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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A_ALL - Static variable in class chemaxon.struc.graphics.MTextAttributes
All identifiers.
A_ALL - Static variable in interface chemaxon.struc.Smolecule
Use all atom and bond property arrays.
A_ASTEREO - Static variable in interface chemaxon.struc.Smolecule
Use atom stereo properties arrays, equals Smolecule.A_PARITY|Smolecule.A_CHIRALITY.
A_ATOMMAP - Static variable in interface chemaxon.struc.Smolecule
Use atom type array.
A_BOLD - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font's bold subattribute.
A_BOND - Static variable in interface chemaxon.struc.Smolecule
Use arrays to store bonds.
A_CHARGE - Static variable in interface chemaxon.struc.Smolecule
Use charge array.
A_CHIRALITY - Static variable in interface chemaxon.struc.Smolecule
Chirality.
A_DX - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the x shift attribute.
A_DY - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the y shift attribute.
A_EXPLH - Static variable in interface chemaxon.struc.Smolecule
Use explicit Hydrogen count array.
A_FONT - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font attribute.
A_FONT_BITS - Static variable in class chemaxon.struc.graphics.MTextAttributes
All font bits.
A_FONTFAMILY - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font family subattribute.
A_FONTSIZE - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font size subattribute.
A_FOREGROUND - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the color attribute.
A_HYBRIDIZATION - Static variable in interface chemaxon.struc.Smolecule
Use hybridization state array.
A_IMPLH - Static variable in interface chemaxon.struc.Smolecule
Use implicit Hydrogen count array.
A_ITALIC - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font's italic subattribute.
A_MASSNO - Static variable in interface chemaxon.struc.Smolecule
Use mass number array.
A_PARITY - Static variable in interface chemaxon.struc.Smolecule
Atom parity.
A_RADICAL - Static variable in interface chemaxon.struc.Smolecule
Use radical array.
A_RGROUP - Static variable in interface chemaxon.struc.Smolecule
Use R-group ID array.
A_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font scale attribute.
A_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the subscript/superscript level attribute.
A_VALENCE - Static variable in interface chemaxon.struc.Smolecule
Use valence array.
AAMAP_MASK - Static variable in class chemaxon.struc.MolAtom
Atom map mask in flags.
AAMAP_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum atom-atom mapping number.
AAMAP_OFF - Static variable in class chemaxon.struc.MolAtom
Atom map offset in flags.
AATOM - Static variable in class chemaxon.jep.context.ReactionContext
 
ABBREV_GROUPS_KEY - Static variable in class chemaxon.standardizer.actions.AliasToGroupAction
Property Key of the abbreviated group modification
ABBREVGROUP - Static variable in class chemaxon.formats.MFileFormat
Chemaxon SMILES Abbreviated Groups.
AbbrevGroupRecognizer - Class in chemaxon.formats.recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
AbbrevGroupRecognizer() - Constructor for class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated.
 
ABBREVIATED_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that abbreviated groups had found in the molecule
ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that only contracted abbreviated groups had found in the molecule
ABBREVIATED_GROUP_WITH_ONLY_EXPANDED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that only expanded abbreviated groups had found in the molecule
ABBREVIATED_GROUPS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "abbrevgroups".
ABBREVIATED_GROUPS_ALLOWED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "abbrevgroupsAllowed".
AbbreviatedGroupChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
AbbreviatedGroupChecker() - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker
Default constructor.
AbbreviatedGroupChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker
Parameterized constructor.
ABS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
Stereogenic centers belonging to ABS represent absolute stereochemistry, i.e.
ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants
Option for absolute stereo matching.
ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants
Option for absolute stereo matching.
ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants
Option for absolute stereo matching.
ABSENT_CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule is chiral, but flag is not added to the molecule
AbsentChiralFlagChecker - Class in chemaxon.checkers
Detects chiral molecules with no chiral flag defined
AbsentChiralFlagChecker() - Constructor for class chemaxon.checkers.AbsentChiralFlagChecker
Initializes the absent chiral flag error checker
AbsentChiralFlagFixer - Class in chemaxon.fixers
Deprecated, for removal: This API element is subject to removal in a future version.
AbsentChiralFlagFixer() - Constructor for class chemaxon.fixers.AbsentChiralFlagFixer
Deprecated.
 
ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "absLabelVisible" or "absLabel".
ABSOLUTE_STEREO_CONFIGURATION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents molecules in which all asymmetric centers have absolute stereo configuration
AbsoluteStereoAction - Class in chemaxon.standardizer.actions
Deprecated, for removal: This API element is subject to removal in a future version.
AbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
Initializes the action with parameters
AbsoluteStereoAction.Type - Enum Class in chemaxon.standardizer.actions
Deprecated.
Type of absolute stereo action
AbsoluteStereoConfigurationChecker - Class in chemaxon.checkers
Detects molecules in which all asymmetric centers have absolute stereo configuration
AbsoluteStereoConfigurationChecker() - Constructor for class chemaxon.checkers.AbsoluteStereoConfigurationChecker
Initializes the absolute stereo configuration checker
AbsoluteStereoFixer - Class in chemaxon.fixers
Deprecated, for removal: This API element is subject to removal in a future version.
AbsoluteStereoFixer() - Constructor for class chemaxon.fixers.AbsoluteStereoFixer
Deprecated.
 
AbstractMRecordReader - Class in chemaxon.marvin.io.formats
Abstract record reader class.
AbstractMRecordReader(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader
Constructs an abstract record reader.
AbstractMRecordReader(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader
 
AbstractStandardizerAction - Class in chemaxon.standardizer
Abstract implementation of the StandardizerAction.
AbstractStandardizerAction(Map<String, String>) - Constructor for class chemaxon.standardizer.AbstractStandardizerAction
Initializes the functionality of the abstract implementation.
AbstractStereoFilter<T extends StereoCenter> - Class in com.chemaxon.calculations.stereoanal.filters
Abstract class for Filter interface.
AbstractStereoFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
 
AbstractStructureChecker - Class in chemaxon.checkers
Abstract base class of all functions checking and repairing chemical structures.
AbstractStructureChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AbstractStructureChecker
Constructor to create a Structure checker instance with the given errorType
AbstractStructureFixer - Class in chemaxon.fixers
This class is the default abstract implementation of StructureFixer interface
AbstractStructureFixer() - Constructor for class chemaxon.fixers.AbstractStructureFixer
Constructor to create a Structure fixer
Ac - Static variable in class chemaxon.core.ChemConst
 
accept(Molecule) - Method in class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter
Accepts molecule if the number of R-group attachments in the molecule is exactly the attachment count specified in the constructor of this filter.
accept(Molecule) - Method in interface chemaxon.util.MolFilter
Returns true if molecule is accepted by the filter.
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
accept(StereoCenterVisitor) - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Accepts visitors.
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
ACCEPT_ONLY_SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
 
Accepted - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
Indicates, that the structure checker puts valid or fixed structures to the output file.
ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
Acceptor sign displayed in GUI.
ACCEPTOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
ACCORD - Static variable in class chemaxon.formats.MFileFormat
ACCORD file format
ACCP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
Atomic contribution with correction terms.
ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
 
ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Constant denoting acidic pKa.
ACT_KEY - Static variable in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
Key of type for parsing and property change
actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Action handler.
ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
action string token of the checker
ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor
action string tokens of the fixer
ACTIONSTRING_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
action string token of the action
ActionStringBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader
An implementation of ConfigurationReader for parsing action strings
ActionStringBasedConfigurationReader(String) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
Default constructor
ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
ActionStringBasedConfigurationReader(String, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
Constructor with custom checker factory
actionStringToken() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the action string token of the checker
actionStringToken() - Element in annotation interface chemaxon.fixers.FixerInfo
Returns the action string token of the fixer.
actionStringToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the action string tokens of the action as a string, divided by comma characters
activateContainerCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
The containing cell of the GraphicComponent will be the active cell of the scene.
active - Variable in class chemaxon.marvin.space.GraphicComponent
Is this component selected or not.
add(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
Add a name to structure converter.
add(StandardizerActionFactory.StandardizerClassDescriptor) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds a standardizer action class descriptor to the factory
add(DPoint3) - Method in class chemaxon.struc.DPoint3
Add the given point to this one.
add(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Calculates the sum of the two vectors
add(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom to the molecule.
add(MolAtom) - Method in class chemaxon.struc.RgMolecule
Adds an atom to the root structure.
add(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Adds an atom to a reactant, product or agent structure.
add(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom to the molecule.
add(MolAtom) - Method in class chemaxon.struc.Sgroup
Adds a new atom to the S-group.
add(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Adds a new atom to the S-group.
add(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new atom to the S-group.
add(MolAtom, boolean) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom to the molecule.
add(MolBond) - Method in class chemaxon.struc.MolAtom
Add a bond if it had not been already added.
add(MolBond) - Method in class chemaxon.struc.Molecule
 
add(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond to the molecule.
add(MolBond) - Method in class chemaxon.struc.RgMolecule
Adds a bond to the root structure.
add(MolBond) - Method in class chemaxon.struc.RxnMolecule
Adds a bond to a reactant, product, agent.
add(MolBond) - Method in class chemaxon.struc.SelectionMolecule
Adds a bond to the graph.
add(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
Add an edge if it had not been already added.
add(MolBond, boolean) - Method in class chemaxon.struc.MoleculeGraph
Add a bond to the molecule.
add(MolBond, boolean) - Method in class chemaxon.struc.SelectionMolecule
Add a bond to the molecule.
add(MolBond, MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
Add an edge to the given atom of the sgroup, if it had not been already added.
add(MProp) - Method in class chemaxon.struc.prop.MListProp
Adds an element.
add(InputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds an input stream containing standardizer specifications to be stored by the output factory
add(String, double) - Method in class chemaxon.jep.ConstantTableBuilder
Adds a double constant to this builder.
add(String, Molecule) - Method in class chemaxon.jep.ConstantTableBuilder
Adds a molecule constant to this builder.
add(String, Molecule[]) - Method in class chemaxon.jep.ConstantTableBuilder
Adds a molecule array constant to this builder.
add(String, String) - Method in class chemaxon.jep.ConstantTableBuilder
Adds a string constant to this builder.
add(URL) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds an input stream containing standardizer specifications to be stored by the output factory
add(Properties) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds a property map containing properties of standardizer actions to be stored by the output factory
ADD - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
Add absolute stereo
ADD_REMOVE_H_ATOMS_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "addRemoveHatomsEnabled".
addAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds an action to the configuration
addActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane
Adds an action listener.
addActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions
Adds an action listener.
addActions(List<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds actions to the configuration
addActionToGroup(String, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds an action to the group
addActionToGroups(Collection<String>, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds an action to a list of groups
addAll(ConstantTable) - Method in class chemaxon.jep.ConstantTableBuilder
Adds all constants in the given table to this builder.
addAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "added atom" list.
addAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "added atom" list.
addAtom(int) - Method in interface chemaxon.struc.WSmolecule
Adds an atom.
addAtom(MolAtom) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "added atom" list.
addAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "added atom" list.
addAtom(Smolecule, int) - Method in interface chemaxon.struc.WSmolecule
Adds an atom from another Smolecule.
addAtom0(MolAtom) - Method in class chemaxon.struc.Molecule
Adds an atom.
addAtom0(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom.
addAtom0(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom.
addAtomPair(int, int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Adds an alignment constraint between the reference and aligned molecule.
addAtomPair(int, int, double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Adds an alignment constraint between the reference and aligned molecule.
addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Adds all atoms and bonds to the specified molecule.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.Molecule
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RgMolecule
 
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule
 
addAtomWithBonds(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom to the molecule.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom without setting its parentGraph and index fields.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom without setting its parentGraph and index fields.
addAttachmentPoint(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point for an atom.
addAttachmentPoint(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point of the given attachment atom and order.
addAttachmentPoint(MolAtom, int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MBracket
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MEFlow
 
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MPolyline
Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRectangle
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRoundedRectangle
Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
Adds the attribute names to the specified list.
addBond(int, int, int) - Method in interface chemaxon.struc.WSmolecule
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.Molecule
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.SelectionMolecule
Adds a bond.
addBondWithoutChangingIt(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond without setting its parentGraph and index fields.
addBracket(MBracket) - Method in class chemaxon.struc.Sgroup
Adds a bracket to this S-group.
addCanvas(Container) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace viewer to the container.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
Adds attribute names to the specified list.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
Adds attribute names to the specified list.
addCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Adds a central atom to this sgroup.
addChar(char) - Method in class chemaxon.struc.graphics.MTextBox
Adds a character to the text.
addCheckerMark(MDocument.CheckerMark) - Method in class chemaxon.struc.MDocument
Adds a checker mark to the document.
addChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup
Adds a child S-group.
AddChiralFlagFixer - Class in chemaxon.fixers
Absent chiral flag fixer.
AddChiralFlagFixer() - Constructor for class chemaxon.fixers.AddChiralFlagFixer
 
addComparator(MolComparator) - Method in class chemaxon.sss.search.MolSearch
Add a comparator to the search object.
addComplex() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Complex number support will be removed without replacement.
addComplexVariable(String, double, double) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Complex number support will be removed without replacement.
addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Adds a new component to this cell.
addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to the active or to the first cell.
addComponent(GraphicComponent, int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to the cell having the given index.
addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule
Adds a reactant, product or agent.
addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule
Adds a reactant, product or agent.
addComponentToEmptyCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to an empty cell.
addConstraintsFromUserMappedAtoms() - Method in class chemaxon.marvin.alignment.Alignment
An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.
addCoordinateSystem(int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a dummy graphic component that represents the coordinate system.
addCrossingBonds(List<MolBond>, List<MolBond>) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the crossing bonds (head and tail) of a ladder-type polymer.
addData(Molecule, MolAtom, String, String) - Method in class chemaxon.marvin.io.MolExportModule
Adds a data sgroup to the given atom in the given molecule with fieldName and value.
addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Adds a line to the data stored in the field.
addDihedralStep(DihedralScanStep) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Add a new step.
addDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent
Forces the component to set all drawing property stored in drawProperties, and leaves the old settings which are not overidden.
addError(Exception) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:
             Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
             
addExplicitHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:
             Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
             
AddExplicitHydrogensAction - Class in chemaxon.standardizer.actions
Hydrogenization standardizer action
AddExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AddExplicitHydrogensAction
Initializes the action
addExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]).
Usage:
             Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
             
addFunction(String, PostfixMathCommandI) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The function table will not be modifiable anymore. No replacement.
addGroup(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Adds a group definition to the group list of the action
addGroup(String) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Adds a group to the list defined by its abbreviation
addHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
addHAtoms(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
addHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
addHeavyAtomLimitChecker(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Creates an input checker by calling CalculatorInputChecker.heavyAtomLimit(int) and adds it to this plugin.
addHelpMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
Adds the help menu to a parent menu.
addHyperlinkListener(JEditorPane) - Static method in class chemaxon.marvin.util.SwingUtil
Adds HTML link handling to an editor pane.
addInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil
Adds the Standardizer tasks specified in the configuration parameter to the inactive tasks list.
addInput(File, String) - Method in class chemaxon.formats.MolConverter.Builder
Adds an input file.
addInput(File, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Builder
Adds an input stream.
addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
addInput(String, String) - Method in class chemaxon.formats.MolConverter.Builder
Adds an input file.
addInput(String, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
addInputChecker(TaggedCalculatorInputChecker) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Adds the specified input checker to this plugin.
addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a label component inside the MarvinView table.
addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a label component inside the MarvinView table.
addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MTextBox
 
addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage
Adds a listener if it is not yet added.
addListToDelete(int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a gl list id to the deletion list
addLonePairs(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
addMatch(int[], int[], int) - Method in class chemaxon.sss.search.MolSearch
 
addMatch(int[], int[], int) - Method in class chemaxon.sss.search.Search
Specifies extra prerequisites of the structure search that queryAtoms[0] must match to targetAtoms[0] only AND queryAtoms[1] must match to targetAtoms[1], etc.
addMatch(int, int) - Method in class chemaxon.sss.search.MolSearch
Adds a fixed matching between the given query and target atoms.
addMatch(int, int) - Method in interface com.chemaxon.search.SimpleSearcher
Adds a fixed matching between the given query and target atoms.
addMenuBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane
Adds a menubar change listener.
addMolecule(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a molecule viewer component inside the MarvinView table.
addMolecule(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a molecule viewer component inside the MarvinView table.
addMolecule(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds a Molecule object to the actual cell of the viewer.
addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment
Add molecule to align
addMolecule(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.
addMoleculeTo(Molecule, int) - Method in class chemaxon.marvin.space.MSpaceEasy
Makes the given cell to be the active cell, and adds the molecule to it.
addMoleculeToEmptyCell(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.
addMoleculeToEmptyCell(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.
addMoleculeWithoutChange(Molecule, boolean) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds a Molecule object to the actual cell of the viewer and resets the view only if required.
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.Alignment
User may define extra weights between colors defined at setColoringScheme.
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
addNodeColorWeight(int, int, double) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint
Point added to a document.
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint
Point added to a document.
addNotify(MDocument) - Method in class chemaxon.struc.MObject
Called when the object is added to a document.
addNumbering - Variable in class chemaxon.marvin.io.MolExportModule
Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.
addObject(MObject) - Method in class chemaxon.struc.MDocument
Adds an object to the document.
addObject(MObject) - Method in class chemaxon.struc.MSelectionDocument
Adds an object to the document.
addOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Adds an owner, that should be notified about the changes in the properties.
addParameters(File) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML config file keeping all previous settings.
addParameters(String) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML string representation keeping all previous settings.
addParametrizedMetric(String, String, String) - Method in class chemaxon.descriptors.MDParameters
Expands the set of parametrized metrics with a new item.
addParametrizedMetricNode(String, String, String) - Method in class chemaxon.descriptors.MDParameters
Adds a ParametrizedMetric node to the DOM tree.
addParametrizedMetricsNode() - Method in class chemaxon.descriptors.MDParameters
Adds the ParametrizedMetrics node to the DOM tree.
addPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
addPopupMenu() - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace popup menu to the JPanel.
addPopupMenu(JPopupMenu) - Method in class chemaxon.marvin.space.MSpaceEasy
 
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
 
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner
Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
Add a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Add a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
Add a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Add a property change listener
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction
Add a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Add a PropertyChangeListener to the listener list.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner
Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
Add a PropertyChangeListener for a specific property.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Add a PropertyChangeListener for a specific property.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
Add a PropertyChangeListener for a specific property.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MSketchPane
Adds a PropertyChangeListener for a specific property.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MViewPane
Adds a PropertyChangeListener for a specific property.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction
Add a PropertyChangeListener for a specific property.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Add a PropertyChangeListener for a specific property.
addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Adds an atom to the list of paradigmatic repeating unit atoms.
addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule
Adds an R-group member.
addRgroupAttachmentPoint(int, int) - Method in class chemaxon.struc.MolAtom
Attaches a new R-group attachment point to this atom by a bond of a specified type.
addRgroupBridgeMember(RgroupBridgeId, Molecule) - Method in class chemaxon.struc.RgMolecule
Adds a definition member to an R-group bridge.
addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule
Creates an RgMolecule containing R-groups of this object from the 'simplified molecule' object made of 'm'.
addSalt(String, Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Adds a salt to the salt list of the action
addSelectionPanel(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
addSelectionPanelAndProgressBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.Molecule
Adds an S-group to this object.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule
Adds an S-group to this object.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule
Adds an S-group to this object.
addSgroupClones(Molecule, Molecule, Molecule) - Method in class chemaxon.struc.Molecule
Adds the S-groups of a child molecule clone to the new parent molecule clone.
addSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule
Adds S-groups to this object and its parent.
addSimpleAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds a non-SgroupAtom atom without setting its parentGraph and index fields.
addSolvent(String, Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Adds a solvent to the solvent list of the action
addStandardConstants() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.
addStandardFunctions() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
These functions will be removed without replacement.
addStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Changes terminal carbon atoms to star atoms (*).
addString(String) - Method in class chemaxon.struc.graphics.MTextBox
Adds a string to the text.
addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
Add a thread-local name to structure converter.
addToolBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
Not used.
addToSelection(MDocument, MSelectionDocument) - Static method in class chemaxon.struc.NoStructure
Adds the selected NoStrutures from the document to the selectionDocument
addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
Add an element to marvinsketch's recent file list
addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
Add an element to marvinview's recent file list
addTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Add a TransferableDescriptor to the MTransferable Registry.
addTransferable(String, String, Integer, Integer, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Deprecated, for removal: This API element is subject to removal in a future version.
addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Add a TransferableDescriptor to the registry, and constructing it by the given parameters.
addUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
Adds the given user-defined comparator to the search.
addUserConstraint(int, int, int, int) - Method in class chemaxon.marvin.alignment.Alignment
Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
addVariable(String, double) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.
addVariableAsObject(String, Object) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.
adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph
Checks whether the molecule has multiple chiral centres
AdvancedCheckerRunner - Class in chemaxon.checkers.runner
CheckerRunner implementation with advanced fixing capabilities.
StructureFixer selection is based on provided fixer class if available, or falls back to StructureCheckerResult based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts.
AdvancedCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(ConfigurationReader, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
affectsPerformance() - Method in enum class chemaxon.calculator.CalculatorTag
Returns whether the presence of this tag affects the performance of the calculator.
Ag - Static variable in class chemaxon.core.ChemConst
 
AGENT - Static variable in class chemaxon.jep.context.ReactionContext
 
AGENTS - Static variable in class chemaxon.struc.RxnMolecule
"Agent" structure type.
Al - Static variable in class chemaxon.core.ChemConst
 
alias - Variable in class chemaxon.marvin.services.ServiceArgument
the alias of the argument
alias() - Element in annotation interface chemaxon.checkers.Persistent
Returns the alias name of the annotated property
ALIAS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias values had found in the molecule
ALIAS_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias value that could be converted to an element had found in the molecule
ALIAS_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias value that could be converted to an abbreviated group had found in the molecule
ALIAS_NONE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias value had found in the molecule
AliasChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting atoms with alias labels.
AliasChecker() - Constructor for class chemaxon.checkers.AliasChecker
Default constructor.
AliasToAtomAction - Class in chemaxon.standardizer.actions
Alias to Atom standardizer action.
AliasToAtomAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToAtomAction
Initializes the action
AliasToGroupAction - Class in chemaxon.standardizer.actions
Alias to Group standardizer action
AliasToGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToGroupAction
Initializes the action with parameters
align() - Method in class chemaxon.marvin.alignment.Alignment
3D alignment on two or more molecules.
align() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
align() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
does a simple one-to-one atom mappin and aligns.
align() - Method in class chemaxon.marvin.alignment.MolAligner
Execute best alignment based on hit map provided earlier
align(int[]) - Method in class chemaxon.marvin.alignment.MolAligner
Calculates and performs the best alignment possible specified by the hit map array.
align(int[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
Rigid alignment on the user defined atom index
align(Molecule) - Method in interface chemaxon.marvin.alignment.MCSAlignment
Align the given molecule to the reference.
ALIGN_AS_IS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
 
ALIGN_BOTTOM - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to bottom of box.
ALIGN_CENTER - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to center of box.
ALIGN_LEFT - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to left edge of box.
ALIGN_RIGHT - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to right edge of box.
ALIGN_TOP - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to top of box.
Alignment - Class in chemaxon.marvin.alignment
3D Alignment aligns two or more 3D molecules onto each other.
Alignment() - Constructor for class chemaxon.marvin.alignment.Alignment
 
Alignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.Alignment
 
ALIGNMENT - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
 
ALIGNMENT - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Alignment
AlignmentAccuracyMode - Enum Class in chemaxon.marvin.alignment
Settings for the representation of a molecular shape.
AlignmentMolecule - Class in chemaxon.marvin.alignment
 
AlignmentMoleculeFactory - Class in chemaxon.marvin.alignment
Creates an AlignmentMolecule form a Molecule based on the settings.
AlignmentMoleculeFactory() - Constructor for class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.marvin.alignment
 
AlignmentPlugin - Class in chemaxon.marvin.calculations
Plugin layer for the AlignmentAPI
AlignmentPlugin() - Constructor for class chemaxon.marvin.calculations.AlignmentPlugin
 
AlignmentProperties - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.ColoringScheme - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.ColorNotSpecifiedCase - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.DegreeOfFreedomType - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.FlexibilityMode - Enum Class in chemaxon.marvin.alignment
Conformational flexibility treatment during the alignment for a pair of a molecule.
AlignmentProperties.NodeType - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.OrientationType - Enum Class in chemaxon.marvin.alignment
 
AlignOnPairedAtoms - Class in chemaxon.marvin.alignment
Overlays two molecules using the user defined atom pairs
Example:
AlignOnPairedAtoms() - Constructor for class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
AlignRigidEasy - Class in chemaxon.marvin.alignment
Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.
AlignRigidEasy() - Constructor for class chemaxon.marvin.alignment.AlignRigidEasy
 
ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
Aliphatic query atom.
ALIPHATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
aliphaticAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.
aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aliphaticAtomCount()
aliphaticBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.
aliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aliphaticBondCount()
aliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of aliphatic ring systems of the molecule.
aliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aliphaticRingCount()
aliphaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
aliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aliphaticRingCount(int)
aliphaticRings() - Method in class chemaxon.calculations.Ring
Identifies the aliphatic rings in the molecule.
aliphaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aliphaticRings()
aliphaticRings(int) - Method in class chemaxon.calculations.Ring
Identifies aliphatic rings in the molecule having a given size (number of atoms).
aliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aliphaticRings(int)
ALL - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption
All atoms can have translation.
ALL - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
ALL_H - Static variable in class chemaxon.struc.MolAtom
Include any Hydrogen atom.
ALL_MATCH_AMBIG - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
Ambiguous aromatic parts of the target Markush structure can be matched by aliphatic and aromatic forms as well.
ALL_PERM - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
 
allringsystems - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
allStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
All stereo centers of molecule.
allStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
All stereo centers with attached data.
Am - Static variable in class chemaxon.core.ChemConst
 
ambient - Static variable in class chemaxon.marvin.space.monitor.Control
 
AMBIGUOUS - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
AMBIGUOUS_AROMATIC_ATOMS_IGNORED - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.DEFAULT.
Usage:
             molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             
AMINOACID - Enum constant in enum class chemaxon.struc.SgroupType
 
AMINOACID_BOND_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "aminoAcidBondColoringEnabled".
ANCHOR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AND - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
Stereogenic centers belonging to an ANDn group (e.g.
AND - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
AND_OR - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Set of enhanced stereo flags.
ANGLE_STEP - Static variable in class chemaxon.struc.MolAtom
 
angle2D(double, double) - Method in class chemaxon.struc.DPoint3
Calculates the absolute angle in the XY plane of the vector pointing from this point to the other point.
angle3D(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculate the angle of two vectors (this and p) in the range 0.0 through pi.
AngleMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring angle between 3 components, the first 2 determines a line, the second 2 another.
AngleMonitor() - Constructor for class chemaxon.marvin.space.monitor.AngleMonitor
Creates a new instance of AngleMonitor
ANIMATE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animate".
ANIMATION_DELAY - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animDelay".
ANIMATION_FPS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animFPS".
ANIMATION_SYNCHRONIZATION - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animSync".
ANIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
ANTI - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, anti (relative configuration).
ANY - Enum constant in enum class chemaxon.struc.SgroupType
 
ANY - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the any atom A.
ANY - Static variable in class chemaxon.struc.MolBond
Any bond type.
ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
 
anyBooleanPropertyTrue(Map<String, String>, String...) - Method in class chemaxon.standardizer.AbstractStandardizerAction
Check the given map, whether there is a String 'true' (case in-sensitive) value for any of the given keys
anyCancelled(CancelObserver...) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
append(Changes) - Method in class chemaxon.standardizer.Changes
Appends a set of changes to the already existing changes.
append(String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
Append text to end of document.
appendChars(int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append a character n times to the string buffer.
appendLeft(String, int) - Method in class chemaxon.marvin.io.MolExportModule
Append a string to the buffer in %-ns format.
appendLine(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Appends line to string buffer with closing '\n' character.
appendLines(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Appends lines to string buffer with closing '\n' character if it is not yet present.
appendMEnd(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Appends the "M END" line to the string buffer.
appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.MDParameters
Extends internal data with a new parametrized metric.
appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.PFParameters
 
appendpHText(String) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Appends the pH text.
appendRight(int, int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append an integer to the buffer in the right hand side of an n-characters wide field.
appendRight(String, int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append a string to the buffer in the right hand side of an n-characters wide field.
apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker
 
apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculator.TaggedCalculatorInputChecker
Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.
apply(Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker
Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.
applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane
Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.
applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane
Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.
Ar - Static variable in class chemaxon.core.ChemConst
 
ARC_BRACES - Static variable in class chemaxon.struc.graphics.MBracket
The default arc angle of the Braces Rectangle in degrees.
ARC_ROUND - Static variable in class chemaxon.struc.graphics.MBracket
The default arc angle of the Rounded Rectangle in degrees.
areArrowsAndLikelyTheSame(MPolyline, MPolyline) - Static method in class chemaxon.marvin.modules.reaction.ReactionEditUtils
Compares type and checks perfect equality of location.
areAttachmentPointsVisible() - Method in class chemaxon.marvin.MolPrinter
Gets the attachment points visibility.
areChildSgroupsVisible() - Method in class chemaxon.struc.Sgroup
Checks whether the child S-groups are visible.
areChildSgroupsVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the child S-groups are visible.
areMonomersTransformed() - Method in class chemaxon.sss.search.SearchOptions
Obtain monomer transformation information.
areNeighbors(int, int) - Method in interface chemaxon.struc.Smolecule
Tests whether two atoms are connected.
arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Are popup menus enabled?
ARO_R - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
Number of aromatic rings.
AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph
Aromatization type for ambiguous 5-membered rings.
AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph
Basic aromatization.
AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph
Huckel aromatization.
AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
General (Daylight conform) aromatization.
AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph
Loose aromatization.
AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph
Substructure aromatization.
AROMATIC - Static variable in class chemaxon.struc.MolAtom
Aromatic query atom.
AROMATIC - Static variable in class chemaxon.struc.MolBond
Aromatic bond type.
AROMATIC_ATOM - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
Aromatic or aliphatic query atom.
AROMATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AROMATIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
aromaticAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic atoms in the molecule.
aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aromaticAtomCount()
aromaticBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic bonds in the molecule.
aromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aromaticBondCount()
AROMATICITY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that aromaticity problem had found in the molecule
AromaticityCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying aromaticity problems, thus errorType property is StructureCheckerErrorType.AROMATICITY
AromaticityCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AromaticityCheckerResult
Constructor which initialize all the properties.
AromaticityErrorChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting aromatization problems.
AromaticityErrorChecker() - Constructor for class chemaxon.checkers.AromaticityErrorChecker
Default constructor.
AromaticityErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AromaticityErrorChecker
Parameterized constructor.
aromaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic ring systems in the molecule (SSSR).
aromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aromaticRingCount()
aromaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
aromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aromaticRingCount(int)
aromaticRings() - Method in class chemaxon.calculations.Ring
Identifies the aromatic rings in the molecule.
aromaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aromaticRings()
aromaticRings(int) - Method in class chemaxon.calculations.Ring
Indentifies aromatic rings in the molecule having a given size (number of rings).
aromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.aromaticRings(int)
aromatize - Variable in class chemaxon.marvin.io.MolExportModule
Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, etc, dearomatize if -1, do nothing if 0.
aromatize() - Method in class chemaxon.struc.MoleculeGraph
Aromatize molecule using the default general aromatization method.
aromatize(boolean) - Method in class chemaxon.struc.MoleculeGraph
Aromatize (using the default general aromatization method) or dearomatize molecule.
aromatize(int) - Method in class chemaxon.struc.Molecule
Aromatizes molecule.
aromatize(int) - Method in class chemaxon.struc.MoleculeGraph
Aromatizes molecule.
aromatize(int) - Method in class chemaxon.struc.RgMolecule
Aromatizes molecule.
aromatize(int, boolean) - Method in class chemaxon.struc.Molecule
Aromatizes molecule.
aromatize(int, boolean) - Method in class chemaxon.struc.MoleculeGraph
Aromatizes molecule.
aromatize(int, boolean) - Method in class chemaxon.struc.RgMolecule
Aromatizes molecule.
aromatize(int, String, boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Aromatize or dearomatize molecule in the specified cell.
AromatizeAction - Class in chemaxon.standardizer.actions
Aromatization standardizer action
AromatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AromatizeAction
Initializes the action with parameters
AromatizeAction.Type - Enum Class in chemaxon.standardizer.actions
Type of aromatization
aromatizeAll(boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Aromatize or dearomatize molecules in all cells.
Aromatizer - Enum Class in com.chemaxon.search.transformation.transformers
Aromatizer transformer.
arrangeComponents() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean).
Usage:
             CleanUtil.arrangeComponents(molecule, true, true);
             
arrangeComponents(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges molecule components (reactants, agents, products, R-group definitions) nicely.
arrangeComponents(MoleculeGraph, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
arrangeComponents(MoleculeGraph, boolean, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
arrangeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange data attached to DataSgroup.
arrangeHydrogenIncerments(Molecule, int, String, double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
arrangeMolecules(MoleculeGraph[], int, int) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice.
arrangeReaction(RxnMolecule) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges reaction components nicely
arrangeRelativeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange data attached to DataSgroup.
arrangeRgroupMembers(RgMolecule) - Method in class chemaxon.marvin.util.MolFragLoader
Arranges R-group definition member coordinates.
arrangeSgBrackets(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange sgroup brackets in the molecule.
ArrayMDocSource - Class in chemaxon.marvin.io
MDocSource implementation for an array of documents or molecules.
ArrayMDocSource(MDocument[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for an array of documents.
ArrayMDocSource(Molecule[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for an array of molecules.
ArrayMDocSource(List<?>) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for a list of documents or molecules.
ARROW_BACK_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Arrow points back.
ARROW_CROSSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Crossed arrow flag.
ARROW_CURVED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Curved arrow flag.
ARROW_DASHED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Dashed arrow flag.
ARROW_EQUILIBRIUM_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Equilibrium arrow flag.
ARROW_GROUP1_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
Mask for the equilibrium and retrosynthetic arrow flags.
ARROW_GROUP2_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
Mask for the curved, dashed and crosed arrow flags.
ARROW_HALF_LEFT - Static variable in class chemaxon.struc.graphics.MPolyline
Only the left half of the arrow head is drawn.
ARROW_HALF_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
Unshifted mask of the half arrow option bits in flags.
ARROW_HALF_RIGHT - Static variable in class chemaxon.struc.graphics.MPolyline
Only the right half of the arrow head is drawn.
ARROW_RETROSYNTHETIC_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Retrosynthetic arrow flag.
arrowFlags - Variable in class chemaxon.struc.graphics.MPolyline
Arrow flags.
As - Static variable in class chemaxon.core.ChemConst
 
ASK - Enum constant in enum class chemaxon.checkers.FixMode
on problem requests user interaction
asProperties(String) - Method in class chemaxon.marvin.common.UserSettings
 
asSet() - Method in enum class chemaxon.calculator.CalculatorTag
Returns a cached set that contains this element only.
associate(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
The given component will depend on this component.
associatedComponents - Variable in class chemaxon.marvin.space.GraphicComponent
Strores components that depend on this component.
asymmetricAtomCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of atoms having four different ligands.
asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.asymmetricAtomCount()
asymmetricAtoms() - Method in class chemaxon.calculations.stereo.Stereochemistry
Retrieves the indexes of atom having four different ligands.
asymmetricAtoms() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.asymmetricAtoms()
asymmetricEuclidean(float[], float[], double) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric Euclidean distance.
asymmetricEuclidean(int[], int[], double) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric Euclidean distance.
asymmetricNormalizedEuclidean(float[], float[], double) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric normalized Euclidean distance.
asymmetricNormalizedEuclidean(int[], int[], double) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric normalized Euclidean distance.
asymmetricTanimoto(float[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric Tanimoto dissimilarity for floating point values.
asymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric Tanimoto dissimilarity for floating point values.
asymmetricXYZSum - Variable in class chemaxon.descriptors.PFParameters
Stores last calculatred asymmetric Tanimoto sum.
asymmetryFactors - Variable in class chemaxon.descriptors.MDParameters
asymmetry ratio of parametrized asymmetric metrics
AsyncCallback<T> - Interface in chemaxon.marvin.services
Callback interface for asynchronous service calls
At - Static variable in class chemaxon.core.ChemConst
 
atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
The atom whose the neighbours are processed.
ATOM - Static variable in class chemaxon.jep.context.AtomContext
 
ATOM - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Calculation domain type: calculation refers to atoms.
ATOM_ATOM_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
This String represents the key of cloned atom, original atom map
ATOM_COUNT - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "atomcount".
ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomFont".
ATOM_FONT_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomFontSize".
ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom maps had found in the molecule
ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomMappingVisible".
ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomNumberingType".
ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
in 6.2.0 use atomNumberingType parameter instead.
ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomPropertiesVisible".
ATOM_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by mapping atom based property values to the surface.
ATOM_QUERY_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that an atom has a query property set.
ATOM_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "atomSet".
ATOM_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomSetColor".
ATOM_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomsize".
ATOM_STRINGS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "atomStrings".
ATOM_SYMBOL_VISIBLE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
 
ATOM_SYMBOLS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomSymbolsVisible".
ATOM_TYPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with the specified symbol had found in the molecule
ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom
Number of atom types in the elements array
ATOM_TYPE_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum atom number.
ATOM_TYPES - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
 
ATOM_VALUE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom values had found in the molecule
atomA - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
atomB - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
AtomChecker - Class in chemaxon.checkers
Descendants of the abstract AtomChecker class check every atom for a specific error or property.
AtomChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomChecker
Constructor to create a Structure checker instance with the given errorType.
AtomContext - Class in chemaxon.jep.context
Expression evaluation context containing an input molecule and an input atom.
AtomContext() - Constructor for class chemaxon.jep.context.AtomContext
Constructor.
atomCount - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
atomCount - Variable in class chemaxon.struc.MoleculeGraph
The number of atoms.
atomCount() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms in the molecule.
atomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of atoms in the molecule including implicit hydrogens.
atomCount() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms in the molecule.
atomCount(int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms of a given element in the molecule.
atomCount(int, int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms of a given element in the molecule.
ATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Atom count of the molecule
AtomIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomIterator
Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
ATOMLIST - Static variable in class chemaxon.sss.search.MarkushFeature
Deprecated.
Expansion type: atom list.
AtomMapChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atom maps.
AtomMapChecker() - Constructor for class chemaxon.checkers.AtomMapChecker
Default constructor
atomMapMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
atomMapMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether atom map numbers should be considered in search.
atomMapMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
atomMapping() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
Array of atom - atom mapping.
AtomNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
Constructs an iterator to process the atoms connecting to the specified atom according to the atom and bond related behavior of this factory.
AtomProperty - Class in chemaxon.marvin.space
The AtomProperty class provides access to chemical properties of Molecule atoms by atom index.
AtomProperty - Class in chemaxon.struc
Class for storing atom property enumerations.
AtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty
 
AtomProperty() - Constructor for class chemaxon.struc.AtomProperty
 
AtomProperty.MoleculeAtomProperty - Class in chemaxon.marvin.space
 
AtomProperty.Radical - Enum Class in chemaxon.struc
Enumeration of the supported radicals.
AtomProperty.SmoleculeAtomProperty - Class in chemaxon.marvin.space
 
AtomQueryPropertyChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms having an query property set.
AtomQueryPropertyChecker() - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.
AtomQueryPropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
Creates a new AtomQueryPropertyChecker instance to detect the given query properties.
AtomQueryPropertyCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying atom query properties, thus errorType property is StructureCheckerErrorType.ATOM_QUERY_PROPERTY by default.
AtomQueryPropertyCheckerResult(StructureChecker, List<MolAtom>, Molecule, String, List<String>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
Constructor which initialize all the properties.
atoms() - Method in class chemaxon.struc.MoleculeGraph
Provides a list view of the atoms in the molecule.
AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters
Selection which contains atom indexes.
AtomSelection(int[], int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated.
AtomSelection(int, int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated.
AtomSelection(List<Integer>, List<Integer>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Constructs an AtomSelection from lists.
atomSet - Variable in class chemaxon.struc.Sgroup
Set for storing the atoms of the s-group's graph.
ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants
Either stereo atom type.
ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants
Stereo atom type mask.
ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants
No stereo atom type specified.
ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants
Specific stereo atom type.
AtomTypeChecker - Class in chemaxon.checkers
A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.
AtomTypeChecker() - Constructor for class chemaxon.checkers.AtomTypeChecker
Default constructor.
AtomTypeChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomTypeChecker
Parameterized constructor providing the possibility for descendants to initialize with their own error type.
AtomTypeChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomTypeChecker
Parameterized constructor.
atomTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
atomTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether atom types should be considered in search.
atomTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
AtomValueChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms with atom value.
AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker
Default constructor.
ATROP - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
 
ATROP - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
Atrop stereo center.
AtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop
Filter for atrop stereo centers.
AtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
 
ATROPISOMER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atropisomers are found in the molecule
AtropisomerChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting atropisomers in the molecule.
AtropisomerChecker() - Constructor for class chemaxon.checkers.AtropisomerChecker
Initializes the atropisomer structure checker
AtropIsomerDetector - Class in chemaxon.marvin.alignment
Molecular mechanics based atropisomer detection.
AtropIsomerDetector() - Constructor for class chemaxon.marvin.alignment.AtropIsomerDetector
 
AtropIsomerDetector.Accuracy - Enum Class in chemaxon.marvin.alignment
 
AtropStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Atrop stereo center implementation.
AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Constructs a new instance of axial stereo center.
AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Constructs a new instance of axial stereo center with attached data.
AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
atropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the atrop stereocenters.
atropStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the atrop stereocenters with attached data.
AtropStereoDescriptor - Class in chemaxon.struc
Descriptor representing atrop stereo information, the rotation of two aromatic rings connected by a single bond (axis), and at least 3 of the ligands in the ring connected to the axis has a non-ring ligand. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.ODD means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.EVEN means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is counter-clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.UNKNOWN means that it can not be decided if it is clockwise or counter-clockwise, but there is no wiggly bond - like a 2D structure without wedge information.. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.WIGGLY means that there is a wiggly bond on either ligand in the ring connected to the axis, or the axis is wiggly.
AtropStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AtropStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AtropStereoDescriptor
 
ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom
S-group attachment point on first and second site.
ATTACH_NONE - Static variable in class chemaxon.struc.MolAtom
There is no S-group attachment point setting on this atom.
ATTACH_UNKNOWN - Static variable in class chemaxon.struc.MolAtom
S-group attachment point information
ATTACH1 - Static variable in class chemaxon.struc.MolAtom
S-group attachment point on first site.
ATTACH2 - Static variable in class chemaxon.struc.MolAtom
S-group attachment point on second site.
ATTACHED_DATA - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that attached data had found in the molecule
ATTACHED_DATA_MATCH_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact match of attached data.
ATTACHED_DATA_MATCH_GENERAL - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for general match of attached data.
ATTACHED_DATA_MATCH_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignoring attached data.
AttachedData - Class in com.chemaxon.calculations.stereoanal.stereocenters
Data object which contains a name and a data (String).
AttachedData(String, String) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
Creates an AttachedData class.
AttachedDataChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting attached data in the molecule.
AttachedDataChecker() - Constructor for class chemaxon.checkers.AttachedDataChecker
Default constructor.
AttachedDataChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AttachedDataChecker
Parameterized constructor.
ATTACHMENT_ATOM - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.
ATTACHMENT_LABEL - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...
ATTACHMENT_MAP - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int).
ATTACHMENT_NONE - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: none (no attachment point data).
ATTACHMENT_POINT - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: R-group attachment.
ATTACHMENT_RLABEL - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String).
Au - Static variable in class chemaxon.core.ChemConst
 
AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Automatic check for structures.
AUTO_RESOLUTION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
AUTO_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "autoscale".
AUTO_TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "autoTabScale".
AUTO_UNGROUP - Static variable in class chemaxon.struc.MoleculeGraph
Automatic ungroup bit in flags.
autoGzip(InputStream) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Detect gzipped InputStream.
AutoMapper - Class in com.chemaxon.mapper
AutoMapper is a tool that performs automated chemical reaction mapping.
AutoMapper() - Constructor for class com.chemaxon.mapper.AutoMapper
Initializes an AutoMapper object
AutoMapper.Options - Class in com.chemaxon.mapper
Option object for set common options when mapping called by static way.
AUTOMATIC_FOG_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "automaticFogEnabled".
AUTOMATIC_REACTION_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "automaticReactionEnabled".
automaticSettingOfGridSize - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat
Image object (java.awt.Image).
AXIAL - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
 
AXIAL - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
Axial stereo center (eg.
AxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial
Filter for axial stereo centers.
AxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
 
AxialStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Axial stereo center implementation.
AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Constructs a new instance of axial stereo center.
AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Constructs a new instance of axial stereo center with attached data.
AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
axialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the axial stereocenters.
axialStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the axial stereocenters with attached data.
AxialStereoDescriptor - Class in chemaxon.struc
 
AxialStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AxialStereoValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AxialStereoDescriptor
 

B

B - Static variable in class chemaxon.core.ChemConst
 
B_FACTOR_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
Ba - Static variable in class chemaxon.core.ChemConst
 
BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "background".
BACKGROUND_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
 
BACKGROUND_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColor - Variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColorMode - Variable in class chemaxon.marvin.space.monitor.Label
 
BACKGROUNDLOAD_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bgloadEnabled".
BACKGROUNDLOAD_PRIORITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bgload".
backgroundThread - Variable in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
balabanIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "ballRadius".
ballPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
ballRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BASE64 - Static variable in class chemaxon.formats.MFileFormat
BASE64 encoded file.
BASIC - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Basic aromatization
BASIC - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
BASIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Constant denoting basic pKa.
BasicStandardizerRunner - Class in chemaxon.standardizer.runner
This is the default implementation of StandardizerActionRunner interface.
BasicStandardizerRunner(StandardizerConfigurationReader) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner
Initialize a BasicStandardizerRunner instance with the StandardizerConfiguration read from the provided configuration reader.
BasicStandardizerRunner(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner
Initialize a BasicStandardizerRunner instance with specified StandardizerConfiguration.
BBB - Class in chemaxon.calculations.bbb
BBB score calculator.
BBB.Property - Class in chemaxon.calculations.bbb
Simple DTO that contains the predicted value, its BBB score and the BBB score multiplied with the corresponding BBB multiplier.
BBBFunction - Enum Class in chemaxon.calculations.bbb
Base phys-chem property calculators and its score functions for BBB score calculation.
BCUT - Class in chemaxon.descriptors
Implements BCUT descriptors.
BCUT() - Constructor for class chemaxon.descriptors.BCUT
Creates a new, empty BCUT descriptor.
BCUT(BCUT) - Constructor for class chemaxon.descriptors.BCUT
Copy constructor.
BCUT(BCUTParameters) - Constructor for class chemaxon.descriptors.BCUT
Creates a new instance according to the parameters.
BCUT(String) - Constructor for class chemaxon.descriptors.BCUT
Creates a new instance according to the parameters.
BCUTGenerator - Class in chemaxon.descriptors
Descriptor generator class for the BCUT descriptor.
BCUTGenerator() - Constructor for class chemaxon.descriptors.BCUTGenerator
Creates and initializes a BCUT descriptor generator object.
BCUTParameters - Class in chemaxon.descriptors
Manages parameters for the BCUT descriptor class.
BCUTParameters() - Constructor for class chemaxon.descriptors.BCUTParameters
Creates an empty object.
BCUTParameters(File) - Constructor for class chemaxon.descriptors.BCUTParameters
Creates a new object based on a given configuration file.
BCUTParameters(String) - Constructor for class chemaxon.descriptors.BCUTParameters
Creates a new object based on a given configuration string.
Be - Static variable in class chemaxon.core.ChemConst
 
beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
Changes the cursor to hourglass at the beginning of a long operation.
bemismurcko - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
bemismurckoloose - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
Bh - Static variable in class chemaxon.core.ChemConst
 
Bi - Static variable in class chemaxon.core.ChemConst
 
BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
descriptor type constants
binaryAsymmetricEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric Euclidean distance of binary descriptors.
binaryAsymmetricNormalizedEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric normalized Euclidean distance of binary descriptors.
binaryAsymmetricNormalizedEuclidean(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics
Calculates the asymmetric normalized Euclidean distance of binary descriptors.
binaryAsymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates asymmetric Tanimoto dissimilarity for binary descriptors.
binaryAsymmetricTanimoto(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics
Calculates asymmetricTanimoto dissimilarity for binary descriptors.
binaryEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the Euclidean distance of two binary descriptors.
binaryNormalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the normalized Euclidean distance of two binary descriptors.
binaryNormalizedEuclidean(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics
Calculates the normalized Euclidean distance of two binary descriptors.
binaryTanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates Tanimoto dissimilarity for binary descriptors.
binaryTanimoto(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics
Calculates Tanimoto dissimilarity for binary descriptors.
binaryTversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates Tversky dissimilarity for binary descriptors.
binaryWeightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric Euclidean distance of binary descriptors.
binaryWeightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.
binaryWeightedAsymmetricNormalizedEuclidean(int[], int, int[], int, float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.
binaryWeightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted Euclidean distance of binary descriptors.
binaryWeightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted normalized Euclidean distance of binary descriptors.
binaryWeightedNormalizedEuclidean(int[], int, int[], int, int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted normalized Euclidean distance of binary descriptors.
Bk - Static variable in class chemaxon.core.ChemConst
 
BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Constant storing the blue rgb value (the basic pKa result color).
BOLD - Static variable in class chemaxon.struc.graphics.MFont
Bold font style.
BOLD - Static variable in class chemaxon.struc.MolBond
"Bold" attribute of the bond.
BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "boldBondWidth".
bond - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
BOND_ANGLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that bond angle problem had found in the molecule
BOND_BOND_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
This String represents the key of cloned bond, original bond map
BOND_DRAGGED_ALONG - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bondDraggedAlong".
BOND_DRAW_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_FACING - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondHashSpacing".
BOND_LENGTH - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that bond length problem had found in the molecule
BOND_LENGTH - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondLength".
BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondLengthVisible".
BOND_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "bondSet".
BOND_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondSetColor".
BOND_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondSpacing".
BOND_TOPOLOGY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule contains bond(s) with topology.
BondAngleChecker - Class in chemaxon.checkers
Bond Angle Checker detects wrong bond angles in 2D structures.
BondAngleChecker() - Constructor for class chemaxon.checkers.BondAngleChecker
Default constructor
BondAngleChecker(double) - Constructor for class chemaxon.checkers.BondAngleChecker
Deprecated.
Not used.
BondAngleCheckerResult - Class in chemaxon.checkers.result
Bond angle checker result.
BondAngleCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongAngleBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondAngleCheckerResult
Constructor which initialize all the properties.
BondAngleFixer - Class in chemaxon.fixers
Bond Angle Fixer fixes wrong bond angles in 2D structures.
BondAngleFixer() - Constructor for class chemaxon.fixers.BondAngleFixer
 
BondChecker - Class in chemaxon.checkers
Descentants of the abstract BondChecker class detect bond related problems.
BondChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.BondChecker
Constructor to create a Structure checker instance with the given errorType.
bondCount - Variable in class chemaxon.struc.MolAtom
Number of bonds.
bondCount - Variable in class chemaxon.struc.MoleculeGraph
The number of bonds.
bondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of bonds in the molecule including bonds of implicit hydrogens.
bondDistance - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bondFacing - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BondInfo - Class in chemaxon.marvin.alignment.atrop
Encapsulates bond info.
BondInfo(int, int, int) - Constructor for class chemaxon.marvin.alignment.atrop.BondInfo
Construct.
BondIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.BondIterator
Constructs an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.
bondlength() - Method in class chemaxon.struc.Molecule
Calculate the regular bond length for the unified structure.
bondlength() - Method in class chemaxon.struc.MoleculeGraph
Calculates the regular bond length.
BondLengthChecker - Class in chemaxon.checkers
Bond Length Checker detects bonds with wrong length in 2D structures.
BondLengthChecker() - Constructor for class chemaxon.checkers.BondLengthChecker
Default constructor
BondLengthChecker(Map<String, String>) - Constructor for class chemaxon.checkers.BondLengthChecker
Deprecated.
Checker has no parameters.
BondLengthCheckerResult - Class in chemaxon.checkers.result
Bond angle checker result.
BondLengthCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongLengthBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondLengthCheckerResult
Constructor which initialize all the properties.
BondLengthFixer - Class in chemaxon.fixers
Bond Length Fixer fixes bonds with wrong length in 2D structures.
BondLengthFixer() - Constructor for class chemaxon.fixers.BondLengthFixer
 
BONDLIST - Static variable in class chemaxon.sss.search.MarkushFeature
Deprecated.
Expansion type: bond list.
BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
Constructs an iterator to process the bonds connecting to the specified atom.
bondRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bonds() - Method in class chemaxon.struc.MolAtom
Provides a list view of the connected bonds of the atom.
bonds() - Method in class chemaxon.struc.MoleculeGraph
Provides a list view of the bonds in the molecule.
bondSkipped(BondInfo, String) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when visited bond is skipped.
bondSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BondTable - Class in chemaxon.core.util
Provides easy lookup of bonds between pair of atoms in a molecule graph.
BondTopologyChecker - Class in chemaxon.checkers
Checker detects bonds with reacting center bond marks.
BondTopologyChecker() - Constructor for class chemaxon.checkers.BondTopologyChecker
Default constructor
bondType(int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines the type of a bond (aromatic bonds are automatically recognized)
bondTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
bondTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether bond types should be considered in search.
bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom
Calculates the average of the bond unit vectors pointing out of this atom.
bondWidth - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor
Boolean option.
booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp
Gets the boolean value.
BORDER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "border".
BORDER_MODE_BRIGHTER_FOREGROUND - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_FOREGROUND_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
borderColor - Variable in class chemaxon.marvin.space.monitor.Label
 
borderColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
borderColorMode - Variable in class chemaxon.marvin.space.monitor.Label
 
BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
boundingBox - Variable in class chemaxon.marvin.space.GraphicComponent
The smallest box containing the graphic component.
BoundingBox - Class in chemaxon.marvin.space
Class for representing a bounding box of any component in the 3D space.
BoundingBox() - Constructor for class chemaxon.marvin.space.BoundingBox
Creates a new instance of BoundingBox but does not set anything.
BoundingBox(float, float, float, float, float, float) - Constructor for class chemaxon.marvin.space.BoundingBox
Creates a bounding box with the given coordinates, computes the center and radius of the box.
Br - Static variable in class chemaxon.core.ChemConst
 
brackets - Variable in class chemaxon.struc.Sgroup
 
BRACKETS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that the molecule contains brackets (S-groups).
BracketsChecker - Class in chemaxon.checkers
Detects brackets (S-groups) in molecules.
BracketsChecker() - Constructor for class chemaxon.checkers.BracketsChecker
Default constructor.
BRIDGEHEAD_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom which is connected to a bridgehead atom.
brightness - Variable in class chemaxon.descriptors.ChemicalFingerprint
number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less pausible)
brightness - Variable in class chemaxon.descriptors.ECFP
The number of bits set in the binary vector storage
brightness - Variable in class chemaxon.descriptors.ReactionFingerprint
number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)
btab - Variable in class chemaxon.struc.MoleculeGraph
Bond table.
bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream
Reads a character and writes into the buffer.
build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
 
build() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
Builds a ValenceCheckOptions object.
build() - Method in class chemaxon.formats.MolConverter.Builder
Builds the MolConverter.
build() - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
build() - Method in class chemaxon.jep.ConstantTableBuilder
Creates a new constant table based on this builder.
build() - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
build() - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Builds a StandardizerActionFactory based on the previously added InputStream instances
build() - Method in class com.chemaxon.search.MatchingOptions.Builder
Creates a search options object with the settings specified by this builder instance.
build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
buildButtonBar() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
 
buildContentPanel() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
 
builder() - Static method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
Creates a new builder.
builder() - Static method in class chemaxon.jep.ConstantTable
Creates a new builder for a constant table.
Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder
 
Builder() - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
 
Builder() - Constructor for class chemaxon.formats.MolConverter.Builder
Constructs an empty Builder object.
Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder
 
Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder
 
Builder() - Constructor for class com.chemaxon.search.MatchingOptions.Builder
Creates a Builder object with the default settings.
Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object with the default settings.
Builder(MatchingOptions) - Constructor for class com.chemaxon.search.MatchingOptions.Builder
Creates a Builder object containing the settings of the given search options object.
Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object containing the settings of the given search options object.
BuildupMcs - Class in com.chemaxon.search.mcs.buildup
Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
BuildupMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.buildup.BuildupMcs
Creates a new BuildupMcs object with the given search options.
BUILT_IN_CHAIN_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in chain colors.
BUILT_IN_CPK_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in cpk colors.
BUILT_IN_RAINBOW_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in rainbow colors.
BUILT_IN_RESIDUE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in residue colors.
BUILT_IN_SECONDARY_STRUCTURE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in secondary structure colors.
BUTTON_MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "buttonmenubar".
BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure
For internal usage only.

C

C - Static variable in class chemaxon.core.ChemConst
 
C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter
Close the underlying stream.
C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter
Flush the output stream and force any buffered output bytes to be written out.
C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator
Name of the 13C chemical shift atom property.
C13 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
13C NMR
Ca - Static variable in class chemaxon.core.ChemConst
 
CACHE_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "cacheMols".
CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for clearing all cached info.
CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in aromatization.
CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for cacheMemory.
CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in graph invariant calculation.
CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in parity calculation.
CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in sssr.
CACHE_REMOVE_TABS - Static variable in class chemaxon.struc.MoleculeGraph
Cache remove option to clear ctab and btab.
cacheMemory - Variable in class chemaxon.struc.MoleculeGraph
 
calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates a "badness" value for the atomic coordinates.
calcBitCount(int) - Static method in class chemaxon.descriptors.Metrics
Counts the number of bits set (1) in the integer parameter.
calcBitCount(int[]) - Static method in class chemaxon.descriptors.Metrics
Counts the number of bits set (1) in a bit vector.
calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the bracket endpoints from the base line of the bracket.
calcCenter() - Method in class chemaxon.struc.MDocument
Calculates the geometrical center.
calcCenter() - Method in class chemaxon.struc.MoleculeGraph
Calculates the geometrical center.
calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument
Calculates the geometrical center.
calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
Calculates the geometrical center.
calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
Calculates the graph invariants with the assumption that hydrogens are removed.
calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the division point of a segment with a given ratio.
calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator
Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator
Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator
Calculate and store in freqCount[] absolute frequency counts per cells.
calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator
Calculate and store in freqCount[] absolute frequency counts per cells.
calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator
Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
calcHeight() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecule height.
calcHybridization() - Method in class chemaxon.struc.MoleculeGraph
Calculates and sets hybridazation state for each atom.
calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the logD value at fixed pH.
calcMaxDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
Calculates the minimum distance between two atoms in the molecule.
calcOrderFromLength() - Method in class chemaxon.struc.MolBond
Calculate the bond order from the atomic distances.
calcOrderFromValence() - Method in class chemaxon.struc.MolBond
Calculate bond order from the types and charges of the two atoms.
calcOutRect() - Method in class chemaxon.struc.MoleculeGraph
Calculates the outer rectangle.
calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the outer rectangle.
calcOutRectCenter() - Method in class chemaxon.struc.MoleculeGraph
Calculates the center of the outer rectangle.
calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the center of the outer rectangle.
CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Calculator rgb offset.
calcSimplePolymerBracket(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the points of a simple polymer bracket that belongs to a bond.
calcStereo2() - Method in class chemaxon.struc.MolBond
Computes the stereochemistry of the bond based on the atomic coordinates.
calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
Computes the stereochemistry of the bond based on the atomic coordinates.
calcStereo2(MolAtom, MolAtom, MolAtom, MolAtom) - Static method in class chemaxon.struc.MolBond
Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates.
calculate() - Method in class chemaxon.marvin.alignment.MMPAlignment
Runs the MCS alignment calculation on the two structures of the constructor.
calculate(int[]) - Method in class chemaxon.marvin.alignment.MolAligner
Calculate best alignment based on the hit map
calculate(Molecule) - Static method in class chemaxon.calculations.bbb.BBB
Calculates the BBB properties and scores of the given Molecule.
calculate(Molecule) - Method in enum class chemaxon.calculations.bbb.BBBFunction
Calculates the BBB property, its score and its multiplied score.
calculate(Molecule) - Static method in class chemaxon.calculations.cnsmpo.CnsMpo
Calculates the CNS MPO properties and scores of the given molecule.
calculate(Molecule) - Method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Calculates the CNS MPO property and its score.
calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
Calculates NMR spectrum for the given input molecule.
calculate(Molecule) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator
 
calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator
 
calculate(Molecule, Molecule, McsSearchOptions) - Method in interface com.chemaxon.search.mcs.upperbound.UpperBoundCalculator
Returns an upper bound for the number of bonds the Maximum Common Substructure of the given molecules may contain.
calculate(Molecule, ProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculate(Molecule, ProgressObserver, DihedralScanListener) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.
calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
 
calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
 
calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
 
calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
Calculates the stereo descriptors of the given molecule.
calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Calculates the coordinates during expand and contract.
calculateCosAFromScalarMul(MolBond, MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.
calculateIntrinsicSolubility(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates intrinsic solubility.
calculatePhDependentSolubility(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates pH-dependent solubility.
calculatePhDependentSolubility(Molecule, double[]) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates pH-dependent solubilities.
calculatePhDependentSolubility(Molecule, double, double, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates pH-dependent solubilities.
calculateSimilarityUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.
calculateUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.
CALCULATIONS_PACK - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Calculations Pack
CalculatorError - Interface in chemaxon.calculator
An error that might occur when a calculator is initialized.
CalculatorInputChecker - Interface in chemaxon.calculator
Instances of this interface are used by calculators to check if they can process an input molecule.
CalculatorPlugin - Class in chemaxon.marvin.plugin
Common base class for calculator plugins.
CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin(Consumer<Molecule>, Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin
 
CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.gui
Common base class for calculator plugin displays.
CalculatorPluginDisplay() - Constructor for class com.chemaxon.calculations.gui.CalculatorPluginDisplay
 
CalculatorPluginOutput<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.cli
Class providing plugin output in table form.
CalculatorPluginOutput() - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput
Default constructor.
CalculatorPluginOutput(CalculatorPlugin) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput
Constructor that sets plugin.
CalculatorPluginService<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin
Base class for types that implement a functionality related to a specific CalculatorPlugin.
CalculatorPluginService() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginService
 
CalculatorTag - Enum Class in chemaxon.calculator
List of optional tags that can be reported by a TaggedCalculator.
calcWidth() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecule width.
call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Performs the calculation and returns the result returned by PluginWorkUnit.getResult().
call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Performs the calculation and returns the result returned by ReusablePluginWorkUnit.getResult().
callback(String, Object) - Method in interface chemaxon.jep.ChemContext
Deprecated, for removal: This API element is subject to removal in a future version.
callback(String, Object) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used for accessing the context, will be removed without replacement.
callback(String, Object) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Deprecated, for removal: This API element is subject to removal in a future version.
Call the appropriate methods directly.
callback(String, Object) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
Call the appropriate methods directly.
callContextFunction(String, List<Object>) - Method in interface chemaxon.jep.ChemContext
Executes the specified context function with the given parameters.
callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.AtomContext
Executes the specified context function with the given parameters.
callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.MolContext
Executes the specified context function with the given parameters.
callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.ReactionContext
Executes the specified context function with the given parameters.
callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
Performs thread-safe asynchronous service call.
callService(DT, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
Performs a service call.
CAN_BE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
canBeCT(int, int) - Method in class chemaxon.struc.MoleculeGraph
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
canBeCT(int, int, boolean) - Method in class chemaxon.struc.MoleculeGraph
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
canBeCT(int, int, boolean) - Method in class chemaxon.struc.RgMolecule
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
canBeCT(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Determines whether the given bond can be a CIS/TRANS or not.
canBeReactionComponent() - Method in class chemaxon.struc.Molecule
Tests whether an object of this class can be a reaction component.
canBeReactionComponent() - Method in class chemaxon.struc.RgMolecule
Tests whether an object of this class can be a reaction component.
canBeReactionComponent() - Method in class chemaxon.struc.RxnMolecule
Tests whether an object of this class can be a reaction component.
canBeSMARTS(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner
Stops the background thread
cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment
Cancel the ongoing calculation
cancel() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
cancel() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Stops the background thread
CancelObserver - Interface in com.chemaxon.calculations.common
Callback to propagate cancel requests into long-running tasks.
CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.
carboaliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
carboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.carboaliphaticRingCount()
carboaromaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
carboaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.carboaromaticRingCount()
carboRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).
carboRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.carboRingCount()
carboRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
carboRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.carboRingCount(int)
carboRings() - Method in class chemaxon.calculations.Ring
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
carboRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.carboRings()
carboRings(int) - Method in class chemaxon.calculations.Ring
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
carboRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.carboRings(int)
CARTRIDGE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem Cartridge
CATIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
CCLENGTH - Static variable in class chemaxon.struc.MolBond
Default bond length.
Cd - Static variable in class chemaxon.core.ChemConst
 
CDParameters - Class in chemaxon.descriptors
Manages parameters the CustomDescriptor class.
CDParameters() - Constructor for class chemaxon.descriptors.CDParameters
Creates an empty object.
CDParameters(int) - Constructor for class chemaxon.descriptors.CDParameters
Creates an empty object of the given type.
CDParameters(File) - Constructor for class chemaxon.descriptors.CDParameters
Creates a new descriptor configured from the given file.
CDParameters(String) - Constructor for class chemaxon.descriptors.CDParameters
Creates a new object based on a given configuration string.
CDX - Static variable in class chemaxon.formats.MFileFormat
ChemDraw CDX file.
CDXML - Static variable in class chemaxon.formats.MFileFormat
ChemDraw CDXML file.
Ce - Static variable in class chemaxon.core.ChemConst
 
CELL - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "cell".
CELL_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
CellOrComponentId - Class in chemaxon.marvin.space
Deprecated, for removal: This API element is subject to removal in a future version.
CellOrComponentId(int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Creates a cell id.
CellOrComponentId(int, int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Creates an id.
cellSize - Variable in class chemaxon.descriptors.MDParameters
size - number of bits - of one descriptor cell
CELLSIZE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The default viewer cell size.
cellwiseWeights - Variable in class chemaxon.descriptors.MDParameters
is cell weights for parametrized metrics
center - Variable in class chemaxon.marvin.space.monitor.Control
 
center - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
centerx() - Method in class chemaxon.marvin.space.BoundingBox
Returns the x coordinate of the center of the box.
centery() - Method in class chemaxon.marvin.space.BoundingBox
Returns the y coordinate of the center of the box.
centerz() - Method in class chemaxon.marvin.space.BoundingBox
Returns the z coordinate of the center of the box.
centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane
Puts the molecule into the center of the display.
Cf - Static variable in class chemaxon.core.ChemConst
 
CFGenerator - Class in chemaxon.descriptors
The CFGenerator class generates topological fingerprints of molecular graphs.
CFGenerator() - Constructor for class chemaxon.descriptors.CFGenerator
Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.
CFGenerator(int) - Constructor for class chemaxon.descriptors.CFGenerator
Deprecated.
since 5.4
CFNS - Static variable in class chemaxon.jep.context.AtomContext
The context function names.
CFNS - Static variable in class chemaxon.jep.context.ReactionContext
The context function names.
CFParameters - Class in chemaxon.descriptors
Manages fingerprint parameters.
CFParameters() - Constructor for class chemaxon.descriptors.CFParameters
Creates an empty object.
CFParameters(File) - Constructor for class chemaxon.descriptors.CFParameters
Creates a new object based on a given configuration file.
CFParameters(String) - Constructor for class chemaxon.descriptors.CFParameters
Creates a new object based on a given configuration string.
chainAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of chain atoms in the molecule excluding hydrogens.
chainAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.chainAtomCount()
chainBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.
chainBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.chainBondCount()
chainTransformers(Transformer...) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a chain transformer.
chainTransformers(List<Transformer>) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a chain transformer.
changeColorMapperColors(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.
Changes - Class in chemaxon.standardizer
The change set of the standardization procedure.
Changes(Molecule) - Constructor for class chemaxon.standardizer.Changes
Initializes the changes object.
Changes(Molecule, StandardizerAction) - Constructor for class chemaxon.standardizer.Changes
Initializes the changes object.
Changes(Molecule, Molecule) - Constructor for class chemaxon.standardizer.Changes
Initializes the changes object.
CHANGING - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
Only reaction center will be mapped
CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).
charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a character of the document.
CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).
CHARGE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).
CHARGE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignore charge searching (charge information is ignored during searching).
CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup
Charge is located on atoms and displayed on atoms.
CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup
Charge is located on atoms but displayed on the whole group (bracket).
CHARGE_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Charge Plugin Group
CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "chargeWithCircle".
CHARGED_H - Static variable in class chemaxon.struc.MolAtom
Include charged Hydrogen atom(s).
chargeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
chargeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether formal charges of atoms should be considered in search.
chargeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
ChargePlugin - Class in chemaxon.marvin.calculations
Plugin class for partial charge calculation.
ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin
Constructor.
check() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
check() - Method in interface chemaxon.checkers.runner.CheckerRunner
Invokes a background thread which will run all checkers on the given molecule
check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
 
check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
 
check(Molecule) - Method in class chemaxon.checkers.InvalidChecker
 
check(Molecule) - Method in interface chemaxon.checkers.StructureChecker
Detects a specific error in the molecule.
check(Molecule) - Method in interface chemaxon.jep.MolCondition
Deprecated.
Returns true if molecule should be processed, false otherwise.
check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AliasChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker
Detects atom of the molecule has atom map.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker
Detects if the current atom of the molecule has atom value.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker
Check the atom of the molecule with index i has no atom map.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker
Detects atom of the molecule is a query atom.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker
Detects if the current atom has free electrons.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.BondTopologyChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker
Examines if the bond is a crossed double bond.
check(Molecule, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker
Detects bond of the molecule is crossing another bond or closer than the limit distance.
check(Molecule, MolBond) - Method in class chemaxon.checkers.QueryBondChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker
 
check(Molecule, E) - Method in class chemaxon.checkers.ComponentChecker
Checks if the component with index i has problem
Check - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Mode
Indicates, that the structurechecker does not automatically fixes.
check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker
Determines if a non chiral molecule contains a chiral flag.
check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker
Determines if all asymmetric centers have absolute stereo configuration
check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
This method contains the current checking mechanism.
check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker
Detects attached data in the molecule
check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker
 
check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker
 
check1(Molecule) - Method in class chemaxon.checkers.BracketsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker
Determines if a non chiral molecule contains a chiral flag.
check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker
Iterates through the components and checks every component.
check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Detects implicitizable hydrogen atoms.
check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.IncorrectTetrahedralStereoChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker
Detects if molecule has charge
check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker
 
check1(Molecule) - Method in class chemaxon.checkers.NonStandardWedgeSchemeChecker
 
check1(Molecule) - Method in class chemaxon.checkers.NonStereoWedgeBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RatomChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RgroupBridgeRatomChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.SolventChecker
 
check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker
 
check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker
 
check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker
Deprecated.
In version 15.8.3 the checker logic was replaced with the logic implemented in Molecule's stereoClean() method.
check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker
 
checkAndWait() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
checkAndWait() - Method in interface chemaxon.checkers.runner.CheckerRunner
Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems
checkAtno(int) - Static method in class chemaxon.struc.MolAtom
Check if the given atomic number is positive and less then atomic type maximum value.
checkBondConsistency() - Method in class chemaxon.struc.MoleculeGraph
 
checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule
Empty implementation, bond consistency is not checked in case of selections.
checkBondConsistency() - Method in class chemaxon.struc.Sgroup
 
checkBonds(MolAtom) - Method in class chemaxon.struc.Sgroup
Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
checkBonds(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
checkConsistency() - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistency() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistency() - Method in class chemaxon.struc.RgMolecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistencyInEmbeddings() - Method in class chemaxon.struc.Sgroup
Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.
checkDocumentVersion(String, String) - Method in class chemaxon.descriptors.MDParameters
Checks if the document is the right version
CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Chemaxon's default checker configuration file name
CheckerInfo - Annotation Interface in chemaxon.checkers
This annotation is responsible for adding GUI based meta data for StructureChecker implementations
CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark
 
CheckerRunner - Interface in chemaxon.checkers.runner
The descendant of CheckerRunner interface has to provide the functionality to run StructureChecker instances automatically
on the given molecule and fix the problems with the associated StructureFixer instances.

Example:

CheckerRunner can be used directly with the checkAndWait method.
CheckerSeverity - Enum Class in chemaxon.checkers
This enum defines the constants which represent the severity of the StructureChecker implementations
checkFilter(String) - Static method in class chemaxon.sss.search.MolSearch
Checks the syntax of the filtering expression.
checkFilter(String, File) - Static method in class chemaxon.sss.search.MolSearch
Checks the syntax of the filtering expression.
checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Checks the input molecule.
checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.
checkSgroupConsistency() - Method in class chemaxon.struc.Molecule
Checks the internal consisitency of S-groups.
checkSgroupConsistency() - Method in class chemaxon.struc.RgMolecule
Checks the consistency of S-groups.
checkSgroupConsistency() - Method in class chemaxon.struc.RxnMolecule
Checks the consistency of S-groups.
checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.Sgroup
Checks whether the parameter s-group contains the atoms of this s-group.
checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup.
checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Checks result types.
checkValence(MolAtom) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
 
checkValence(MoleculeGraph) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
 
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject
Is it a valid object in the document?
CHEM_CURATOR_COMPOUND - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Compound
CHEM_CURATOR_FULL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Full
chemaxon.calculations - package chemaxon.calculations
Contains chemical computation modules.
chemaxon.calculations.bbb - package chemaxon.calculations.bbb
BBB score calculator.
chemaxon.calculations.cip - package chemaxon.calculations.cip
 
chemaxon.calculations.clean - package chemaxon.calculations.clean
 
chemaxon.calculations.cnsmpo - package chemaxon.calculations.cnsmpo
CNS MPO score calculator.
chemaxon.calculations.dipole - package chemaxon.calculations.dipole
 
chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize
 
chemaxon.calculations.nmr - package chemaxon.calculations.nmr
 
chemaxon.calculations.nmr.io - package chemaxon.calculations.nmr.io
 
chemaxon.calculations.stereo - package chemaxon.calculations.stereo
 
chemaxon.calculator - package chemaxon.calculator
 
chemaxon.checkers - package chemaxon.checkers
Structure checkers can be used to filter drawing mistakes or special structural elements.
chemaxon.checkers.result - package chemaxon.checkers.result
This package is used to identify problems found in molecules.
chemaxon.checkers.runner - package chemaxon.checkers.runner
This package supports the automatic running of structure checkers.
chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader
Extension package of the automatic runner functionality.
chemaxon.common.util - package chemaxon.common.util
 
chemaxon.core - package chemaxon.core
 
chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo
 
chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck
 
chemaxon.core.util - package chemaxon.core.util
 
chemaxon.descriptors - package chemaxon.descriptors
 
chemaxon.descriptors.scalars - package chemaxon.descriptors.scalars
 
chemaxon.fixers - package chemaxon.fixers
Structure fixers can be used to fix problems identified by structure checker instances.
chemaxon.formats - package chemaxon.formats
Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.
chemaxon.formats.factory - package chemaxon.formats.factory
 
chemaxon.formats.recognizer - package chemaxon.formats.recognizer
Provides classes to recognize files of various file formats.
chemaxon.jep - package chemaxon.jep
Chemical Terms Evaluator classes.
chemaxon.jep.context - package chemaxon.jep.context
Specific chemical terms evaluation contexts.
chemaxon.license - package chemaxon.license
Classes related licenses, license handling, validating, GUI and documentation.
chemaxon.marvin - package chemaxon.marvin
Contains utility classes for rendering molecules.
chemaxon.marvin.alignment - package chemaxon.marvin.alignment
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
chemaxon.marvin.alignment.atrop - package chemaxon.marvin.alignment.atrop
Utilities for AtropIsomerDetector.
chemaxon.marvin.beans - package chemaxon.marvin.beans
Provides bean classes for creating Marvin based user interface.
chemaxon.marvin.calculations - package chemaxon.marvin.calculations
Provides specific plugin, plugin loader and table form output implementations.
chemaxon.marvin.common - package chemaxon.marvin.common
Contains a class for handling user settings.
chemaxon.marvin.io - package chemaxon.marvin.io
Provides classes for molecule import and export through data streams.
chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats
Core package of any import/export module.
chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles
 
chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.
chemaxon.marvin.modules.reaction - package chemaxon.marvin.modules.reaction
 
chemaxon.marvin.plugin - package chemaxon.marvin.plugin
Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.
chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent
Classes to achieve concurrent processing of calculator plugins.
chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
Calculator plugin common GUI classes.
chemaxon.marvin.services - package chemaxon.marvin.services
Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.
chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice
 
chemaxon.marvin.services.json - package chemaxon.marvin.services.json
 
chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice
 
chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap
 
chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice
 
chemaxon.marvin.sketch - package chemaxon.marvin.sketch
Contains the sketcher's core classes and various sketching modes.
chemaxon.marvin.sketch.swing.modules.documentstyle - package chemaxon.marvin.sketch.swing.modules.documentstyle
 
chemaxon.marvin.space - package chemaxon.marvin.space
Contains the core classes of MarvinSpace including the graphic canvas and the basic visualizer classes.
chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
chemaxon.marvin.uif.dialog - package chemaxon.marvin.uif.dialog
 
chemaxon.marvin.util - package chemaxon.marvin.util
Contains some utilities for example for molecule cleaning and Swing.
chemaxon.marvin.util.codeassist - package chemaxon.marvin.util.codeassist
 
chemaxon.marvin.view - package chemaxon.marvin.view
Control records in MarvinView.
chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing
Swing support for MarvinView tables.
chemaxon.naming - package chemaxon.naming
Name to Structure conversion.
chemaxon.naming.document - package chemaxon.naming.document
Document to Structure (D2S) conversion.
chemaxon.naming.document.annotate - package chemaxon.naming.document.annotate
 
chemaxon.sss - package chemaxon.sss
 
chemaxon.sss.screen - package chemaxon.sss.screen
 
chemaxon.sss.search - package chemaxon.sss.search
 
chemaxon.sss.search.options - package chemaxon.sss.search.options
 
chemaxon.standardizer - package chemaxon.standardizer
Contains packages for structure standardization.
chemaxon.standardizer.actions - package chemaxon.standardizer.actions
Contains basic standardizer actions.
chemaxon.standardizer.advancedactions - package chemaxon.standardizer.advancedactions
Contains advanced standardizer actions.
chemaxon.standardizer.concurrent - package chemaxon.standardizer.concurrent
Contains classes for concurrent execution of standardization.
chemaxon.standardizer.configuration - package chemaxon.standardizer.configuration
Contains classes for handling configurations of standardizer.
chemaxon.standardizer.configuration.reader - package chemaxon.standardizer.configuration.reader
Contains classes for handling configuration deserialization.
chemaxon.standardizer.runner - package chemaxon.standardizer.runner
Contains classes for executing standardization based on a configuration.
chemaxon.struc - package chemaxon.struc
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.
chemaxon.struc.graphics - package chemaxon.struc.graphics
Contains graphics MDocument elements.
chemaxon.struc.prop - package chemaxon.struc.prop
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
chemaxon.struc.sgroup - package chemaxon.struc.sgroup
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.
chemaxon.util - package chemaxon.util
Provides general utility classes.
chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
 
chemaxon.util.iterator - package chemaxon.util.iterator
Provides iterator classes for molecules and their components.
ChemConst - Class in chemaxon.core
 
ChemConst() - Constructor for class chemaxon.core.ChemConst
 
ChemContext - Interface in chemaxon.jep
Interface of expression evaluation contexts.
ChemContext.ProvidesFunction - Annotation Interface in chemaxon.jep
Repeatable annotation used on ChemContext implementations to declare the context functions supported by the ChemContext.callContextFunction(String, List) method.
ChemContext.ProvidesFunctionContainer - Annotation Interface in chemaxon.jep
Container for the repeatable ChemContext.ProvidesFunction annotation.
ChemicalFingerprint - Class in chemaxon.descriptors
The ChemicalFingerprint class implements topological fingerprints as a type of MolecularDescriptors.
ChemicalFingerprint() - Constructor for class chemaxon.descriptors.ChemicalFingerprint
Creates a new, empty instance of ChemicalFingerprint without allocating internal storage.
ChemicalFingerprint(CFParameters) - Constructor for class chemaxon.descriptors.ChemicalFingerprint
Creates a new instance of ChemicalFingerprint according to the parameters given.
ChemicalFingerprint(ChemicalFingerprint) - Constructor for class chemaxon.descriptors.ChemicalFingerprint
Copy constructor.
ChemicalFingerprint(String) - Constructor for class chemaxon.descriptors.ChemicalFingerprint
Creates a new instance of ChemicalFingerprint according to the parameters given.
ChemJEP<C extends ChemContext> - Class in chemaxon.jep
Expression parser and evaluator for chemical expressions.
ChemJEP() - Constructor for class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Direct creation of a ChemJEP object will no longer be supported, use the Evaluator.compile(java.lang.String) methods instead.
ChemJEP(Class<? extends C>) - Constructor for class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Direct creation of a ChemJEP object will no longer be supported, use the Evaluator.compile(java.lang.String) methods instead.
CHEMLOCATOR_PERSONAL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemLocator Personal
CHEMLOCATOR_SERVER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemLocator Server
CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents molecules marked with "absolute stereo" flag.
chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of chiral centers.
chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.chiralCenterCount()
chiralCenterCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Calculates the number of tetrahedral stereogenic centers.
chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry
Determines the chiral center atoms.
chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.chiralCenters()
ChiralFlagChecker - Class in chemaxon.checkers
Implementation of AbstractStructureChecker detecting "absolute stereo flag" on molecule.
ChiralFlagChecker() - Constructor for class chemaxon.checkers.ChiralFlagChecker
Constructs ChiralFlagChecker instance
ChiralFlagErrorChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).
ChiralFlagErrorChecker() - Constructor for class chemaxon.checkers.ChiralFlagErrorChecker
Default constructor
CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants
Axially chiral atom with M configuration.
CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants
Chirality mask in flags.
CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants
Axially chiral atom with P configuration.
CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants
Pseudo-asymmetric chiral atom of r configuration.
CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants
Chiral atom of R configuration.
CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants
Pseudo-asymmetric chiral atom of s configuration.
CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants
Chiral atom of S configuration.
CHIRALITY_SUPPORT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "chiralitySupport".
CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants
R/S shown always.
CHIRALITYSUPPORT_ALL_POSSIBLE - Static variable in interface chemaxon.struc.StereoConstants
R/S shown always and highlight possible chiral centers as well.
CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants
R/S not shown for any molecule.
CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants
R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.
CIPStereoCalculator - Class in chemaxon.calculations.cip
Stereo calculator with the Cahn, Ingold, Prelog priority rules.
CIPStereoDescriptorIface - Interface in chemaxon.struc
Cahn-Ingold-Prelog (CIP) stereodescriptor interface.
CIPStereoDescriptorIface.CIPType - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue - Interface in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AtropStereoValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AxialStereoValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.CisTransStereoValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue - Enum Class in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue - Enum Class in chemaxon.struc
 
CIPStereoRecognizer - Class in chemaxon.core.calculations.stereo
Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial, cis/trans and atrop stereo features.
CIPStereoRecognizer() - Constructor for class chemaxon.core.calculations.stereo.CIPStereoRecognizer
 
CIRCULAR_RGROUP_REFERENCE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule with circular R-group definition found
CircularRGroupReferenceChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting circular R-group references.
CircularRGroupReferenceChecker() - Constructor for class chemaxon.checkers.CircularRGroupReferenceChecker
Initializes the checker
CIS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
2 dimension: The rigid part's maximal indexed ligands placed in the same half-plane according to the rigid part.
0 dimension: CIS stereo value was set on the double bond for it's maximal indexed ligands.
CIS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
Deprecated, for removal: This API element is subject to removal in a future version.
CIS - Static variable in interface chemaxon.struc.StereoConstants
Cis double bond.
CIS_TRANS - Static variable in interface chemaxon.struc.StereoConstants
Cis and trans double bond mask.
CisDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
Filter for CIS double bonds.
CisDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
 
cisDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the CIS double bonds.
CISTRANS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
 
CISTRANS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
Cis-trans stereo center.
CISTRANS - Enum constant in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType
Double bond stereoisomers.
CisTransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
Filter for cis-trans stereo centers.
CisTransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
 
cisTransDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the CIS-TRANS double bonds.
cisTransDoubleBondsWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the CIS-TRANS double bonds with attached data.
CisTransStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Cis-trans stereo center implementation.
CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Constructs a new instance of cis-trans stereo center.
CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Constructs a new instance of cis-trans stereo center with attached data.
CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
CisTransStereoDescriptor - Class in chemaxon.struc
 
CisTransStereoDescriptor(CIPStereoDescriptorIface.CIPValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.CisTransStereoDescriptor
 
Cl - Static variable in class chemaxon.core.ChemConst
 
CLASS - Static variable in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
Property key for Service class name as String
className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
 
clean(int) - Method in class chemaxon.formats.MolConverter.Builder
Enables cleaning.
clean(int) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder
Enables cleaning.
clean(int, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
clean(int, String) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).
clean(int, String, int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Clean the specified cell.
clean(int, String, MProgressMonitor) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
clean(MoleculeGraph, int) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates.
clean(MoleculeGraph, int, String) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates.
clean(MoleculeGraph, int, String, MProgressMonitor) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates.
Clean2DAction - Class in chemaxon.standardizer.advancedactions
Clean molecule graph in 2D standardizer action
Clean2DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean2DAction
Initializes the action with parameters
Clean2DAction.Type - Enum Class in chemaxon.standardizer.advancedactions
Type of clean action (partial, full, template based or convert 3D to 2D)
clean3d(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
clean3d(Molecule, int) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
Clean3DAction - Class in chemaxon.standardizer.advancedactions
Clean molecule graph in 3D standardizer action
Clean3DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean3DAction
Initializes the action with parameters
cleanAll(int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Clean all cells.
Cleaner - Class in chemaxon.calculations.clean
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.
Cleaner() - Constructor for class chemaxon.calculations.clean.Cleaner
 
CleanFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which cleans the molecule in 2d
CleanFixer() - Constructor for class chemaxon.fixers.CleanFixer
 
CLEANING_2D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "clean2dOpts".
CLEANING_3D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "clean3dOpts".
CLEANING_DIMENSION - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "cleanDim".
CLEANING_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "cleanOpts".
cleanup() - Method in class chemaxon.marvin.space.GraphicComponent
 
cleanup() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
cleanup() - Method in class chemaxon.marvin.space.PharmacophorePoint
 
cleanupRemovedRgroupMember(MoleculeGraph, int) - Method in class chemaxon.struc.RgMolecule
Clean-up after R-group removal.
CleanUtil - Class in chemaxon.marvin.util
Utility methods for cleaning.
CleanUtil() - Constructor for class chemaxon.marvin.util.CleanUtil
 
clear() - Method in class chemaxon.descriptors.BCUT
Clears the descriptor, all values are set to zero.
clear() - Method in class chemaxon.descriptors.ChemicalFingerprint
Clears the fingerprint: sets all bins to store zero value.
clear() - Method in class chemaxon.descriptors.CustomDescriptor
Clears the descriptor: sets all cells to store zero value.
clear() - Method in class chemaxon.descriptors.ECFP
Clears the fingerprint, all values are set to zero.
clear() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Clears the fingerprint: sets all bins to store zero value.
clear() - Method in class chemaxon.descriptors.ReactionFingerprint
Clears the fingerprint: sets all bins to store zero value.
clear() - Method in class chemaxon.descriptors.ScalarDescriptor
Clears the descritor: sets its value to zero value.
clear() - Method in class chemaxon.descriptors.ShapeDescriptor
Clears the fingerprint, all values are set to zero.
clear() - Method in class chemaxon.formats.MolConverter.Builder
Clears all settings.
clear() - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
clear() - Method in interface chemaxon.jep.ChemContext
Clears the context.
clear() - Method in class chemaxon.jep.context.AtomContext
Clears the context.
clear() - Method in class chemaxon.jep.context.MolContext
Clears the context.
clear() - Method in class chemaxon.jep.context.ReactionContext
Clears the context.
clear() - Method in class chemaxon.marvin.space.BoundingBox
Clears all previously set coordinate from the box.
clear() - Method in class chemaxon.marvin.space.monitor.Monitor
Deletes all items from selectedItems.
clear() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Clears the configuration of action
clear() - Method in class chemaxon.struc.MDocument
Clears the document.
clear() - Method in class chemaxon.struc.MolAtom
Clear query properties, charge, and hcount.
clear() - Method in class chemaxon.struc.Molecule
Clears the molecule.
clear() - Method in class chemaxon.struc.MoleculeGraph
Clears the molecule.
clear() - Method in class chemaxon.struc.MPropertyContainer
Clears properties.
clear() - Method in class chemaxon.struc.MSelectionDocument
Clears the document.
clear() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Clears the display.
CLEAR - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
Remove absolute stereo
clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
clearCachedInfo(int) - Method in class chemaxon.struc.MoleculeGraph
Deletes the cached information depending on the given options.
clearChangesInUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Used in initializing searches.
clearCheckerMarks() - Method in class chemaxon.struc.MDocument
Clears the checker marks
clearClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Clears the clipboard by creating an empty Transferable and placing it on the clipboard.
clearClipboardConditionally() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Clears the clipboard, if ClipboardHandler.isClearClipboardBeforeExport() is true.
clearComparators() - Method in class chemaxon.sss.search.MolSearch
Delete all comparator from the search object.
clearExtraLabel() - Method in class chemaxon.struc.MolAtom
Clears the extra label.
clearExtraLabels() - Method in class chemaxon.struc.Molecule
Clears extra atom labels.
clearForImport(String) - Method in class chemaxon.struc.Molecule
Initializes molecule for import.
clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph
Clears the bonds vector, the properties, the flags, and sets the origin coordinates to 0.
clearForImport(String) - Method in class chemaxon.struc.RgMolecule
Clear the edges vector and the properties.
clearForImport(String) - Method in class chemaxon.struc.RxnMolecule
Clear the edges vector and the properties.
clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane
Reset undo queue.
clearInactiveTasks(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil
Clears the inactive tasks list.
ClearIsotopesAction - Class in chemaxon.standardizer.actions
Clear isotopes standardizer action
ClearIsotopesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearIsotopesAction
Initializes the action
clearLines() - Method in class chemaxon.struc.graphics.MTextBox
Clears all lines.
clearMatch() - Method in class chemaxon.sss.search.MolSearch
 
clearMatch() - Method in class chemaxon.sss.search.Search
Clears the extra prerequisites of the structure search specified using addMatch calls.
clearObjects() - Method in class chemaxon.struc.Molecule
 
clearObjects() - Method in class chemaxon.struc.RgMolecule
 
clearObjects() - Method in class chemaxon.struc.RxnMolecule
Deletes the graphical objects from this.
clearObjects() - Method in class chemaxon.struc.Sgroup
Clears all MObject-s that belong to this S-groups.
clearProperties() - Method in class chemaxon.struc.MolAtom
Removes all properties from this atom.
clearProperties() - Method in class chemaxon.struc.MolBond
Removes all properties from this bond.
clearProperties() - Method in class chemaxon.struc.Molecule
Clears RDfile/SDfile properties.
clearQProps() - Method in class chemaxon.struc.MolAtom
Clears query props.
clearSavedAtomIndices() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
clearSelection(int) - Method in class chemaxon.marvin.space.GraphicScene
Sets all components and parts of components to be unselected in the given cell.
clearSelections() - Method in class chemaxon.marvin.space.GraphicCell
Sets all components and parts of components to be unselected.
clearSets() - Method in class chemaxon.struc.MDocument
Clears the atomSets and the bondSets.
ClearStereoAction - Class in chemaxon.standardizer.actions
Clear stereo standardizer action
ClearStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearStereoAction
Initializes the action with parameters
ClearWedgeFixer - Class in chemaxon.fixers
Clears wedges.
ClearWedgeFixer() - Constructor for class chemaxon.fixers.ClearWedgeFixer
 
CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Flag that indicates an import operation
CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Flag that indicates an export operation
CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Undefined clipboard operation state identifier
CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Temporary property name to mark the molecule if it comes from a file via the clipboard
ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer
Facade of the Clipboard handling in Marvin.
clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Clipboard operation type.
clipSurface(BoundingBox) - Method in class chemaxon.marvin.space.SurfaceComponent
The bounding box of the surface can be used to determine 6 clipping planes and clip (do not draw) parts lying outside of the box.
clone() - Method in class chemaxon.checkers.AbstractStructureChecker
 
clone() - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
clone() - Method in class chemaxon.checkers.SubstructureChecker
 
clone() - Method in class chemaxon.core.util.BondTable
 
clone() - Method in class chemaxon.descriptors.BCUT
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.ChemicalFingerprint
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.CustomDescriptor
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.ECFP
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.MolecularDescriptor
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.ReactionFingerprint
Creates a copy with identical internal state.
clone() - Method in class chemaxon.descriptors.ScalarDescriptor
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.HAcc
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.HDon
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.Heavy
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.LogD
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.LogP
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.Mass
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.scalars.TPSA
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.ShapeDescriptor
 
clone() - Method in class chemaxon.fixers.StructureFixerDescriptor
 
clone() - Method in class chemaxon.formats.MolConverter.Builder
Clones the object.
clone() - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
clone() - Method in class chemaxon.sss.search.MolSearchOptions
 
clone() - Method in class chemaxon.sss.search.SearchOptions
Makes an identical copy of this SearchObject.
clone() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
clone() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
 
clone() - Method in class chemaxon.standardizer.actions.AliasToGroupAction
 
clone() - Method in class chemaxon.standardizer.actions.AromatizeAction
 
clone() - Method in class chemaxon.standardizer.actions.ClearStereoAction
 
clone() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
 
clone() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
clone() - Method in class chemaxon.standardizer.actions.ExpandAction
 
clone() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
clone() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
 
clone() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
 
clone() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
 
clone() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
 
clone() - Method in class chemaxon.standardizer.actions.TautomerizeAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
clone() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.TransformAction
 
clone() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
 
clone() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
clone() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
 
clone() - Method in class chemaxon.struc.CTransform3D
 
clone() - Method in class chemaxon.struc.DPoint3
Make an identical copy.
clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
clone() - Method in class chemaxon.struc.graphics.MBracket
 
clone() - Method in class chemaxon.struc.graphics.MChemicalStruct
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MEFlow
 
clone() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
clone() - Method in class chemaxon.struc.graphics.MEllipse
 
clone() - Method in class chemaxon.struc.graphics.MFont
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MMidPoint
 
clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
 
clone() - Method in class chemaxon.struc.graphics.MPolyline
 
clone() - Method in class chemaxon.struc.graphics.MRectangle
 
clone() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
 
clone() - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
clone() - Method in class chemaxon.struc.graphics.MTextBox
 
clone() - Method in class chemaxon.struc.MDocument
Creates a clone.
clone() - Method in class chemaxon.struc.MObject
Creates a clone.
clone() - Method in class chemaxon.struc.MolAtom
Clones the atom.
clone() - Method in class chemaxon.struc.MolBond
Make a copy of this object.
clone() - Method in class chemaxon.struc.Molecule
Makes an identical copy of the molecule.
clone() - Method in class chemaxon.struc.MoleculeGraph
Make an identical copy of the molecule.
clone() - Method in class chemaxon.struc.MPoint
 
clone() - Method in class chemaxon.struc.MPropertyContainer
Clones this object.
clone() - Method in class chemaxon.struc.prop.MBooleanProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MDoubleProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MHCoords3DProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MIntegerProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MMoleculeProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MObjectProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MStringProp
Clones the object.
clone() - Method in class chemaxon.struc.QueryBond
Make a copy of this object.
clone() - Method in class chemaxon.struc.RgMolecule
Clone the markush structure.
clone() - Method in class chemaxon.struc.RxnMolecule
Make an identical copy of the reaction structure.
clone() - Method in class chemaxon.struc.SelectionMolecule
Create a clone of this SelectionMolecule.
clone() - Method in class chemaxon.struc.sgroup.SgroupAtom
Clones the S-group superatom and it's SuperatomSgroup as well.
clone() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Clones the SuperatomSgroup (and not the Molecule).
cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
Copies the specified atoms.
cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies the specified atoms.
cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
Clones this bond.
cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.QueryBond
Clones this bond.
cloneBondTable(BondTable) - Static method in class chemaxon.core.util.BondTable
Clones the bond table.
cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MHashProp
Clones the object.
cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MListProp
Clones the object.
cloneConfiguration() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Clones the configuration
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
Copies the specified atoms and bonds of this molecule to another one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies the specified atoms of this molecule graph to another one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Copies the specified atoms of this graph to another one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Copies the specified nodes and edges of this graph to another one.
clonecopy(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions
Copies parameters to other.
clonecopy(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions
Copies all search options to other.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
Makes another molecule identical to this one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Make another molecule identical to this one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Make another molecule identical to this one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Make another molecule identical to this one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
Copies the clones of atoms and bonds of this graph to another one.
clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies the specified atoms and bonds of this molecule graph to another one.
clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
Copies the specified atoms and bonds of this graph to another one.
clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions
 
clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions
Copies all search options except search type to other.
clonecopyWithoutSgroups(Molecule) - Method in class chemaxon.struc.Molecule
Copies the all the contents except the S-groups into another molecule object.
cloneDocument() - Method in class chemaxon.struc.MDocument
Creates a clone.
cloneDocument() - Method in class chemaxon.struc.MSelectionDocument
Creates a clone.
cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom
Clones the S-group superatom partially.
cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker
 
cloneItem() - Method in class chemaxon.checkers.InvalidChecker
 
cloneItem() - Method in interface chemaxon.checkers.StructureChecker
Returns a clone of this StructureChecker instance
cloneItem() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
cloneItem() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
cloneItem() - Method in interface chemaxon.standardizer.StandardizerAction
Returns a clone of this StandardizerAction instance
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
Deprecated.
as of Marvin 6.3.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.3.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Deprecated.
as of Marvin 6.3.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Deprecated.
as of Marvin 6.3.
Not supported feature.
cloneMainMolecule() - Method in class chemaxon.struc.MDocument
Creates a clone.
cloneMainMoleculeGraph() - Method in class chemaxon.struc.MDocument
Creates a clone.
cloneMFont() - Method in class chemaxon.struc.graphics.MFont
Creates a clone.
cloneMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
cloneMolecule() - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 2014.09.01.0 use Molecule.clone() instead
cloneMoleculeWithDocument() - Method in class chemaxon.struc.Molecule
Makes an identical copy of the molecule and its document.
cloneMoleculeWithDocument() - Method in class chemaxon.struc.RgMolecule
 
cloneMoleculeWithDocument() - Method in class chemaxon.struc.RxnMolecule
 
cloneProp() - Method in class chemaxon.struc.MDocument.Prop
Creates a clone.
cloneProp() - Method in class chemaxon.struc.MProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MObjectProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MStringProp
Clones the object.
cloneSets(MDocument) - Method in class chemaxon.struc.MDocument
Clones the atom/bond sets from doc.
cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.Sgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.Sgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.DataSgroup
Gets a new DataSgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets a new Sgroup instance.
cloneStructure() - Method in class chemaxon.struc.Sgroup
Gets the clone of the structure stored.
cloneTemporraryObjects(MDocument) - Method in class chemaxon.struc.MDocument
 
close() - Method in class chemaxon.formats.MolConverter
Closes the exporter and the output stream.
close() - Method in class chemaxon.formats.MolExporter
Closes the MolExportModule and the underlying stream.
close() - Method in class chemaxon.formats.MolImporter
Close the underlying input stream.
close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Interrupts parsing.
close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
 
close() - Method in class chemaxon.marvin.io.MDocSource
Closes the underlying input stream(s).
close() - Method in class chemaxon.marvin.io.MolExportModule
Close the stream.
close() - Method in class chemaxon.marvin.io.MRecordImporter
Closes the input stream.
close() - Method in interface chemaxon.marvin.io.MRecordReader
Closes the input stream.
close() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
 
close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
Closes the importers.
close() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Closes the output.
close() - Method in interface com.chemaxon.calculations.common.ProgressObserver
Notifies that the represented task has completed (either successfully or because of a failure), and no further work will be done.
close() - Method in class com.chemaxon.calculations.util.CloseableLineIterator
Deprecated.
 
close(int) - Method in class chemaxon.formats.MolConverter
Closes the exporter.
close(int) - Method in class chemaxon.formats.MolExporter
Closes the MolExportModule and, optionally, the underlying stream.
close(int) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Closes the output.
CloseableLineIterator - Class in com.chemaxon.calculations.util
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed without replacement.
CLOSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Closed flag.
closeSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane
Closes the sketcher window that belongs the the specified cell.
closeWindow(int) - Method in class chemaxon.marvin.beans.MViewPane
Closes the detached viewer window of the specified cell.
closeWindows() - Method in class chemaxon.marvin.beans.MarvinPane
Closes all windows opened by this MarvinPane.
Cm - Static variable in class chemaxon.core.ChemConst
 
CmdlineUtils - Class in com.chemaxon.calculations.util
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed without replacement.
CML - Static variable in class chemaxon.formats.MFileFormat
Chemical Markup Language.
Cn - Static variable in class chemaxon.core.ChemConst
 
CnsMpo - Class in chemaxon.calculations.cnsmpo
CNS MPO score calculator.
CnsMpo.Property - Class in chemaxon.calculations.cnsmpo
Simple DTO that contains the predicted value and its CNS MPO score.
CnsMpoFunction - Enum Class in chemaxon.calculations.cnsmpo
Base phys-chem property calculators and its score functions for CNS MPO calculation.
Co - Static variable in class chemaxon.core.ChemConst
 
CodeAssistConfiguration() - Constructor for class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
 
CodeAssistFactory - Class in chemaxon.marvin.util.codeassist
Manages the creation of Chemical Terms related components, such as the Code Assist text field, toolbars, favorite and macro handling components, and validation response component.
CodeAssistFactory.CodeAssistConfiguration - Class in chemaxon.marvin.util.codeassist
Helper class for CodeAssistFactory to set up CodeAssist
codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Add mass number information to the given code.
colDec - Variable in class chemaxon.descriptors.PFParameters
atom set colors
color - Variable in class chemaxon.marvin.space.GraphicComponent
 
color - Variable in class chemaxon.marvin.space.MoleculeComponent
 
color - Variable in class chemaxon.marvin.space.SurfaceComponent
 
COLOR_MAPPER_BLUE_TO_GREEN - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in blue-cyan-green palette will be used.
COLOR_MAPPER_BLUE_TO_RED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in blue-lightgray-red palette will be used.
COLOR_MAPPER_FIRE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in "fire" palette will be used.
COLOR_MAPPER_GREEN_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in green-cyan-blue palette will be used.
COLOR_MAPPER_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in rainbow palette will be used.
COLOR_MAPPER_RED_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in red-lightgray-blue palette will be used.
COLOR_MAPPER_REVERSE_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in reverse rainbow palette will be used.
COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "colorScheme".
color3 - Variable in class chemaxon.marvin.space.SurfaceComponent
 
ColorGenerator - Class in chemaxon.marvin.util
A final class which provides a static access to a color distant color creator class.
ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator
 
coloring(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
 
COLORING_ALL - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for setting all coloring options, currently scaffold and R-groups.
COLORING_NONE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for no hit coloring.
COLORING_RGROUPS - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for R-group coloring.
COLORING_SCAFFOLD - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for scaffold coloring.
colorType - Variable in class chemaxon.marvin.space.MoleculeComponent
 
COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "cols".
com.chemaxon.calculations.admet - package com.chemaxon.calculations.admet
 
com.chemaxon.calculations.cli - package com.chemaxon.calculations.cli
 
com.chemaxon.calculations.common - package com.chemaxon.calculations.common
Common components of Calculator APIs.
com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal
API of the elemental analysis functionality.
com.chemaxon.calculations.elemanal.factory - package com.chemaxon.calculations.elemanal.factory
 
com.chemaxon.calculations.gui - package com.chemaxon.calculations.gui
 
com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility
 
com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal
API of the Stereo Analysis Plugin.
com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters
Core filter classes.
com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop
Atrop stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial
Axial stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans
Cis-trans stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral
Tetrahedral stereo filter implementations.
com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters
Stereocenter implementations of Stereo Analysis API.
com.chemaxon.calculations.stereoisomers - package com.chemaxon.calculations.stereoisomers
 
com.chemaxon.calculations.util - package com.chemaxon.calculations.util
 
com.chemaxon.common.annotations - package com.chemaxon.common.annotations
 
com.chemaxon.mapper - package com.chemaxon.mapper
 
com.chemaxon.search - package com.chemaxon.search
Tools for chemical search.
com.chemaxon.search.mcs - package com.chemaxon.search.mcs
Contains classes for finding the maximum common substructure (MCS) of molecular structures.
com.chemaxon.search.mcs.buildup - package com.chemaxon.search.mcs.buildup
Contains MCS algorithm implementation based on the "build up" method.
com.chemaxon.search.mcs.maxclique - package com.chemaxon.search.mcs.maxclique
Contains MCS algorithm implementation based on the "maximum clique" method.
com.chemaxon.search.mcs.upperbound - package com.chemaxon.search.mcs.upperbound
Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.
com.chemaxon.search.transformation - package com.chemaxon.search.transformation
 
com.chemaxon.search.transformation.transformers - package com.chemaxon.search.transformation.transformers
 
com.chemaxon.version - package com.chemaxon.version
 
combine(Collection<? extends CalculatorInputChecker>) - Static method in interface chemaxon.calculator.CalculatorInputChecker
Combines the given checkers into a single one that reports all errors reported by the given checkers.
compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator
 
compareAtoms(int, int) - Method in class chemaxon.sss.search.MolComparator
Compares atoms of indices a1 and a2.
compareBonds(int, int) - Method in class chemaxon.sss.search.MolComparator
Compares bonds of indices b1 and b2.
compareHit(int[], int) - Method in class chemaxon.sss.search.MolComparator
Checks a partial hit during the search algorithm.
compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Comparison method which uses the priority field for ordering.
compareTo(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
compareTo(Object) - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
compile(String) - Method in class chemaxon.jep.ChemJEP
Compiles the expression string to an inner structure.
compile(String) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, C) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, C, ConstantTable) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, Class<? extends C>) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, Class<? extends C>, ConstantTable) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, Class<? extends C>, SymbolTable) - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
COMPILE_ERROR - Static variable in class chemaxon.jep.ChemJEP
The compilation error message.
COMPLETE - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
All atoms will be mapped
component - Variable in class chemaxon.marvin.space.monitor.Control
 
COMPONENT - Enum constant in enum class chemaxon.struc.SgroupType
 
COMPONENT_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_ENTIRE - Static variable in class chemaxon.marvin.space.GraphicComponent
Indicates if the entire component is selected by picking.
COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
componentBecameSelected() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if a component became selected previously.
componentBecameSelected(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if a component became selected previously in the given cell.
componentBecameUnselected() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if a component became unselected previously.
componentBecameUnselected(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if a component became unselected previously in the given cell.
ComponentChecker<E> - Class in chemaxon.checkers
Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).
ComponentChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.ComponentChecker
Constructor to create a Structure checker instance with the given errorType.
ComponentElement - Class in chemaxon.marvin.space
Class to identify parts of GraphicComponents mainly during selection.
ComponentElement(ComponentElement) - Constructor for class chemaxon.marvin.space.ComponentElement
Copies the given ComponentElement.
ComponentElement(GraphicComponent, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement of a simple (not structured) GraphicComponent.
ComponentElement(GraphicComponent, int, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement of a complex (structured) GraphicComponent.
ComponentElement(GraphicComponent, int, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement.
ComponentElement(GraphicComponent, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement.
componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Hides windows if the parent frame is hidden.
componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Does nothing.
componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Does nothing.
componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MViewPane
 
componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Shows windows if the parent frame is hidden.
composition() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
composition(int) - Method in class chemaxon.calculations.ElementalAnalyser
Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
COMPOSITION - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "composition".
COMPRESS - Static variable in class chemaxon.formats.MdlCompressor
Compression flag.
compressedData - Variable in class chemaxon.descriptors.PFParameters
Buffer for compressed data, used in MolecularDescriptor.toData( final int[] ).
computeFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Computes the scaling factor for the unscaled NMR spectrum function.
computeFunctionScale(double, double[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
 
computeSurface(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MSpaceEasy
Activates the container cell of the MoleculeVisualizer, and computes its Connolly surface.
computeSurface(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Computes the given type of surface in the active cell of the viewer.
ConcurrentStandardizerProcessor - Class in chemaxon.standardizer
Performs standardization of molecules in concurrent mode.
ConcurrentStandardizerProcessor() - Constructor for class chemaxon.standardizer.ConcurrentStandardizerProcessor
 
ConcurrentStandardizerProcessor.MolTransformer - Interface in chemaxon.standardizer
Molecule transformer.
CONFIDENCE - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the confidence that the structure is correct.
config - Variable in class chemaxon.checkers.StructureCheckOptions
The configuration of the structure check.
CONFIG_DIR - Static variable in class chemaxon.jep.Evaluator
Default directory for storing configuration files.
CONFIG_PATH_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction
The key of configuration path parameter of the abstract action.
configFilePath - Variable in class chemaxon.descriptors.MDParameters
location of the configuration file
ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader
This interface is provided for classes which can read the configuration of CheckerRunner.
ConfigurationUtility - Class in chemaxon.standardizer.configuration
Utility to manage standardizer configuration
ConfigurationUtility() - Constructor for class chemaxon.standardizer.configuration.ConfigurationUtility
 
CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "confirmTransfer".
CONFORMATION - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
CONFORMATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Conformation Plugin Group
CONFORMER_CONFORMERS - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
CONFORMER_HASVALIDCONFORMER - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
CONFORMER_LECONFORMER - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
ConformerPlugin - Class in chemaxon.marvin.calculations
Plugin class for conformer calculation.
ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin
Constructor.
CONJUGATED - Static variable in class chemaxon.struc.MolBond
Conjugation state of the bond.
connectedMode(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether the common substructures should be connected or they can consist of multiple fragments.
connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule
 
connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
Sets the original connections to the new atom.
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject
 
constant - Variable in class chemaxon.marvin.services.ServiceArgument
field indicates constant argument
constants() - Method in class chemaxon.jep.ConstantTable
Returns an immutable set containing the names of the constants in this table.
constantTable() - Method in class chemaxon.jep.ChemJEP
Returns the constant table used by this parser.
constantTable() - Method in class chemaxon.jep.Evaluator
Returns the table of predefined constants (molecules, molecule sets and other constants defined in the built-in and the user-defined jep.script).
ConstantTable - Class in chemaxon.jep
Immutable table of constants used in a Chemical Terms evaluator.
ConstantTableBuilder - Class in chemaxon.jep
A builder for a ConstantTable.
containerFrame - Variable in class chemaxon.marvin.space.MSpaceEasy
 
contains(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
Tells whether the given location is inside the box.
contains(MDocument) - Method in class chemaxon.struc.MDocument
Tests whether the document contains all objects of another document.
contains(MObject) - Method in class chemaxon.struc.MDocument
Searches an object in the document.
contains(MolAtom) - Method in class chemaxon.struc.MolBond
 
contains(MolAtom) - Method in class chemaxon.struc.Molecule
Checks if the molecule graph contains the specified atom.
contains(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Checks if the molecule graph contains the specified atom.
contains(MolAtom) - Method in class chemaxon.struc.RgMolecule
Checks if the root structure or an R-group contains the specified node.
contains(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Checks if a reactant, agent or product structure contains the specified node.
contains(MolAtom) - Method in class chemaxon.struc.Sgroup
Is this atom contained by the s-group?
contains(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.
contains(MolBond) - Method in class chemaxon.struc.RgMolecule
Checks if the root structure or an R-group contains the specified edge.
contains(MolBond) - Method in class chemaxon.struc.RxnMolecule
Checks if a reactant, agent or product structure contains the specified edge.
contains(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Does the molecule graph contain the specified fragment?
contains(MProp) - Method in class chemaxon.struc.MPropertyContainer
Tests whether the container contains the specified property object.
contains(MProp) - Method in class chemaxon.struc.prop.MCollectionProp
Tests whether the collection contains the specified property.
containsAllAtomsOf(Sgroup) - Method in class chemaxon.struc.Sgroup
Checks if the S-group contains the atoms of another S-group.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.MObject
Checks if the object contains the specified atom reference.
containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Tells whether the component is in the cell.
containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the component exists in the scene.
containsConstant(String) - Method in class chemaxon.jep.ConstantTable
Returns true if this table contains the given constant.
containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule graph contains coordinate bonds.
containsLadderTypePolymer() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the structure of this sgroup contains a ladder-type repeating unit.
containsMulticenterSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule contains Multicenter S-groups.
containsOnlyOne(Class<?>) - Method in class chemaxon.struc.MDocument
Deprecated, for removal: This API element is subject to removal in a future version.
containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
 
containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom
Returns true if this atom has a mapping for the specified property key.
containsPropertyKey(String) - Method in class chemaxon.struc.MolBond
Returns true if this bond has a mapping for the specified property key.
containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if molecule contains pseudo atom.
containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule contains SRU S-groups.
CONTEXT - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the context of the structure recognized in the text.
CONTEXT_INDEX - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: index of the hit inside the context.
contract(int) - Method in class chemaxon.struc.Sgroup
Sets the state to Sgroup.XSTATE_C.
contract(int) - Method in interface chemaxon.struc.sgroup.Expandable
Contracts the S-group.
contract(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Contracts this S-group.
contract(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Contracts this S-group.
ContractGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule
ContractGroupFixer() - Constructor for class chemaxon.fixers.ContractGroupFixer
 
contractOrExpandSgroups(int, String, boolean) - Method in class chemaxon.marvin.view.MDocStorage
Contract or expand S-groups in the specified cell.
contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.view.MDocStorage
Contract or expand S-groups in all molecules.
contractSgroups() - Method in class chemaxon.struc.Molecule
Contracts all S-groups.
contractSgroups(int) - Method in class chemaxon.struc.Molecule
Contracts all S-groups.
ContractSgroupsAction - Class in chemaxon.standardizer.actions
Standardizer action contracting s-groups of the target molecule
ContractSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ContractSgroupsAction
Initializes the action
control - Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
 
control - Variable in class chemaxon.marvin.space.monitor.Monitor
 
control(int) - Method in class chemaxon.marvin.space.monitor.Control
Does control on z event.
control(int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
One part of the molecule being in one of the end of the torsion bond will be rotated around the bond.
control(int) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Passes the control event to the control.
control(int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Changes the location say translates the component of the control in the global coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Changes the orientation that is rotates the component of the control in the global coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Changes the location say translates the component of the control in its local coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Changes the orientation say rotates the component of the control in its local coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Causes the monitor's controll to take action with 1 parameter.
control(int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
Resizes the component in z direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
control(int, int) - Method in class chemaxon.marvin.space.monitor.Control
Does control on x-y events.
control(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
Does nothing.
control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Changes the location say translates the component of the control in the global coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Changes the orientation say rotates the component of the control in the global coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Changes the location say translates the component of the control in its local coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Changes the orientation say rotates the component of the control in its local coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Causes the monitor's controll to take action with 2 parameters.
control(int, int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
Resizes the component in x, y direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
Control - Class in chemaxon.marvin.space.monitor
Transformation on a GraphicComponent that changes the coordinates, and not just the view.
Control() - Constructor for class chemaxon.marvin.space.monitor.Control
Creates a new instance of Control
convert() - Method in class chemaxon.formats.MdlCompressor
Compression/decompression
convert() - Method in class chemaxon.formats.MolConverter
Convert the next molecule.
convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor
(Un)compress the specified molfile or SDfile.
convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
 
convert(TransferDataImporter) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Convert transfer data available on clipboard in one of the requested flavors.
convert(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Creates an MDL mol or compressed mol representation of the molecule.
convert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule
Convert a molecule to a string or byte array.
convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
 
convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
 
convert(Molecule, Map<String, Map<?, ?>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
This method converts the entities contained in this result according to the convertData.
convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.ModeConverter
 
convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.TypeConverter
 
convert(String, boolean) - Method in interface chemaxon.naming.NameConverter
Convert a name into the corresponding structure.
convert(String, int) - Static method in class chemaxon.formats.MdlCompressor
(Un)compress the specified molfile or SDfile.
ConvertAliasToGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the aliases to contracted abbreviated groups in the molecule
ConvertAliasToGroupFixer() - Constructor for class chemaxon.fixers.ConvertAliasToGroupFixer
 
ConvertConstants - Class in chemaxon.checkers.result
This class contains convert relevant constants
ConvertConstants() - Constructor for class chemaxon.checkers.result.ConvertConstants
 
convertCoordinateBondsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Converts coordinate bonds to data sgroups (attached data) with field name MRV_COORDINATE_BOND.
ConvertDoubleBondsAction - Class in chemaxon.standardizer.actions
Convert double bonds standardizer action
ConvertDoubleBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertDoubleBondsAction
Initializes the action with parameters
ConvertDoubleBondsAction.Type - Enum Class in chemaxon.standardizer.actions
Type of conversion
convertExplicitHToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts explicit Hydrogen atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts explicit Hydrogen atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.
convertExplicitLonePairsToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts explicit lone pairs from a molecule to implicit.
convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts implicit Hydrogen atoms of the molecule to explicit.
convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit lone pairs of the atoms of a molecule to explicit.
convertPageSettingsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX.
ConvertPiMetalBondsAction - Class in chemaxon.standardizer.actions
Convert Pi-Metal coordinate bond to coordinate bond action.
ConvertPiMetalBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertPiMetalBondsAction
Initializes a convert pi-metal bond action
ConvertPseudoToGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the pseudo informations to contracted abbreviated groups in the molecule
ConvertPseudoToGroupFixer() - Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer
 
convertResult(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
This method converts the result by changing the atoms and bonds back to the original instead of the cloned ones
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker
Handles the mapping of a cloned and expanded molecule result to the original molecule.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker
This implementation does nothing.
ConvertToAtomFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information
ConvertToAtomFixer() - Constructor for class chemaxon.fixers.ConvertToAtomFixer
 
ConvertToCarbonFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms
ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer
 
ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond
ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
 
ConvertToElementalFormFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms
ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer
 
ConvertToEnhancedStereoAction - Class in chemaxon.standardizer.actions
Convert to enhanced stereo standardizer action
ConvertToEnhancedStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Initializes the action with parameters
convertToFrags() - Method in class chemaxon.struc.Molecule
Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.
ConvertToIonicFormFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.
ConvertToIonicFormFixer() - Constructor for class chemaxon.fixers.ConvertToIonicFormFixer
 
ConvertToPlainDoubleBondFixer - Class in chemaxon.fixers
Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.
ConvertToPlainDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToPlainDoubleBondFixer
 
ConvertToSingleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the bond to single bond.
ConvertToSingleBondFixer() - Constructor for class chemaxon.fixers.ConvertToSingleBondFixer
 
convertToSmilingFormat(Molecule) - Static method in class chemaxon.formats.MFileFormatUtil
Tries to convert a molecule to a SMILES related format.
convertToSmilingFormat(MProp) - Static method in class chemaxon.formats.MFileFormatUtil
Try to convert a property to text with a SMILES related format argument.
convertToString(MDocument, String, int) - Static method in class chemaxon.formats.MolExporter
Converts the document to text format.
convertToString(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler
Converts the value associated with the given key in the given MPropertyContainer to string.
convertToString(MProp, String) - Static method in class chemaxon.marvin.io.MPropHandler
Converts the property to text format.
convertToString(String) - Method in class chemaxon.struc.MProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop
Deprecated, for removal: This API element is subject to removal in a future version.
convertToString(String, int) - Method in class chemaxon.struc.MProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts crossed double bond to wiggly
ConvertToWigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToWigglyDoubleBondFixer
 
convertTransform(CTransform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle
 
COORDDEP - Static variable in class chemaxon.struc.MProp
Coordinate dependent property.
COORDINATE - Static variable in class chemaxon.struc.MolBond
Coordinate bond flag.
COORDINATE_BOND_STYLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "coordinateBondStyle".
COORDINATE_BOND_STYLE_AT_MULTICENTER - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "coordinateBondStyleAtMulticenter".
CoordinationSystemErrorChecker - Class in chemaxon.checkers
Detects errors of multicenter coordination systems.
CoordinationSystemErrorChecker() - Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker
Default constructor
COORDS_UPDATE - Static variable in interface chemaxon.struc.sgroup.Expandable
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, no replacement.
Not supported feature.
COPOLYMER - Enum constant in enum class chemaxon.struc.SgroupType
 
COPOLYMER_ALT - Enum constant in enum class chemaxon.struc.SgroupType
 
COPOLYMER_BLK - Enum constant in enum class chemaxon.struc.SgroupType
 
COPOLYMER_RAN - Enum constant in enum class chemaxon.struc.SgroupType
 
COPY_AS_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
Default format to be selected on Copy as dialog.
COPY_AS_IMAGE_BITMAP - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version. 
COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version. 
COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version. 
COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version. 
COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated, for removal: This API element is subject to removal in a future version.
since 5.3.3 has no sense
CopyOptConstants - Interface in chemaxon.marvin.util
Deprecated, for removal: This API element is subject to removal in a future version.
since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this interface either non exists in the new implementation or its value has changed. See the constants own description for details.
copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket
Copies line properties to another line object.
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow
 
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline
Copies line properties to another line object.
correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
countAllAtoms() - Method in class chemaxon.struc.MolAtom
Counts all atoms represented by this atom.
countAllAtoms() - Method in class chemaxon.struc.Sgroup
Counts the total number of atoms recursively.
countAllAtoms() - Method in class chemaxon.struc.sgroup.SgroupAtom
Counts all atoms represented by this atom.
countEnumerations() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the number of all enumerated structures, no arithmetic overflow because counts in BigInteger.
countEnumerationsMagnitude() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures.
countExpandableContractableSgroups() - Method in class chemaxon.struc.Molecule
Counts the expandable and contractable S-groups.
countOrderedComponentSgroups() - Method in class chemaxon.struc.Molecule
Counts the ordered component S-groups.
countRecords(MProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.view.MDocStorage
Counts the total number of records and sets the size of the document storage.
countRecordsInFraction(double, int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
Deprecated, for removal: This API element is subject to removal in a future version. 
COVALENT_COUNTER_ION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that incorrectly drawn covalent counter ion had found in the molecule
COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Covalent hydration error remark.
CovalentCounterionChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).
CovalentCounterionChecker() - Constructor for class chemaxon.checkers.CovalentCounterionChecker
Default constructor
covalentRadiusOf(int, int) - Static method in class chemaxon.struc.MolAtom
Gets the covalent radius in C-C bond length units.
Cr - Static variable in class chemaxon.core.ChemConst
 
crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
create() - Static method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Constructs a new StereoisomerSettings object with default settings.
create(byte[]) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule
Deprecated, for removal: This API element is subject to removal in a future version.
create(byte[], AlignmentProperties.DegreeOfFreedomType) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule
Deserializes an AlignmentMolecule from a byte array.
create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
create(Molecule, Molecule) - Method in interface com.chemaxon.search.CustomMatcherFactory
Creates a custom matcher for atom and bond pairs of the given query and target structures.
create(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
Creates a similarity calculator object according to the user defined parameters.
create(String) - Static method in class chemaxon.util.DotfileUtil
Opens a dotfile for writing.
create(String, int, int) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
Creates a similarity calculator object according to the user defined parameters.
create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas
Constructs an elemental analysis from molecular formula.
createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Deprecated.
Constructs an elemental analysis from molecular formula.
createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value
createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value
createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value and type
createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value and type
createAromatizedSearcher(AromatizationMethod) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that considers aromatization differences of the input molecule.
createAromatizedSearcher(AromatizationMethod, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher which considers aromatization according to the specified rules and initializes it with the specified search options.
createArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
Creates an array property.
createArrayXSD(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
Creates an array property from the XSD type.
createAtomIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
createAtomNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an iterator to get the atom neighbours of the specified atom.
createBondIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.
createBondNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an iterator to get the bonds connecting to the specified atom.
createBondTable(int, int) - Static method in class chemaxon.core.util.BondTable
Creates a new bond table for a molecule graph with the specified number of atoms and bonds.
createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
 
createChemicalTermsTextPane() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
createChemicalTermsTextPane(boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
createChemicalTermsTextPane(CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(String, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
 
createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument
Creates a ServiceArgument constant based on string value and argument type.
Supported types are String, Integer, Long, Double, Float and Boolean
createDefaultParameterPanel(Class, String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory
 
createDefaultParameterPanel(String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory
Creates default parameter panel based on XML config.
createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph
Creates a dehydrogenized version of the molecule.
createEMF(String, String) - Static method in class chemaxon.util.ImageExportUtil
Creates a .NET based EMF picture.
createErrorMessage(StandardizerConfiguration) - Static method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Creates an error message based on an invalid configuration
createExportModule() - Method in class chemaxon.formats.MFileFormat
Creates the export module.
createExportModule(String) - Method in interface chemaxon.formats.factory.MolExportModuleFactory
Creates the export module.
createExportModule(String) - Method in class chemaxon.formats.MFileFormat
Creates the export module.
createExportModule(String) - Static method in class chemaxon.formats.MFileFormatUtil
Creates an export module for the specified format.
createExportModule(String, String) - Static method in class chemaxon.formats.MFileFormatUtil
Creates an export module for the specified format with the specified encoding.
createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
createGData() - Method in class chemaxon.marvin.space.SurfaceComponent
 
createGearch() - Method in class chemaxon.struc.Molecule
 
createGearch() - Method in class chemaxon.struc.MoleculeGraph
 
createGearch() - Method in class chemaxon.struc.RgMolecule
 
createGearch() - Method in class chemaxon.struc.RxnMolecule
 
createGearch() - Method in class chemaxon.struc.SelectionMolecule
 
createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
CreateGroupAction - Class in chemaxon.standardizer.advancedactions
Create Group standardizer action
CreateGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.CreateGroupAction
Initializes a create group standardizes action
createImage(Buffer, int, int) - Method in class chemaxon.marvin.space.GraphicScene
 
createImportMod(MolInputStream) - Static method in class chemaxon.marvin.io.MRecordImporter
Creates an importer for the specified molecule input stream.
createImportMod(String) - Static method in class chemaxon.marvin.io.MRecordImporter
Creates an importer for the specified molecule format.
createImportModule() - Method in interface chemaxon.formats.factory.MolImportModuleFactory
Creates the molecule import module.
createImportModule() - Method in class chemaxon.formats.MFileFormat
Creates the molecule import module.
createInDocumentAt(DPoint3, MDocument) - Static method in class chemaxon.struc.NoStructure
Creates a NoStructure at the given location.
createInDocumentFrom(Molecule, MDocument) - Static method in class chemaxon.struc.NoStructure
Creates a NoStructure from the given component.
createLicenseManagerPanel() - Static method in class chemaxon.license.LicenseManager
Creates the main panel which is used for end-user license managing.
createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3.1, replaced by SwingUtil.createMenu
createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
Utility method to create a menu with a label specified as a resource.
createMenu(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu with a label specified as a resource.
createMenuItem(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu with a label specified as a resource.
createMenuItem(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu with a label specified as a resource.
createMenuItem(ResourceBundle, String, Class<?>, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu item with a label specified as a resource.
createMessagePane(String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a message pane with HTML text content.
createMMoleculeProp(String) - Static method in class chemaxon.marvin.io.MPropHandler
 
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the major tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the major tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Returns the molecule form with largest distribution.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the major tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the canonical tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the modified input molecule (e.g.
createMol() - Method in class chemaxon.formats.MolImporter
Deprecated, for removal: This API element is subject to removal in a future version.
As of 23.15, no replacement
createMol() - Method in class chemaxon.marvin.io.formats.mdl.MolImport
Creates a new target molecule object.
createMol() - Method in class chemaxon.marvin.io.MolImportModule
Creates a new target molecule object for the import.
createMol() - Method in class chemaxon.marvin.io.MRecordImporter
Creates an empty target molecule for import.
createMolConverter(InputStream, OutputStream, String[], int[]) - Static method in class chemaxon.formats.MolConverter
Creates a MolConverter instance with the attributes specified in the parameters.
createMolecule() - Method in class chemaxon.struc.Sgroup
Creates a molecule object that contains only this group.
createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Creates a molecule object that contains only one SuperatomSgroup identical to this one.
createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.
createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Creates a MoleculeIterator object for iterating through a molecule array (Molecule[]).
createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Creates a MoleculeIterator object for iterating through collection of molecules (Molecule objects).
createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter
Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.
createNeighbourBonds(Molecule, MolBond, boolean) - Static method in class chemaxon.checkers.StructureCheckerHelper
This method returns a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond
createNew() - Static method in class chemaxon.marvin.calculations.HlbPlugin.Builder
Constructs a new HlbPlugin instance.
createNew(Molecule) - Static method in class chemaxon.marvin.alignment.MCSAlignment.Factory
Constructs a new instance of ConformationAlignment class.
createNewCell() - Method in class chemaxon.marvin.space.GraphicScene
Sets an empty cell to be the active cell.
createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
Creates identical attributes for the next section.
createNoCancelObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed without replacement.
createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates the parameter panel.
createPartialMappingMatcher() - Method in interface com.chemaxon.search.CustomMatcherFactory
 
createReaction(MoleculeGraph, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
Creates a reaction.
createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule
Creates a reaction.
createRecognizer() - Method in interface chemaxon.formats.factory.RecognizerFactory
Creates a recognizer module.
createRecognizer() - Method in class chemaxon.formats.MFileFormat
Creates a recognizer module.
createRecognizer(String) - Method in class chemaxon.formats.MFileFormat
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead
createRecordReader(MolInputStream, String) - Method in interface chemaxon.formats.factory.MRecordReaderFactory
Creates the record reader.
createRecordReader(MolInputStream, String) - Method in class chemaxon.formats.MFileFormat
Creates the record reader.
createRecordReader(InputStream, String) - Static method in class chemaxon.formats.MFileFormatUtil
Creates a record reader for an input stream.
createRecordReader(InputStream, String, String, String) - Static method in class chemaxon.formats.MFileFormatUtil
Creates a record reader for an input stream.
createResult(Molecule, List<StructureCheckerResult>) - Method in class chemaxon.checkers.ReactionChecker
This method a merged StructureCheckerResult from the List of StructureCheckerResult which contains the problems of the components in the reaction
createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AliasChecker
 
createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomChecker
 
createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.PseudoAtomChecker
 
createResult(Molecule, List<MolBond>) - Method in class chemaxon.checkers.BondChecker
 
createResult(Molecule, List<E>) - Method in class chemaxon.checkers.ComponentChecker
Creates a StructureCheckerResult from a List containing the components.
createResultView(String, MolPanel) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
 
createRgComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.
createRotationAboutBond(MolBond, double) - Static method in class chemaxon.marvin.util.CleanUtil
Creates a rotation transformation about a bond.
createRxnComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.
createSavedCoordsArray(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Creates an empty array for the atomic coordinates of a structure.
createScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
Creates a scalar property.
createScalar(String, String, MProgressMonitor) - Static method in class chemaxon.marvin.io.MPropHandler
Creates a scalar property.
createScalarXSD(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
Creates a scalar property from the XSD type.
createSearcher(Transformer, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Constructs a searcher with the specified parameters.
createSearcherWithoutAromatization() - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that does not handle aromatization.
createSearcherWithoutAromatization(MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that doesn't consider aromatization.
createSearcherWithoutAromatization(SimpleSearcher, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher with the specified search options, other parameters (query, target, etc.) are copied from the specified searcher if possible (in case of BaseMolSearch).
createSelectionPanel(int) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
createSelectionPanelAndProgressBar() - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
createServiceHandler() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
 
createServiceHandler() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
 
createServiceHandler() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
 
createServiceHandler() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
 
createServiceHandler() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
 
createSgroupIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an s-group iterator for the specified molecule of the factory.
createSmolecule() - Method in class chemaxon.struc.MoleculeGraph
Creates a Smolecule represenation of this molecule.
createSpacePanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates space panel with given molecules, creates colored surface to each molecule.
createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Creates standardized molecule, the original input molecule is cloned.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Deprecated, for removal: This API element is subject to removal in a future version.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
createStatistics - Variable in class chemaxon.descriptors.MDGenerator
indicates if statistical data has to be gathered during generation
createStrictNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed without replacement.
createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a sub-panel with a title.
createTopLeftConstraints() - Static method in class chemaxon.marvin.util.SwingUtil
Creates GridBagConstraints for the top left component.
createUserDefined(String, String, String, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, String, long) - Static method in class chemaxon.formats.MFileFormat
Creates a user-defined format descriptor.
createUserDefined(String, List<String>, List<String>, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, Map<String, Integer>, long) - Static method in class chemaxon.formats.MFileFormat
Creates a user-defined format descriptor.
createViewPanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates view panel with given molecules, places molecule properties in formatted texts.
createViewPanel(Molecule[], int, int, int, int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates view panel with given molecules, places molecule properties in formatted texts.
createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<T>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Constructs the specified visitor implementation.
CRITICAL_ERROR_MSG - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Critical error message.
cross(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Calculates the cross product of the two vectors
CROSSED - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
Crossed double bond type
CROSSED_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that crossed double bond had found in the molecule
CrossedDoubleBondChecker - Class in chemaxon.checkers
A descendant of BondChecker for the detection of unspecified double bonds represented by crossed bond type.
CrossedDoubleBondChecker() - Constructor for class chemaxon.checkers.CrossedDoubleBondChecker
Default constructor
CrossedDoubleBondFixer - Class in chemaxon.fixers
Deprecated, for removal: This API element is subject to removal in a future version.
CrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.CrossedDoubleBondFixer
Deprecated.
 
CROSSLINK - Enum constant in enum class chemaxon.struc.SgroupType
 
Cs - Static variable in class chemaxon.core.ChemConst
 
CSMDL_IN - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
CSMOL_OUT - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Compressed Molfiles and Rgfiles.
CSRDF - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Compressed RDfiles.
CSRXN_OUT - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Compressed Rxnfiles.
CSSDF_OUT - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Compressed SDfiles.
cssr - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
CSSR - Enum constant in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
Complete set of smallest rings.
CSV - Static variable in class chemaxon.formats.MFileFormat
 
ctab - Variable in class chemaxon.struc.MoleculeGraph
Connection table.
CTransform3D - Class in chemaxon.struc
3D transformation matrix.
CTransform3D() - Constructor for class chemaxon.struc.CTransform3D
Constructs an identity transformation.
CTransform3D(CTransform3D) - Constructor for class chemaxon.struc.CTransform3D
Copy constructor.
CTSPECIFIC_H - Static variable in class chemaxon.struc.MolAtom
Deprecated.
As of Marvin 5.11
Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.
CTUMASK - Static variable in interface chemaxon.struc.StereoConstants
Double bond stereo mask.
CTUNKNOWN - Static variable in interface chemaxon.struc.StereoConstants
Deprecated.
As of Marvin 6.1,
Usage:
 In the specified methods the CIS|TRANS or
 CIS|TRANS|CTUNSPEC values are used instead.
 
CTUNSPEC - Static variable in interface chemaxon.struc.StereoConstants
Unspecified double bond.
Cu - Static variable in class chemaxon.core.ChemConst
 
CubeRecognizer - Class in chemaxon.formats.recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
CubeRecognizer() - Constructor for class chemaxon.formats.recognizer.CubeRecognizer
Deprecated.
 
currentBond - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Current bond pointer of the iterator.
currentMetricIndex - Variable in class chemaxon.descriptors.MDParameters
index of the parametrized metric currently in use
cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Move the cursor down.
cursorLeft(boolean) - Method in class chemaxon.struc.graphics.MTextBox
 
cursorRight(boolean) - Method in class chemaxon.struc.graphics.MTextBox
 
cursorToRowEnd(boolean) - Method in class chemaxon.struc.graphics.MTextBox
 
cursorToRowStart(boolean) - Method in class chemaxon.struc.graphics.MTextBox
 
cursorUp(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Moves the cursor up.
CUSTOM_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
custom name property
CustomDescriptor - Class in chemaxon.descriptors
The CustomDescriptor class implements a generic molecular descriptor class which supports third party or use defined descriptors.
CustomDescriptor() - Constructor for class chemaxon.descriptors.CustomDescriptor
Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.
CustomDescriptor(int, int) - Constructor for class chemaxon.descriptors.CustomDescriptor
Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.
CustomDescriptor(CDParameters) - Constructor for class chemaxon.descriptors.CustomDescriptor
Creates a new instance of CustomDescriptor according to the parameters given.
CustomDescriptor(CustomDescriptor) - Constructor for class chemaxon.descriptors.CustomDescriptor
Copy constructor.
CustomDescriptor(String) - Constructor for class chemaxon.descriptors.CustomDescriptor
Creates a new instance of CustomDescriptor according to the parameters given.
CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "customizationEnabled".
CustomMatcher - Interface in com.chemaxon.search
Interface for custom matching of atoms and bonds during search.
customMatcherFactory - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
CustomMatcherFactory - Interface in com.chemaxon.search
Factory interface for creating CustomMatcher objects.
customMatching(CustomMatcherFactory) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets the factory to be used to create a custom matcher.
customMatching(CustomMatcherFactory) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
customPaletteColors - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
CXON - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Object Notation.
CXSMARTS - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Extended SMARTS.
CXSMILES - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Extended SMILES.
cyclomaticNumber() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the smallest number of graph edges which must be removed such that no circuit remains.

D

D2S - Static variable in class chemaxon.formats.MFileFormat
Any document format recognized by Document to Structure (doc, odt, ...).
data - Variable in class chemaxon.descriptors.MDParameters
buffer for external data format generation, used in MolecularDescriptor.toData()
DATA - Enum constant in enum class chemaxon.struc.SgroupType
 
DATA_COLLECTION_CONSENT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
DATA_COLLECTION_SERVER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
DataSgroup - Class in chemaxon.struc.sgroup
Data Sgroup.
DataSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.DataSgroup
Creates a Data S-group with the specified parent.
DataSgroup(DataSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.DataSgroup
Copy constructor.
DataSgroup(DataSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.DataSgroup
Copy constructor.
DataSgroupCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.
DataSgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DataSgroupCheckerResult
Constructor which initialize all the properties.
date() - Element in annotation interface com.chemaxon.common.annotations.SubjectToRemoval
 
Db - Static variable in class chemaxon.core.ChemConst
 
DBS_ALL - Static variable in interface chemaxon.struc.StereoConstants
Double bond stereo checking for all double bonds.
DBS_MARKED - Static variable in interface chemaxon.struc.StereoConstants
Double bond stereo checking for marked double bonds only.
DBS_NONE - Static variable in interface chemaxon.struc.StereoConstants
No double bond stereo checking.
deactivateActiveCell() - Method in class chemaxon.marvin.space.GraphicScene
Sets the active cell to be no longer active.
DEAROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
General dearomatization.
DEAROM_HUCKELCHECK - Static variable in class chemaxon.struc.MoleculeGraph
Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
DEAROM_HUCKELCHECK_EX - Static variable in class chemaxon.struc.MoleculeGraph
Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
dearomatize() - Method in class chemaxon.struc.Molecule
Dearomatize molecule.
dearomatize() - Method in class chemaxon.struc.MoleculeGraph
Dearomatize molecule.
dearomatize(int) - Method in class chemaxon.struc.MoleculeGraph
Dearomatize molecule.
DearomatizeAction - Class in chemaxon.standardizer.actions
Dearomatization standardizer action
DearomatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DearomatizeAction
Initializes the action
DearomatizeFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the aromatic rings in the molecule into Kekule representation.
DearomatizeFixer() - Constructor for class chemaxon.fixers.DearomatizeFixer
 
DEBUG - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "debug".
Debye - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit
Debye unit.
DEBYE_TO_EA - Static variable in class chemaxon.calculations.dipole.DipoleResult
Debye to eA conversion upon multiplication.
decForm - Variable in class chemaxon.descriptors.MDParameters
to format floating point output
decode(String, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
Reads attributes of the next section from a string.
decode(String, MFont, MTextAttributes.MFontCreator, double) - Method in class chemaxon.struc.graphics.MTextAttributes
Reads attributes of the next section from a string.
decodeHIsotopeMass(int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Extract H isotope information from the given Chemaxon compressed mol format code of the atom.
decompress(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Uncompresses input byte array and stores the uncompressed array in params.data.
DECOMPRESS - Static variable in class chemaxon.formats.MdlCompressor
Decompression.
decorateSubPanel(JPanel, String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates border and title for a panel.
decQProp(String) - Method in class chemaxon.struc.MolAtom
Decrements the value of a query property.
DECREASE_LINEAR - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will decrease when getting farther from the atom center.
DECREASE_RECIPROCAL_SQUARE - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will decrease when getting farther from the atom center.
DECREASE_SQUARE - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will decrease when getting farther from the atom center.
decValenceProp() - Method in class chemaxon.struc.MolAtom
Decrements the value of the valence property.
DEF_IONICSTRENGTH - Static variable in class chemaxon.marvin.calculations.pKaPlugin
The default ionic strength of the pKa calculation models (small and large).
DEF_MAXIONS - Static variable in class chemaxon.marvin.calculations.pKaPlugin
The default value of the number of ionizable atoms to consider.
DEF_TEMPERATURE - Static variable in class chemaxon.marvin.calculations.pKaPlugin
The default temperature in Kelvins.
Default - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView
 
DEFAULT - Enum constant in enum class chemaxon.descriptors.MetricsType
 
DEFAULT - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption
Default error handling.
DEFAULT - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
default factory id
DEFAULT - Static variable in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
DEFAULT - Static variable in class chemaxon.standardizer.StandardizerActionFactory
default factory id
DEFAULT - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default attributes object.
DEFAULT_ARROW_HEAD_LENGTH - Static variable in class chemaxon.struc.graphics.MPolyline
Default arrow head length.
DEFAULT_ARROW_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
Default arrow head width.
DEFAULT_ASYMMETRY_FACTOR - Static variable in class chemaxon.descriptors.MDParameters
 
DEFAULT_BALL_RADIUS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.CFParameters
 
DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.RFParameters
 
DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.CFParameters
 
DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.RFParameters
 
DEFAULT_BOND_DISTANCE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_BOND_RADIUS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_BOND_WIDTH - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_CACHE_SIZE - Static variable in class com.chemaxon.mapper.AutoMapper
default cache size
DEFAULT_CACHE_SIZE_PROPERTY - Static variable in class com.chemaxon.mapper.AutoMapper
cache size property key
DEFAULT_CHECKERS_CONFIG_PATH - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
path to default checker configuration list
DEFAULT_COLOR - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_COLOR - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
DEFAULT_CONFIG_FILE - Static variable in class com.chemaxon.calculations.gui.PluginFactory
The default config file name.
DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Chemaxon's default checker configuration path
DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.standardizer.StandardizerActionFactory
Chemaxon's default standardizer action configuration path
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
The default location of Chemaxon standard checker runner configuration
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Chemaxon's default checker configuration file schema path
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.standardizer.StandardizerActionFactory
Chemaxon's default standardizer action configuration file schema path
DEFAULT_DIAMETER - Static variable in class chemaxon.descriptors.ECFPParameters
 
DEFAULT_DISSIMILARITY_THRESHOLD - Static variable in interface chemaxon.sss.SearchConstants
Default threshold value for similarity search.
DEFAULT_EQUILIBRIUM_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
Default equilibrium head width.
DEFAULT_FUZZINESS_FACTOR - Static variable in class chemaxon.descriptors.PFParameters
 
DEFAULT_FUZZY_CUTOFF - Static variable in class chemaxon.descriptors.PFParameters
 
DEFAULT_FUZZY_LOWER_BOUND - Static variable in class chemaxon.descriptors.PFParameters
 
DEFAULT_H_BALL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_BOND_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_JOINT_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_SPACEFILL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_STICK_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_ISOVALUE - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
DEFAULT_L_BALL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_BOND_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_JOINT_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_SPACEFILL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_STICK_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.CFParameters
default values for parameters
DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.ECFPParameters
default values for parameters
DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.RFParameters
default values for parameters
DEFAULT_LINE_WIDTH - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_LOWER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters
default values for parameters
DEFAULT_M_BALL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_BOND_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_JOINT_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_SPACEFILL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_STICK_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_MAX_CONSIDERED_RING_SIZE - Static variable in class com.chemaxon.search.mcs.McsSearchOptions
DEFAULT_MAX_CROSS_SIZE - Static variable in class chemaxon.struc.graphics.MPolyline
Default maximum cross size.
DEFAULT_NEAR_EDGE - Static variable in class chemaxon.marvin.space.GraphicCell
 
DEFAULT_OPTIONS - Static variable in interface chemaxon.struc.sgroup.Expandable
Default expansion/contraction options.
DEFAULT_OUTPUT_PRECISION - Static variable in class chemaxon.descriptors.MDParameters
 
DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.HBParameters
default values for parameters
DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.LDParameters
 
DEFAULT_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
the default priority value
DEFAULT_PROBE_RADIUS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
DEFAULT_RADIUS - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
DEFAULT_RANDOM_SEED - Static variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Default random seed.
DEFAULT_RECURSION_LEVEL - Static variable in class chemaxon.sss.screen.HashCode
 
DEFAULT_RESOLUTION - Static variable in class chemaxon.descriptors.PFParameters
default values
DEFAULT_RESOLUTION - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
DEFAULT_RETROSYNTHETIC_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
Default retrosynthetic head width.
DEFAULT_RLOGIC_RANGE - Static variable in class chemaxon.struc.RgMolecule
Default R-logic range.
DEFAULT_SALT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
Default salt dictionary file path.
DEFAULT_SAMPLING_ACCURACY - Static variable in class chemaxon.marvin.alignment.AtropIsomerDetector
DEFAULT_SAVE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "defaultSaveFormat".
DEFAULT_SCALE_FACTOR - Static variable in class chemaxon.descriptors.MDParameters
constants, default parameter values
DEFAULT_SEARCHTYPE - Static variable in interface chemaxon.sss.SearchConstants
Default search type equals SUBSTRUCTURE.
DEFAULT_SERVICE_CONFIGURATION_PATH - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
Path to default services configuration xml
DEFAULT_SERVICE_DESCRIPTOR_EDITOR_PROVIDER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service descriptor editor provider class
DEFAULT_SERVICE_DESCRIPTOR_READER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service descriptor reader class
DEFAULT_SERVICE_DESCRIPTOR_WRITER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service descriptor writer class
DEFAULT_SERVICE_DIALOG_PROVIDER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service dialog provider class
DEFAULT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Control
 
DEFAULT_SOLVENT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Default solvent dictionary file path.
DEFAULT_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader
path to default standardizer action configuration list
DEFAULT_STEP_SIZE - Static variable in class chemaxon.descriptors.scalars.LDParameters
 
DEFAULT_STICK_RADIUS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_SUPERSCRIPT_DELTAY - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default value of the y shift attribute in superscripts
DEFAULT_SUPERSCRIPT_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default value of the font scale attribute in superscripts
DEFAULT_SUPERSCRIPT_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default value of the superscript level attribute in superscripts
DEFAULT_TAG_NAME - Static variable in class chemaxon.jep.Evaluator
Default SDFile tag to store the evaluation result.
DEFAULT_THICKNESS - Static variable in class chemaxon.struc.graphics.MPolyline
Default line thickness.
DEFAULT_TIMEOUT_LIMIT - Static variable in class chemaxon.sss.search.SearchOptions
 
DEFAULT_TOOL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "defaultTool".
DEFAULT_UNGROUP - Static variable in class chemaxon.struc.Molecule
Do not ungroup and do not expand S-group's children.
DEFAULT_UPPER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters
 
DEFAULT_USER_CHECKER_FILENAME - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
Default user defined checker file name for fallback.
DEFAULT_USER_SERVICE_CONFIGURATION_FILENAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
name of default user service configuration file
DEFAULT_VALUE - Static variable in class chemaxon.core.util.BondTable
The default (null) value in the matrix.
DEFAULT_WEIGHT - Static variable in class chemaxon.descriptors.MDParameters
 
DEFAULT_XML_CONFIG - Static variable in class chemaxon.descriptors.PFParameters
 
defaultCategories() - Static method in class com.chemaxon.calculations.solubility.SolubilityCategories
Creates default categories.
DefaultExternalStructureCheckerResult - Class in chemaxon.checkers.result
This descendant of DefaultStructureCheckerResult also implements the ExternalStructureCheckerResult interface thus providing a default implementation base class for external structure checkers' results.
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
Constructor which initialize all the properties.
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
Constructor which initialize all the properties.
DefaultPluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent
Work unit performing plugin calculation and returning the cached results.
DefaultPluginWorkUnit(CalculatorPluginOutput<?>, boolean) - Constructor for class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
Constructor.
DefaultSolubilityCategory - Enum Class in com.chemaxon.calculations.solubility
Default solubility categories.
DefaultStructureCheckerResult - Class in chemaxon.checkers.result
This class is the default implementation of StructureCheckerResult
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
Constructor which initialize all the properties.
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
Constructor which initialize all the properties.
defaultWeight - Variable in class chemaxon.descriptors.MDParameters
value for all missing weight parameters
dehydrogenize(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
deleteAllUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Deletes all comparator added by the user.
deleteChar() - Method in class chemaxon.struc.graphics.MTextBox
Removes the character under the cursor.
deleteCharBackward() - Method in class chemaxon.struc.graphics.MTextBox
Removes the character before the cursor (backspace).
deleteUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
Deletes a given user defined comparator if found.
density - Variable in class chemaxon.descriptors.MDGenerator
 
DENY_IF_NOT_SPECIFIED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
 
description() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the description of the checker
description() - Element in annotation interface chemaxon.fixers.FixerInfo
Returns the description of the fixer.
description() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the description of the action
description() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
 
description() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
 
description() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
Description.
DESCRIPTION - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
description of checker
DESCRIPTION - Static variable in class chemaxon.fixers.StructureFixerDescriptor
description of fixer
DESCRIPTION - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
description of action
DESCRIPTOR_URI - Static variable in class chemaxon.marvin.services.json.JsonServiceDescriptor
Property key for Service descriptor as String
DescriptorGenerator - Class in chemaxon.descriptors
Simple class for generating molecular descriptors (fingerprints).
DescriptorGenerator(String) - Constructor for class chemaxon.descriptors.DescriptorGenerator
Creates a new instance using the given descriptor type with its default configuration parameters.
DescriptorGenerator(String, String) - Constructor for class chemaxon.descriptors.DescriptorGenerator
Creates a new instance using the given descriptor type with the given XML configuration.
descrType - Variable in class chemaxon.descriptors.CDParameters
descriptor type
descrValue - Variable in class chemaxon.descriptors.ScalarDescriptor
descriptor value
desiredLength(int, int, int, int) - Static method in class chemaxon.struc.MolBond
Desired length of a bond between two atoms in Angstroms.
destroySketcher() - Method in class chemaxon.marvin.beans.MViewPane
Closes all detached sketcher windows.
DETACH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "detach".
DETACHABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "detachable".
detectRecordPositions(IntVector) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
 
detectRecordPositions(IntVector) - Method in interface chemaxon.marvin.io.MRecordReader
Detects positions of records in the input stream.
determinant() - Method in class chemaxon.struc.CTransform3D
Computes the determinant of the matrix.
determinant2D() - Method in class chemaxon.struc.CTransform3D
Computes the determinant of the 2D matrix.
determineArrowDistance(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
Project the point (x,y,z) to the line of the reaction arrow 'ar'.
determinePosition(DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox
Deprecated, for removal: This API element is subject to removal in a future version.
use MTextBox.determinePosition(Graphics, DPoint3, boolean) in case you have a special graphics context to be used for font calculations.
determinePosition(Graphics, DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox
Determines the character index based on the passed view coordinate.
determineType(double, double, double) - Method in class chemaxon.struc.RxnMolecule
Determines whether a point should be in a reactant, in a product or in an agent.
determineType(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
Determines whether a point should be in a reactant, in a product or in an agent.
DICE - Enum constant in enum class chemaxon.descriptors.MetricsType
 
diffuse - Static variable in class chemaxon.marvin.space.monitor.Control
 
DihedralControl - Class in chemaxon.marvin.space.monitor
This control is to change a dihedral angle that is torsion a GraphicComponent.
DihedralControl(DihedralMonitor) - Constructor for class chemaxon.marvin.space.monitor.DihedralControl
Creates a new instance of DihedralControl
DihedralMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring dihedral.
DihedralMonitor() - Constructor for class chemaxon.marvin.space.monitor.DihedralMonitor
Creates a new instance of DihedralMonitor
DihedralRotator - Class in chemaxon.marvin.alignment
Rotates a dihedral in a 3D molecule
DihedralRotator(Molecule) - Constructor for class chemaxon.marvin.alignment.DihedralRotator
creates a rotator object
DihedralScanListener - Interface in chemaxon.marvin.alignment.atrop
Callback to track dihedral scan steps.
DihedralScanResult - Class in chemaxon.marvin.alignment.atrop
Results of a dihedral scan.
DihedralScanResult(BondInfo) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanResult
Construct for a dihedral.
dihedralScanStep(BondInfo, DihedralScanStep, Molecule, Molecule) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when a dihedral scan step is performed.
DihedralScanStep - Class in chemaxon.marvin.alignment.atrop
One step in a dihedral scan.
DihedralScanStep(double, double) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanStep
Construct.
DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph
Dimension bits in flags.
DIPOLE - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
DipoleCalculator - Class in chemaxon.calculations.dipole
Calculates the components of the dipole vector.
DipoleCalculator.Builder - Class in chemaxon.calculations.dipole
Builder class for dipole moment calculation.
DipoleResult - Class in chemaxon.calculations.dipole
Dipole moment calculation result.
DipoleResult(double, double, double, DipoleResult.Unit, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult
Constructor.
DipoleResult(double, double, double, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult
Constructor.
DipoleResult.Unit - Enum Class in chemaxon.calculations.dipole
Dipole moment units.
dirty - Variable in class chemaxon.sss.search.SearchOptions
This flag is set to true whenever any of the options change.
DISABLE_SPECIAL_NODES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "disableSpecialNodes".
disableNewEmfGenerator() - Static method in class chemaxon.util.ImageExportUtil
Disables the new .NET based EMF generator.
Discarded - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
Indicates, that the structure checker puts invalid structures to the discarded file.
discardedPath - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the invalid/unfixable output structures
DisconnectMetalAtomsAction - Class in chemaxon.standardizer.actions
Disconnect metal atoms standardizer action
DisconnectMetalAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DisconnectMetalAtomsAction
Initializes the disconnect metal atoms action
display(GLAutoDrawable) - Method in class chemaxon.marvin.space.GraphicScene
Warning: this function should not be called directly, use refresh() or redraw() instead.
DISPLAY_BOND_ORDER - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DISPLAY_QUALITY - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated since Marvin 6.4. No settings is used intead of this, only High Quality exists from now on.
displayBondOrder - Variable in class chemaxon.marvin.space.MoleculeComponent
 
displayChanged(GLAutoDrawable, boolean, boolean) - Method in class chemaxon.marvin.space.GraphicScene
Called by the system.
displayInMarvinSpace - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Display in MarvinSpace is enabled or not.
dispose(GLAutoDrawable) - Method in class chemaxon.marvin.space.GraphicScene
 
DISSIMILARITY_PROPERTY_NAME - Static variable in interface chemaxon.sss.SearchConstants
Name of the mrv/sdf property which stores the dissimilarity values.
distance(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculates the distance between two points.
distance(MolAtom, MolAtom) - Static method in class chemaxon.checkers.StructureCheckerHelper
Calculates the distance of two atoms.
DISTANCE_CONSTANT - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the distance measured from the atom center extended by a constant value.
DISTANCE_FROM_VDW - Static variable in class chemaxon.marvin.space.SurfaceColoring
In case of distance weighted property mapping is the distance measured from the atom center extended by the van der Waals radius.
DISTANCE_FROM_VDW_EXTENDED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the distance measured from the atom center extended by the van der Waals radius plus a constant, typically the probe radius.
DISTANCE_WEIGHTED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Will all affecting properties be mapped onto the surface weighted by atom distances.
distance2D(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculates the distance between two points in the XY plane.
DistanceBasedMetalloceneFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts incorrectly drawn metallocenes into multicenter based coordinate bond representation.
DistanceBasedMetalloceneFixer() - Constructor for class chemaxon.fixers.DistanceBasedMetalloceneFixer
 
distanceCount(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
Counts the given value in a row of the distance matrix.
distanceDegree(int) - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
distanceFrom(double, double) - Method in class chemaxon.struc.MObject
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlow
 
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MObject
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MPoint
Gets the 2D distance from the specified point.
distanceFrom(MoleculeGraph, double, double, CTransform3D) - Static method in class chemaxon.struc.graphics.MChemicalStruct
Gets the 2D distance from the specified point.
DistanceMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring distance between 2 components.
DistanceMonitor() - Constructor for class chemaxon.marvin.space.monitor.DistanceMonitor
Creates a new instance of DistanceMonitor
distanceRangeStore() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
DIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Divalent radical center.
DIVALENT_SINGLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Divalent radical center with singlet electronic configuration.
DIVALENT_TRIPLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Divalent radical center with triplet electronic configuration.
DNA - Static variable in class chemaxon.formats.MFileFormat
DNA sequence.
DO_NOT_FIX - Enum constant in enum class chemaxon.checkers.FixMode
on problem do nothing
DOC_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: name of the principal author(s) of a document.
DOC_CREATION_DATE - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the date on which the document was created.
DOC_LAST_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: name of the last (most recent) author of a document.
DOC_PATENT_ASSIGNEES - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the assignees of the patent, separated by newline characters.
DOC_PATENT_ID - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the patent identifier.
DOC_PATENT_INVENTORS - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the inventors of the patent, separated by newline characters.
DOC_PATENT_IPC - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the IPC classification(s) for the patent, separated by newline characters.
DOC_PATENT_IPCR - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the IPCR classification(s) for the patent, separated by newline characters.
DOC_TITLE - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the title of the document.
doColoring() - Method in class chemaxon.marvin.space.SurfaceColoring
This function has to be called after proper parametrization of the SurfaceColoring object in case of custom properties.
doColoring(int) - Method in class chemaxon.marvin.space.SurfaceColoring
This function has to be called after proper parametrization of the SurfaceColoring object in case of built-in properties.
docProduced(MDocStorage, MDocument, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
Document retrieved from source.
document - Variable in class chemaxon.descriptors.MDParameters
contains the XML document
DOCUMENT - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the file name of the source document.
DOCUMENT_TO_STRUCTURE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Document to Structure
DocumentAnnotator - Class in chemaxon.naming.document.annotate
Generate a chemically annotated HTML view of a document.
DocumentAnnotator(File) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given document file.
DocumentAnnotator(InputStream) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator(InputStream, DocumentAnnotator.DocumentType) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator.DocumentType - Enum Class in chemaxon.naming.document.annotate
Document type enum for DocumentAnnotator.
DocumentAnnotator.Listener - Interface in chemaxon.naming.document.annotate
The interface for a DocumentAnnotator progress event listener.
DocumentAnnotator.ProgressInfo - Class in chemaxon.naming.document.annotate
Represents the state of progress during a document annotation process.
DocumentAnnotatorOptions - Class in chemaxon.naming.document.annotate
Represents various options regarding how a document should be annotated, both in terms of input and output.
DocumentAnnotatorOptions.Builder - Class in chemaxon.naming.document.annotate
A builder for DocumentAnnotatorOptions, allowing for options to be built using a fluent interface.
DocumentAnnotatorOptions.ImageFormat - Enum Class in chemaxon.naming.document.annotate
A list of supported image formats for popups in the annotated document.
DocumentStyleAPI - Class in chemaxon.marvin.sketch.swing.modules.documentstyle
API for DocumentStyle management.
DocumentStyleAPI() - Constructor for class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI
 
DocumentToStructure - Class in chemaxon.naming.document
A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files.
DocumentToStructure() - Constructor for class chemaxon.naming.document.DocumentToStructure
 
done() - Method in interface com.chemaxon.calculations.common.ProgressObserver
Deprecated, for removal: This API element is subject to removal in a future version.
Implement ProgressObserver.close() instead, and create instances of this interface in a try-with-resources block.
DONOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
Donor sign displayed in GUI.
DONOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
DONR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
DONT_REMOVE_LAST_COMPONENT_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
Property key for "Don't Remove Last Component" option
DOODLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule with serious scanning or drawing issue had found
doPaste() - Method in class chemaxon.marvin.beans.MarvinPane
Invokes Paste actions.
doPaste() - Method in class chemaxon.marvin.beans.MSketchPane
Invokes Paste action.
doPaste() - Method in class chemaxon.marvin.beans.MViewPane
Invokes Paste action.
doSetSetSeqs(Molecule[], int, String) - Method in class chemaxon.marvin.view.MDocStorage
 
DOTDISCONNECTED_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "dotdisconnectedformalchargeformula".
DOTDISCONNECTED_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "dotdisconnectedformula".
DOTDISCONNECTED_ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "dotdisconnectedisotopeformalchargeformula".
DOTDISCONNECTED_ISOTOPE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "dotdisconnectedisotopeformula".
dotDisconnectedFormula() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the dot-disconnected molecular formula of a multifragment molecule.
dotDisconnectedIsotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the dot-disconnected isotope formula of a multifragment molecule.
dotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the dot-disconnected isotope formula of a multifragment molecule.
DotfileUtil - Class in chemaxon.util
Utility class for configuration file handling.
DotfileUtil() - Constructor for class chemaxon.util.DotfileUtil
 
DOTTED_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
DOUBLE - Static variable in class chemaxon.struc.MolBond
Double bond type.
DOUBLE_BOND - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
DOUBLE_BOND_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule contains either double bonds which are not valid
DOUBLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond
Double or aromatic query bond type.
doubleStringWidth(String, MFont, FontMetrics, Graphics) - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets the width of a string as a floating point number.
doubleValue() - Method in class chemaxon.struc.prop.MDoubleProp
Gets the double floating point value.
DOWN - Static variable in class chemaxon.struc.MolBond
Single bond down flag.
DOWN_WEDGE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "downWedge".
DPoint3 - Class in chemaxon.struc
Point in three dimensional space.
DPoint3() - Constructor for class chemaxon.struc.DPoint3
Construct a zero point.
DPoint3(double, double, double) - Constructor for class chemaxon.struc.DPoint3
Construct a point from the specified coordinates.
DPoint3(DPoint3) - Constructor for class chemaxon.struc.DPoint3
Copy constructor.
DRAGGABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "draggable".
draw() - Method in class chemaxon.marvin.space.GraphicCell
Makes the vieport draw this cell.
draw() - Method in class chemaxon.marvin.space.GraphicComponent
Draws the coordinate system of the component.
draw() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the MacroMolecule as letting its visualizers draw its parts.
draw() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
draw() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Draws the molecular surface, and recomputes it if the coordinates of the molecule have been changed.
draw() - Method in class chemaxon.marvin.space.MoleculeComponent
Called by GraphicCell from the Jogl rendering thread and draws the molecule.
draw() - Method in class chemaxon.marvin.space.monitor.AngleMonitor
Draws the anglemonitor as lines between the components, and an arc between the lines.
draw() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Draws dotted lines between the components, and a circle around the middle line.
draw() - Method in class chemaxon.marvin.space.monitor.DistanceMonitor
Draws solid line between the measured elements.
draw() - Method in class chemaxon.marvin.space.monitor.Label
Does nothing, because a label is drawn in plane or as a transparent component.
draw() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Draws nothing.
draw() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Draws the component if it is opaque.
draw() - Method in class chemaxon.marvin.space.PharmacophorePoint
Draws the entire component if it is opaque.
draw() - Method in class chemaxon.marvin.space.SurfaceComponent
Draws the surface if drawtype was DOTTED_TYPE or FILLED_TYPE.
draw(GL2) - Method in class chemaxon.marvin.space.BoundingBox
Draws the box with the given GL2 in line mode.
DRAW_TYPE_BALL - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_BALL_AND_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_BALL_AND_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_SPACEFILL - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPES - Static variable in class chemaxon.marvin.space.PharmacophoreArrow
 
DRAW_TYPES - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
draw2D - Variable in class chemaxon.marvin.space.monitor.Label
 
draw2DPart() - Method in class chemaxon.marvin.space.GraphicComponent
A component which draws (partly) in plane should overwrite this method.
draw2DPart() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the 2D parts of its visualizers.
draw2DPart() - Method in class chemaxon.marvin.space.monitor.Label
Draws the label when it is set to be drawn in plane.
draw2DPart() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Draws the Control of the PositionMonitor.
drawAtomSelection(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
drawAtomSelection(int) - Method in class chemaxon.marvin.space.MoleculeComponent
To make selection faster we don't draw the atoms themself into the selection buffer, but we draw simple polygons instead.
drawBorders() - Method in class chemaxon.marvin.space.GraphicCell
Draw borders of the cell.
drawBoundingBox() - Method in class chemaxon.marvin.space.GraphicComponent
Vizualises the bounding box.
drawCell() - Method in class chemaxon.marvin.space.GraphicCell
Draws all components of the cell.
drawCoordinateAxes() - Method in class chemaxon.marvin.space.GraphicComponent
Draws the local coordinate axes, the origin is the transformation center
drawHydrogens - Variable in class chemaxon.marvin.space.MoleculeComponent
 
drawProperties - Variable in class chemaxon.marvin.space.GraphicComponent
Common drawing related properties that affect all three quality modes.
drawRawSurface() - Method in class chemaxon.marvin.space.SurfaceComponent
 
drawRelation - Variable in class chemaxon.marvin.space.monitor.Label
 
drawSelection(int) - Method in class chemaxon.marvin.space.GraphicComponent
Draws the component in the given mode (usually in selection mode), the rendering mode is for checking.
drawSelection(int) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the component in the given mode (usually in selection mode).
drawSelection(int) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
drawSelection(int) - Method in class chemaxon.marvin.space.MoleculeComponent
 
drawSelection(int) - Method in class chemaxon.marvin.space.SurfaceComponent
 
drawSmoothBackground() - Method in class chemaxon.marvin.space.GraphicCell
 
drawSphere() - Method in class chemaxon.marvin.space.GraphicCell
Draws the rotation sphere.
drawSurface() - Method in class chemaxon.marvin.space.SurfaceComponent
 
drawTransparentPart() - Method in class chemaxon.marvin.space.GraphicComponent
A component having transparent parts should override this method, drawing the transparent parts here.
drawTransparentPart() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the transparent parts of its visualizers.
drawTransparentPart() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
drawTransparentPart() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Draws the surface if it was transparent or mesh.
drawTransparentPart() - Method in class chemaxon.marvin.space.MoleculeComponent
Draws the molecule if the drawing type was wire.
drawTransparentPart() - Method in class chemaxon.marvin.space.monitor.Label
Renders the label in 3d as a transparent object.
drawTransparentPart() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Draws transparent parts of the component if there is any.
drawTransparentPart() - Method in class chemaxon.marvin.space.PharmacophorePoint
Draws transparent parts of the component if there is any.
drawTransparentPart() - Method in class chemaxon.marvin.space.SurfaceComponent
Draws the surface if drawtype was MESH_TYPE or TRANSPARENT_TYPE.
drawType - Variable in class chemaxon.marvin.space.GraphicComponent
The actual drawing type of the component.
drawType - Variable in class chemaxon.marvin.space.MoleculeComponent
 
drawTypes - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
dropBinaryVector() - Method in class chemaxon.descriptors.ECFP
Drops the binary vector storage.
Ds - Static variable in class chemaxon.core.ChemConst
 
DT_FORMATTED - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: formatted.
DT_NUMERIC - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: numeric.
DT_TEXT - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: text.
DT_UNSPEC - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: unspecified.
DT_URL - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: url.
DUPLICATE - Static variable in interface chemaxon.sss.SearchConstants
Duplicate search (formerly called perfect).
Dy - Static variable in class chemaxon.core.ChemConst
 
DynamicArgument<CT,RT> - Class in chemaxon.marvin.services
ServiceArguments implementing this interface should support automatic evaluation of arguments before service call based on context.
NOTE: subclasses MUST HAVE default constructor to use from Marvin Sketch
DynamicArgument() - Constructor for class chemaxon.marvin.services.DynamicArgument
 
DynamicArgument(String) - Constructor for class chemaxon.marvin.services.DynamicArgument
 
DYNAMICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin
pKa's prefix (acidic/basic) does depend on the submitted micro state

E

E - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
 
E_SINK - Static variable in class chemaxon.struc.graphics.MEFlow
Electron sink.
E_SOURCE - Static variable in class chemaxon.struc.graphics.MEFlow
Electron source.
eA - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit
Atomic charge unit * Angstrom.
eccentricity(int) - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
ECFP - Class in chemaxon.descriptors
The ECFP class implements Extended-Connectivity Fingerprints (ECFPs) as a type of MolecularDescriptors.
ECFP() - Constructor for class chemaxon.descriptors.ECFP
Creates a new, empty instance of ECFP without allocating internal storage.
ECFP(ECFP) - Constructor for class chemaxon.descriptors.ECFP
Copy constructor.
ECFP(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFP
Creates a new instance of ECFP according to the parameters given.
ECFP(String) - Constructor for class chemaxon.descriptors.ECFP
Creates a new instance of ECFP according to the parameters given.
ECFP_FCFP - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Molecular Descriptors
ECFPFeature - Class in chemaxon.descriptors
Class for representing the substructural features of ECFP fingerprints.
ECFPFeatureLookup - Class in chemaxon.descriptors
Class for retrieving the substructural features of ECFP fingerprints.
ECFPFeatureLookup() - Constructor for class chemaxon.descriptors.ECFPFeatureLookup
Creates a new ECFPFeatureLookup instance with the default ECFP configuration parameters.
ECFPFeatureLookup(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup
Creates a new ECFPFeatureLookup instance with the given ECFP configuration parameters.
ECFPFeatureLookup(String) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup
Creates a new ECFPFeatureLookup instance with the given ECFP configuration parameters.
ECFPGenerator - Class in chemaxon.descriptors
The ECFPGenerator class generates ECFP fingerprints of molecular graphs.
ECFPGenerator() - Constructor for class chemaxon.descriptors.ECFPGenerator
Creates a new instance of ECFPGenerator, which can be used to generate ECFP fingerprints for an arbitrary number of molecules.
ECFPParameters - Class in chemaxon.descriptors
Manages ECFP fingerprint parameters.
ECFPParameters() - Constructor for class chemaxon.descriptors.ECFPParameters
Creates an empty object.
ECFPParameters(File) - Constructor for class chemaxon.descriptors.ECFPParameters
Creates a new object based on a given configuration file.
ECFPParameters(String) - Constructor for class chemaxon.descriptors.ECFPParameters
Creates a new object based on a given configuration string.
EDITABLE - Static variable in class chemaxon.marvin.beans.MViewPane
Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinView in a new window.
EDITABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "editable".
EDITOR_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
editor class name property of checker
EDITOR_CLASS_NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
editor class name property of standardizer action
editorClassName() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the name of the checker's editor
editorClassName() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the editor class name of the action
electronegOf(int) - Static method in class chemaxon.struc.MolAtom
Gets 10 times the electronegativity value for the specified element.
electronRadious - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
 
ELEMENT_COUNT - Static variable in class chemaxon.core.ChemConst
Number of elements in the periodic system
ELEMENT_COUNT - Static variable in class chemaxon.struc.MolAtom
Number of elements in the periodic system
ElementalAnalyser - Class in chemaxon.calculations
Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyser() - Constructor for class chemaxon.calculations.ElementalAnalyser
 
ElementalAnalyserPlugin - Class in chemaxon.marvin.calculations
Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.ElementalAnalyserPlugin
 
ElementalAnalyserPlugin.ResultType - Enum Class in chemaxon.marvin.calculations
Represents the different result types of the elemental analyser plugin.
ElementalAnalysis - Interface in com.chemaxon.calculations.elemanal
Calculates molecular formula, mass, MS mass and composition.
elementList - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
ELEMENTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "elements".
EMF - Static variable in class chemaxon.formats.MFileFormat
Windows Enhanced Metafiles.
EMPTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule structure was empty
EMPTY - Static variable in class chemaxon.jep.ConstantTable
An empty constant table.
EMPTY - Static variable in class chemaxon.struc.MolAtom
Empty atom type.
EMPTY_MOLECULE - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
In case of standardization error an empty molecule is provided on the output
EmptyStructureChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting structures having no atoms.
EmptyStructureChecker() - Constructor for class chemaxon.checkers.EmptyStructureChecker
Default constructore
ENABLED_2D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "2dviewerEnabled".
ENABLED_3D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "3dviewerEnabled".
enableDefaultHeavyAtomLimits() - Static method in interface chemaxon.calculator.TaggedCalculator
Sets the global input checker to one that uses the default heavy atom limits.
enclosesPoint(double, double) - Method in class chemaxon.struc.graphics.MBracket
Checks if a specified point is enclosed by this bracket.
encode(MFont, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
Returns the string representation of the attributes.
encoding - Variable in class chemaxon.marvin.io.PositionedInputStream
The encoding.
END_CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: key of the molecule property which contains the ending character offset since the beginning of the document, for text formats (html, xml, txt).
endGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream
Ends grabbing lines.
endHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
Changes the hourglass cursor back to normal at the end of a long operation.
ENDO - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, endo (relative configuration).
endRecord(boolean) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
It must be called at the end of record.
endReuse(int) - Method in class chemaxon.struc.Molecule
End reusing atoms.
endReuse(int) - Method in class chemaxon.struc.RgMolecule
End reusing atoms.
endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument
Tests whether the document ends with the specified character.
endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Tests whether this text portion ends with the specified character.
EnhancedStereo - Class in com.chemaxon.calculations.stereoanal.stereocenters
Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.
EnhancedStereo(StereoConstants.EnhancedStereoType) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Creates enhanced stereo representation.
EnhancedStereo(StereoConstants.EnhancedStereoType, int) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Creates enhanced stereo representation.
EnhancedStereoGroup - Class in com.chemaxon.calculations.stereoanal.stereocenters
Enhanced stereo descriptor class.
EnhancedStereoGroup(EnhancedStereo, List<TetrahedralStereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
Creates enhanced stereo group.
enqueueUpdate() - Method in class chemaxon.marvin.view.swing.TableSupport
Enqueues an update task.
ENTRY_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Configuration entry separator token of the action string
EPS - Static variable in class chemaxon.formats.MFileFormat
Encapsulated PostScript vector image format.
EPSILON - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
 
EPSILON - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
The microspecies is ignored if its distribution is less than EPSILON for all pH values.
equals(CTransform3D, double) - Method in class chemaxon.struc.CTransform3D
 
equals(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether two attributes objects equal or not.
equals(Object) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
 
equals(Object) - Method in class chemaxon.checkers.AbstractStructureChecker
 
equals(Object) - Method in class chemaxon.checkers.AromaticityErrorChecker
 
equals(Object) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
equals(Object) - Method in class chemaxon.checkers.AttachedDataChecker
 
equals(Object) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
 
equals(Object) - Method in class chemaxon.checkers.result.AromaticityCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.BondAngleCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.BondLengthCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
 
equals(Object) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.ReactionCheckerResult
Deprecated.
 
equals(Object) - Method in class chemaxon.checkers.result.RgroupCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.SgroupCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.SubstructureCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
equals(Object) - Method in class chemaxon.checkers.ValencePropertyChecker
 
equals(Object) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
 
equals(Object) - Method in class chemaxon.fixers.StructureFixerDescriptor
 
equals(Object) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
 
equals(Object) - Method in class chemaxon.marvin.space.ComponentElement
 
equals(Object) - Method in class chemaxon.sss.search.MarkushFeature
Deprecated.
 
equals(Object) - Method in class chemaxon.sss.search.SearchHit
 
equals(Object) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
equals(Object) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
 
equals(Object) - Method in class chemaxon.struc.AtropStereoDescriptor
 
equals(Object) - Method in class chemaxon.struc.AxialStereoDescriptor
 
equals(Object) - Method in class chemaxon.struc.CisTransStereoDescriptor
 
equals(Object) - Method in class chemaxon.struc.CTransform3D
 
equals(Object) - Method in class chemaxon.struc.DPoint3
Two points equal if their coordinates equal.
equals(Object) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.MFont
Tests whether two font objects equal.
equals(Object) - Method in class chemaxon.struc.graphics.MMidPoint
Two midpoints equal if their parent lines are the same and the polyline point indices also equal.
equals(Object) - Method in class chemaxon.struc.graphics.MRectanglePoint
Two rectangle points equal if their parent rectangles are the same and they are on the same corner or edge.
equals(Object) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether two attributes objects equal or not.
equals(Object) - Method in class chemaxon.struc.MPoint
Two points equal if their location equals.
equals(Object) - Method in class chemaxon.struc.prop.MBooleanProp
 
equals(Object) - Method in class chemaxon.struc.prop.MCollectionProp
 
equals(Object) - Method in class chemaxon.struc.prop.MDoubleArrayProp
 
equals(Object) - Method in class chemaxon.struc.prop.MDoubleProp
 
equals(Object) - Method in class chemaxon.struc.prop.MHashProp
 
equals(Object) - Method in class chemaxon.struc.prop.MHCoords3DProp
 
equals(Object) - Method in class chemaxon.struc.prop.MIntegerArrayProp
 
equals(Object) - Method in class chemaxon.struc.prop.MIntegerProp
 
equals(Object) - Method in class chemaxon.struc.prop.MListProp
 
equals(Object) - Method in class chemaxon.struc.prop.MMoleculeProp
 
equals(Object) - Method in class chemaxon.struc.prop.MObjectProp
 
equals(Object) - Method in class chemaxon.struc.prop.MStringProp
 
equals(Object) - Method in class chemaxon.struc.StereoActivePart
 
equals(Object) - Method in class chemaxon.struc.TetrahedralStereoDescriptor
 
equalsHead(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the head bonds equal the given bonds.
equalsNext(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether the attributes of two neighboring sections equal or not.
equalsTail(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the tail bonds equal the given bonds.
equalsTo(Object, int[]) - Method in class chemaxon.struc.AtropStereoDescriptor
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.AxialStereoDescriptor
 
equalsTo(Object, int[]) - Method in interface chemaxon.struc.CIPStereoDescriptorIface
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.CisTransStereoDescriptor
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.StereoActivePart
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.TetrahedralStereoDescriptor
 
EQUILIBRIUM - Static variable in class chemaxon.struc.RxnMolecule
Resonance arrow, the same as the two-headed double reaction arrow.
Er - Static variable in class chemaxon.core.ChemConst
 
ERROR - Enum constant in enum class chemaxon.checkers.CheckerSeverity
This severity level should used for StructureChecker implementations which search for serious problems in a Molecule
errorList - Variable in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
ErrorProcessor - Interface in chemaxon.util
Error processing interface.
ErrorReport - Class in com.chemaxon.calculations.stereoanal
Error reporting class.
ErrorReport(AtomSelection, String) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport
Constructs new error report.
ErrorReport(AtomSelection, String, Optional<? extends StereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport
Constructs new error report.
errors() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Error reports.
errorType - Variable in class chemaxon.checkers.AbstractStructureChecker
The error type of the current checker.
Es - Static variable in class chemaxon.core.ChemConst
 
ESCAPE_CHAR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "escapeChar".
estimateNumRecords() - Method in class chemaxon.formats.MolImporter
Estimates the total number of records.
estimateNumRecords() - Method in class chemaxon.marvin.io.ArrayMDocSource
Estimates the total number of records.
estimateNumRecords() - Method in class chemaxon.marvin.io.MDocSource
Estimates the total number of records.
estimateProgress() - Method in interface chemaxon.util.iterator.MoleculeIterator
Estimates the iteration progress.
Eu - Static variable in class chemaxon.core.ChemConst
 
euclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the Euclidean distance.
euclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the Euclidean distance.
EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType
 
evaluate(C) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression.
evaluate(StandardizerRunner.ErrorHandlingPolicy, StandardizerResult) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
 
evaluate(CT) - Method in class chemaxon.marvin.services.DynamicArgument
Evaluates the dynamic argument based on context
evaluate_boolean(C) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result boolean.
evaluate_booleans(C) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result to boolean[].
evaluate_double(C) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result to double.
evaluate_doubles(C) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result to double[].
EVALUATION_ERROR - Static variable in class chemaxon.jep.ChemJEP
The evaluation error message.
Evaluator - Class in chemaxon.jep
Evaluates Chemical Terms expressions.
Evaluator() - Constructor for class chemaxon.jep.Evaluator
Default constructor.
Evaluator(Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File, Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Evaluator(String) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(String, Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(String, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
EVALUATOR_DEFAULTS_FILE - Static variable in class chemaxon.jep.Evaluator
Default Function/Plugin settings filename.
EVALUATOR_NAMED_MOLS_FILE - Static variable in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
EVALUATOR_SCRIPT_FILE - Static variable in class chemaxon.jep.Evaluator
Initial script filename.
EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
 
EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
 
EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
 
EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
Deprecated, for removal: This API element is subject to removal in a future version.
EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
Deprecated, for removal: This API element is subject to removal in a future version.
EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
Deprecated, for removal: This API element is subject to removal in a future version.
EVEN - Static variable in class chemaxon.calculations.stereo.Stereochemistry
 
EVERY_WEIGHT_IS_ONE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
 
EXACT_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction
Key of exact for parsing and property change
EXACT_MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "exactmass".
exactMass() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.
exactMass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
exactMassPrecision() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the precision of the monoisitopic weight (number of significant decimal digits).
exactQueryAtomMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
exactQueryAtomMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether generic query atoms should be matched only to atoms of exactly the same type.
exactQueryAtomMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
exactQueryBondMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether generic query bonds should be matched only to bonds of exactly the same type.
exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
EXCLUDE_XX - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
EXCLUDED_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
excludeString - Variable in class chemaxon.standardizer.actions.ContractSgroupsAction
 
excludeString - Variable in class chemaxon.standardizer.actions.ExpandSgroupsAction
 
excludeString - Variable in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
exclusiveSelection() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
exclusiveSelection() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
exclusiveSelection() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
exclusiveSelection(int) - Method in class chemaxon.marvin.space.GraphicCell
Exclusive selection in the given component.
exclusiveSelection(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the the given part of the component to be selected, and sets every other parts not to be selected.
exclusiveSelection(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Exclusive selection in the given component in its container cell.
exit() - Method in class chemaxon.marvin.beans.MarvinPane
Closes all windows opened by this MarvinPane and saves user initialization file.
exit(int) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Terminate execution with given status code.
EXO - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, exo (relative configuration).
expand(int) - Method in class chemaxon.struc.Sgroup
Sets the state to Sgroup.XSTATE_X or Sgroup.XSTATE_XC.
expand(int) - Method in interface chemaxon.struc.sgroup.Expandable
Expands the S-group.
expand(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Expands this S-group unless it has expandable child s-group because in that case our calculations' behaviour can not be predicted.
expand(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Expands this S-group.
Expandable - Interface in chemaxon.struc.sgroup
Expandable interface for S-groups.
ExpandAction - Class in chemaxon.standardizer.actions
Expand stoichiometry standardizer action
ExpandAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ExpandAction
Initializes the action with parameters
ExpandGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which expands all abbreviated groups in the molecule
ExpandGroupFixer() - Constructor for class chemaxon.fixers.ExpandGroupFixer
 
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker
Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BondAngleChecker
 
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker
This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker
This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.OverlappingAtomsChecker
 
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.OverlappingBondsChecker
 
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker
This implementation does nothing.
expandOther(int, Molecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated.
as of Marvin 6.2. use SuperatomSgroup.expand(int) instead on the s-groups desired to be expanded
expandSgroups() - Method in class chemaxon.struc.Molecule
Expands all S-groups.
expandSgroups(int) - Method in class chemaxon.struc.Molecule
Expands all S-groups.
ExpandSgroupsAction - Class in chemaxon.standardizer.actions
Standardizer action expanding s-groups of the target molecule
ExpandSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ExpandSgroupsAction
Initializes the action
EXPLICIT_H - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that explicit hydrogen had found in the molecule
EXPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated, for removal: This API element is subject to removal in a future version.
since 5.3
EXPLICIT_LONE_PAIR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that explicit lone pair had found in the molecule
ExplicitHydrogenChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting explicit hydrogens.
ExplicitHydrogenChecker() - Constructor for class chemaxon.checkers.ExplicitHydrogenChecker
Default constructor All types of explicit hydrogens will be searched.
ExplicitHydrogenChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ExplicitHydrogenChecker
Parameterized constructor If map contains lonely/charged/mapped/isotopic/radical/wedged keys with value false then hydrogens with these types won't be detected.
ExplicitHydrogenFixer - Class in chemaxon.fixers
Deprecated, for removal: This API element is subject to removal in a future version.
ExplicitHydrogenFixer() - Constructor for class chemaxon.fixers.ExplicitHydrogenFixer
Deprecated.
 
ExplicitHydrogenResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying explicit hydrogen problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.
ExplicitHydrogenResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.ExplicitHydrogenResult
Constructor which initialize all the properties.
explicitHydrogens - Variable in class chemaxon.marvin.plugin.CalculatorPlugin
explicit hydrogens of the input molecule stored here key: index of the "parent" atom on the input molecule value: the hydrogen atom
ExplicitLonePairChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting lone pair type atoms.
ExplicitLonePairChecker() - Constructor for class chemaxon.checkers.ExplicitLonePairChecker
Default constructor
export(NMRSpectrum, double, double, double) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Returns the x-y point pairs of an NMR spectrum.
exportToBinFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter
Creates a binary representation of the document.
exportToBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Creates a binary representation of the molecule.
exportToBinFormat(String) - Method in class chemaxon.struc.MDocument
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String).
exportToBinFormat(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
exportToFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter
Creates a string representation of the document.
exportToFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Creates a string representation of the molecule.
exportToFormat(String) - Method in class chemaxon.struc.MDocument
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String)
exportToFormat(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
exportToJcampDX(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Exports the NMR spectrum into JCAMP-DX format.
exportToJcampDX(NMRSpectrum, int) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Exports the NMR spectrum into JCAMP-DX format.
exportToMol(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Returns a molecule with its NMR spectrum property.
exportToMol(NMRSpectrum, String) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Returns a molecule with its NMR spectrum property.
exportToObject(MDocument, String) - Static method in class chemaxon.formats.MolExporter
Creates a String, byte[] or Image representation of the document.
exportToObject(Molecule[], String, MolExportModule) - Static method in class chemaxon.formats.MolExporter
Creates a String, byte[] or Image representation of the given molecules.
exportToObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Creates a String, byte[] or Image representation of the molecule.
exportToObject(String) - Method in class chemaxon.struc.MDocument
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String)
exportToObject(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
extend(float) - Method in class chemaxon.marvin.space.BoundingBox
Makes the bounding box being larger or smaller by the given value in each direction.
EXTENDED_ATOMTYPES - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
 
extendSelection() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
extendSelection() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
extendSelection() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
extendSelection(int) - Method in class chemaxon.marvin.space.GraphicCell
Additive selection in the given component, so the previously picked part of the component will be selected, and all selection remains as is.
extendSelection(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the the given part of the component to be selected, and leaves other parts as they are.
extendSelection(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Additive selection in the given component in its container cell.
EXTERNAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type for externally developed StructureChecker classes
ExternalStructureChecker - Class in chemaxon.checkers
ExternalStructureChecker class provides a super class for externally implemented structure checkers.
ExternalStructureChecker(String) - Constructor for class chemaxon.checkers.ExternalStructureChecker
This constructor creates an external structure checker instance with the given error code
ExternalStructureCheckerResult - Interface in chemaxon.checkers.result
This interface is an extension of StructureCheckerResult that supports external StructureChecker development.
EXTRA_BONDS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "extraBonds".
EXTRA_TEMPLATES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "xtmpls".
extraFlavor - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
 
EZ_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule contains double bonds, that can be cis or trans
EZ_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "ezVisible".
EZDoubleBondChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting double bonds, that can be cis or trans.
EZDoubleBondChecker() - Constructor for class chemaxon.checkers.EZDoubleBondChecker
Initializes the EZ double bond checker

F

F - Static variable in class chemaxon.core.ChemConst
 
F_ARCHIVE - Static variable in class chemaxon.formats.MFileFormat
General archive format that stores a file in another format.
F_BINARY - Static variable in class chemaxon.formats.MFileFormat
Import/export module handles binary (byte array) data.
F_COORDS - Static variable in class chemaxon.formats.MFileFormat
The format can store atom coordinates if this flag is set.
F_EXPORT - Static variable in class chemaxon.formats.MFileFormat
Export is possible if this flag is set.
F_GRAPHICS - Static variable in class chemaxon.formats.MFileFormat
File format readable by a graphics program (image viewer, ray tracer etc.).
F_IMAGE - Static variable in class chemaxon.formats.MFileFormat
2D image file format, readable by image viewers.
F_IMPORT - Static variable in class chemaxon.formats.MFileFormat
Import is possible if this flag is set.
F_MIXED - Static variable in class chemaxon.formats.MFileFormat
Storage of records in different formats is possible if this flag is set.
F_MOL_MISSING - Static variable in class chemaxon.marvin.io.MRecord
Molecule (or reaction) is missing from the record.
F_MOLECULE - Static variable in class chemaxon.formats.MFileFormat
The format can store molecule(s) if this flag is set.
F_MULTIPLE_RECORDS_LEGAL - Static variable in class chemaxon.formats.MFileFormat
The format is designed to store multiple records if this flag is set.
F_MULTIPLE_RECORDS_POSSIBLE - Static variable in class chemaxon.formats.MFileFormat
The import/export modules can handle files with multiple records if this flag is set, but according to the format definition it is not legal.
F_OBJECT - Static variable in class chemaxon.formats.MFileFormat
Import/export module creates or reads a java object.
F_REACTION - Static variable in class chemaxon.formats.MFileFormat
The format can store reaction(s) if this flag is set.
F_RECOGNIZER - Static variable in class chemaxon.formats.MFileFormat
Format recognizer exists if this flag is set.
F_SINGLE_LINE - Static variable in class chemaxon.formats.MFileFormat
Format uses one line per structure.
F_USER_DEFINED - Static variable in class chemaxon.formats.MFileFormat
User defined format.
F_XML - Static variable in class chemaxon.formats.MFileFormat
The format is XML based if this flag is set.
Factory() - Constructor for class chemaxon.marvin.alignment.MCSAlignment.Factory
 
fadeSelected() - Method in class chemaxon.marvin.space.GraphicComponent
A descendant should overwrite this method to have its selection became faded.
fadeSelected() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The selected visualizers will be hidden.
fadeSelected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
fadeSelected() - Method in class chemaxon.marvin.space.MoleculeComponent
The selected atoms will be faded.
fadeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all selected components to faded.
fadeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Sets the drawing mode of all selected elements to faded so it will be hardly visible, and prevents them from clicking.
fadeUnselected() - Method in class chemaxon.marvin.space.GraphicComponent
A descendant should overwrite this method to have all but its selection became faded.
fadeUnselected() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The unselected visualizers will be hidden.
fadeUnselected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
fadeUnselected() - Method in class chemaxon.marvin.space.MoleculeComponent
The unselected atoms will be faded.
fadeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all selected components to faded.
fadeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Sets the drawing mode of all unselected elements to faded so it will be hardly visible, and prevents them from clicking.
FALSE - Static variable in class chemaxon.jep.ChemJEP
Logical result value: FALSE.
FAST - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
Atomic contribution, only for some selected atoms and ring centers.
FAST - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
 
FAST - Enum constant in enum class com.chemaxon.search.mcs.SearchMode
Fast search mode.
FAST_COORDS - Static variable in interface chemaxon.struc.sgroup.Expandable
Fast coordinate calculation in expand.
FASTA - Static variable in class chemaxon.formats.MFileFormat
FASTA file format
FASTA_DNA - Static variable in class chemaxon.formats.MFileFormat
FASTA file format with DNA sequence
FASTA_PEPTIDE - Static variable in class chemaxon.formats.MFileFormat
FASTA file format with peptide sequence
FASTA_RNA - Static variable in class chemaxon.formats.MFileFormat
FASTA file format with RNA sequence
FastUpperBoundCalculator - Class in com.chemaxon.search.mcs.upperbound
This class implements a simple upper bound calculator for the MCS problem.
FastUpperBoundCalculator() - Constructor for class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator
 
Fe - Static variable in class chemaxon.core.ChemConst
 
fileEndPosition - Variable in class chemaxon.marvin.io.MRecord
 
files - Variable in class chemaxon.checkers.StructureCheckOptions
List of the input files
fileStartPosition - Variable in class chemaxon.marvin.io.MRecord
 
FILLED_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
fillInStackTrace() - Method in exception chemaxon.naming.NameFormatException
 
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.Molecule
Adds all atoms and bonds to the specified molecule.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RgMolecule
Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RxnMolecule
Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
fillWithNulls() - Method in class chemaxon.marvin.view.MDocStorage
Set all stored document entries to null.
filter(List<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Filter stereo centers.
FILTER_DIM0 - Static variable in class chemaxon.formats.MolExporter
Molecule filter for cleaning 0D molecules only.
FILTER_ONE_ATTACHMENT - Static variable in class chemaxon.marvin.util.MolFragLoader
Filter object for accepting fragments with one attachment point.
FILTER_TWO_ATTACHMENTS - Static variable in class chemaxon.marvin.util.MolFragLoader
Filter object for accepting fragments with two attachment points.
FILTER_VALENCE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Filter constant: valence filter.
FilteredCase(String) - Constructor for exception chemaxon.naming.NameFormatException.FilteredCase
 
FilteredCase(String, Throwable) - Constructor for exception chemaxon.naming.NameFormatException.FilteredCase
 
filterGroups(StandardizerConfiguration, String[]) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility
Filters the action list of a configuration to a configuration containing only the actions that are in the target groups (or in all groups).
FINAL_CLEAN_ID - Static variable in class chemaxon.standardizer.configuration.ConfigurationUtility
Deprecated, for removal: This API element is subject to removal in a future version.
It's not required anymore.
FINAL_CLEAN_ID - Static variable in class chemaxon.standardizer.Standardizer
Deprecated, for removal: This API element is subject to removal in a future version. 
find() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Performs MCS search according to the specified options.
findAll() - Method in class chemaxon.sss.search.Search
Looks for all matching patterns in the molecule.
findAllGroups() - Method in class chemaxon.sss.search.Search
Returns the group hits corresponding to all hits.
findAllHits() - Method in class chemaxon.sss.search.MolSearch
 
findAllHits() - Method in class chemaxon.sss.search.Search
Looks for all matching patterns in the molecule.
findAllSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule
Finds all smallest S-groups containing the specified atom.
findAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Finds an atom in the atoms array.
findAtomClone(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Finds the clone of an atom.
findAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem
Returns the atomic number of the element in the periodic system specified by its symbol.
findAttachAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the attachment atom of attachment point with the smallest order.
findBasicFrags(Class<C>) - Method in class chemaxon.struc.MoleculeGraph
Determines the disconnected fragments and puts them into an array.
findBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Finds a bond in the bonds array.
findComponentIds() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by MoleculeGraph.getFragIds(int) and MoleculeGraph.FRAG_BASIC.
Usage:
             mol.getFragIds(MoleculeGraph.FRAG_BASIC);
             
findComponentIds(int[]) - Method in class chemaxon.struc.MoleculeGraph
Assigns a component ID to each connected component formed by the specified atom indexes.
findContainingMulticenterSgroup(MolAtom) - Method in class chemaxon.struc.Molecule
Gets the containing multicenter S-group of a multicenter atom.
findContractableSgroup() - Method in class chemaxon.struc.Molecule
Finds an expanded residue.
findCrossingBonds() - Method in class chemaxon.struc.Sgroup
Finds the crossing bonds.
findCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Finds the crossing bonds.
findCrossingBonds() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Finds the crossing bonds.
findExpandableSgroup() - Method in class chemaxon.struc.Molecule
Finds a contracted residue.
findFirst() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Overlays the molecule to align on the reference using the predefined atom pairs.
findFirst() - Method in class chemaxon.sss.search.Search
Looks for the first matching pattern in the target molecule.
findFirstGroup() - Method in class chemaxon.sss.search.Search
Returns the group hit corresponding to the first hit.
findFirstHit() - Method in class chemaxon.sss.search.MolSearch
 
findFirstHit() - Method in class chemaxon.sss.search.Search
Looks for the first matching pattern in the target molecule.
findFormats(String, long, long) - Static method in class chemaxon.formats.MFileFormatUtil
Gets a list of formats.
findFrag(int, int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Determines the subgraph connected to the specified atom.
findFrag(int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.6, replaced by MoleculeGraph.findFrag(int, int, MoleculeGraph) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:
             mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
             
findFragById(int, int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Determines the subgraph corresponding to the specific fragment ID.
findFrags() - Method in class chemaxon.struc.Molecule
Determines the disconnected fragments and puts them into an array.
findFrags(Class<C>) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.6, replaced by MoleculeGraph.findFrags(Class, int) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:
             mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
             
findFrags(Class<C>, int) - Method in class chemaxon.struc.Molecule
Determines the disconnected fragments and puts them into an array.
findFrags(Class<C>, int) - Method in class chemaxon.struc.MoleculeGraph
Determines the disconnected fragments and puts them into an array.
findInArray(Object[], int[], int, Object) - Static method in class chemaxon.struc.MoleculeGraph
Finds an object in an array.
findMcs(Matcher) - Method in class com.chemaxon.search.mcs.buildup.BuildupMcs
Performs an approximate calculation of the maximal common edge subgraph of the two input molecules.
findMcs(Matcher) - Method in class com.chemaxon.search.mcs.maxclique.MaxCliqueMcs
Finds the MCS and all related data (components and mappings).
findMcs(Matcher) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Finds the MCS and all related data (fragments and mappings).
findNext() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Randomizes dihedral angles of the input conformation for flexible molecules and aligns.
findNext() - Method in class chemaxon.sss.search.Search
Looks for the next matching pattern in the target molecule.
findNextGroup() - Method in class chemaxon.sss.search.Search
Returns the group hit corresponding to the next hit.
findNextHit() - Method in class chemaxon.sss.search.MolSearch
 
findNextHit() - Method in class chemaxon.sss.search.Search
Searches for the next hit.
findNextHit() - Method in interface com.chemaxon.search.SimpleSearcher
Searches for the next hit.
findRgroupBridgeId(int) - Method in class chemaxon.struc.RgMolecule
Finds the corresponding RgroupBridgeId for an R-group index.
findRgroupIndex(int) - Method in class chemaxon.struc.RgMolecule
Finds the index of an R-group based on the R-group number.
findScriptLastSectionIndex(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Finds the end of a subscript or superscript.
findSelectedSgroup() - Method in class chemaxon.struc.MSelectionDocument
Gets the smallest sgroup that belongs to the selection.
findSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule
Finds the largest S-group that contains the specified atom.
findSgroupOf(MolAtom) - Method in class chemaxon.struc.Molecule
Finds the smallest S-group related to the specified atom.
findSmallestSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule
Finds the smallest S-group that contains the specified atom.
findSmallestSgroupContaining(MolAtom) - Method in class chemaxon.struc.Sgroup
Finds the smallest S-group containing the specified node.
findSmallestSgroupOf(MolAtom) - Method in class chemaxon.struc.Sgroup
Finds the smallest S-group that has the specified node.
FINGERPRINT - Static variable in class chemaxon.jep.context.MolContext
 
FingerprintGenerator - Interface in chemaxon.jep
Fingerprint generator used in Chemical Terms match functions.
finishCancel() - Method in exception chemaxon.marvin.view.MDocStorage.CancellationException
This method should be called after catching the exception.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MPolyline
Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.MObject
Finish cloning a document.
firstPage - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
The first page of the document that should be annotated.
firstPage(Integer) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
fix - Variable in class chemaxon.checkers.StructureCheckOptions
Fix mode - deprecated.
fix() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
Checks the structure, then fixes the problems based on configuration.
NOTE: FixMode and fixerClassName from configuration is used to choose best fixer.
fix() - Method in interface chemaxon.checkers.runner.CheckerRunner
Runs all StructureChecker on the given molecule and after that fixes all identified problems with the first StructureFixer which is associated with the current problem.
fix(StructureCheckerResult) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
Fixes the given result based on the fixer defined for the checker.
fix(StructureCheckerResult) - Method in interface chemaxon.checkers.runner.CheckerRunner
Fixes the problem identified by result with the first StructureFixer which is associated with the StructureCheckerErrorType of the result.
fix(StructureCheckerResult) - Method in class chemaxon.fixers.AbsentChiralFlagFixer
Deprecated.
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.AbsoluteStereoFixer
Deprecated.
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.AddChiralFlagFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.BondAngleFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.BondLengthFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.CleanFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ClearWedgeFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ContractGroupFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertAliasToGroupFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertPseudoToGroupFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToAtomFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToCarbonFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToElementalFormFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToIonicFormFixer
Checker results contain atoms from the alkali metal and alkaline earth metal groups and their ionic counterparts of N, O, S atoms.
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToPlainDoubleBondFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToSingleBondFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToWigglyDoubleBondFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.CrossedDoubleBondFixer
Deprecated.
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.DearomatizeFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.DistanceBasedMetalloceneFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ExpandGroupFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ExplicitHydrogenFixer
Deprecated.
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.FlipWedgeBondFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.IsotopeFixer
Deprecated.
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MapMoleculeFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MapReactionFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MetalloceneFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.NeutralizeChargeFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.PartialCleanFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RearomatizeFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RearrangeWedgesFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAliasFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomMapFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomQueryPropertyFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomValueFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAttachedDataFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBondFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBondTopologyFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBracketsFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveChiralFlagFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveExplicitHydrogenFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveInvalidChiralFlagFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveRadicalFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveReactingCenterBondMarkFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveStereoCareBoxFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveValencePropertyFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveZCoordinateFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RgroupAttachmentFixer
 
fix(StructureCheckerResult) - Method in interface chemaxon.fixers.StructureFixer
Fixes one molecule problem identified by the result
fix(StructureCheckerResult) - Method in class chemaxon.fixers.SubstructureFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.UngroupFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ValenceFixer
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.WedgeCleanFixer
Deprecated.
 
fix(StructureCheckerResult) - Method in class chemaxon.fixers.WigglyDoubleBondFixer
Deprecated.
 
fix(StructureChecker, StructureCheckerResult) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
Tries to fix the problem detected by the specified checker, or falls back to result based behavior.
Fix - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Mode
Indicates, that the structurechecker does automatically fix.
FIX - Enum constant in enum class chemaxon.checkers.FixMode
on problem applies preferred fix if possible
FIX_CHARGE - Static variable in class chemaxon.struc.MolAtom
Valence checking will replace radicals with charges if this flag is set.
FIX_MODE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
fix mode property
fixable(StructureCheckerResult) - Method in class chemaxon.fixers.PartialCleanFixer
Gets whether the result is fixable.
fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.graphics.MPolyline
 
fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.graphics.MRectangle
 
fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.MObject
Sets the parent object for this object.
FIXED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType
Do not move this molecule
fixElectronContainers(MDocument, boolean, boolean) - Static method in class chemaxon.struc.MDocument
Removes unnecesarry MElectronContainers from the give MDocument corresponding to lone pair display options, if an electron of a MEFlow arrow has been removed the arrow is removed as well.
FIXER_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
fixer class name property
FIXERFACTORYCONFIG_XML - Static variable in class chemaxon.fixers.StructureFixerFactory
Deprecated.
default fixer configuration file name
FixerInfo - Annotation Interface in chemaxon.fixers
This annotation is responsible for adding UI based meta data for StructureFixer implementations
FixerPriorityComparator - Class in chemaxon.fixers
Comparator of structure fixer for priority Default fixer and order of fixers is defined this way.
FixerPriorityComparator() - Constructor for class chemaxon.fixers.FixerPriorityComparator
 
Fixes - Annotation Interface in chemaxon.fixers
This annotation is used to annotate the StructureFixer implementations which StructureCheckerErrorType can be fixed by the current fixer
FixesExternal - Annotation Interface in chemaxon.fixers
This annotation is used to annotate the StructureFixer implementations which error codes (identified by a unqie String) can be fixed by the current fixer
fixMidPointClones(MObject[], MObject[]) - Static method in class chemaxon.struc.graphics.MPolyline
Fixes the parents of the cloned MMidPoints.
FixMode - Enum Class in chemaxon.checkers
fix mode options
fixProperties() - Method in class chemaxon.struc.MoleculeGraph
Delegates to tracker's fixProperties().
fixProperties() - Method in class chemaxon.struc.RxnMolecule
 
fixReaction(Molecule, boolean, MolEditor) - Static method in class chemaxon.marvin.modules.reaction.ReactionEditUtils
Fixes a possibly broken reaction.
fixRectanglePointClones(MObject[], MObject[]) - Static method in class chemaxon.struc.graphics.MRectangle
Fixes the parents of the cloned MRectanglePoints.
fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.Molecule
Fix a property containing reference to the molecule.
fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.MoleculeGraph
Fix a property containing reference to the molecule.
fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.RgMolecule
Fix a property containing reference to the molecule.
fixSgroups - Variable in class chemaxon.marvin.io.formats.mdl.MolImport
 
Fl - Static variable in class chemaxon.core.ChemConst
 
flag() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Returns the enhanced stereo flag (eg.
flatten() - Method in class chemaxon.struc.MPropertyContainer
Flattens hierarchically specified RDF properties.
flavor - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
The DataFlavor represented by the implementation.
flip() - Method in class chemaxon.marvin.space.monitor.DihedralControl
Torsion will affect the other part of the component.
FlipWedgeBondFixer - Class in chemaxon.fixers
Flips wedge bonds.
FlipWedgeBondFixer() - Constructor for class chemaxon.fixers.FlipWedgeBondFixer
 
FLOAT_ARRAY - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
 
FLOAT_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
 
floatDescr - Variable in class chemaxon.descriptors.CustomDescriptor
storage for the floating point descriptors
flush() - Method in class chemaxon.formats.MolExporter
Flushes the output stream and forces any buffered output bytes to be written out.
Fm - Static variable in class chemaxon.core.ChemConst
 
FMT_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_IMAGE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_MOL - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_MRV - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_PLAINTEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_RXN - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_SMILES - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_STRING - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version.
will be deleted, no need to this constant
FMT_STRUCTURE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated, for removal: This API element is subject to removal in a future version. 
FOG_FACTOR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "fogFactor".
FONT_DEFAULT_SCALE - Static variable in class chemaxon.struc.graphics.MTextBox
 
foregroundColor - Variable in class chemaxon.marvin.space.monitor.Label
 
foregroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
forIntValue(int) - Static method in enum class chemaxon.struc.AtomProperty.Radical
Gets the AtomProperty.Radical that's int value is the given parameter.
FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "formalchargeformula".
formalCharge() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the formal (total) charge of the molecule.
format - Variable in class chemaxon.checkers.StructureCheckOptions
The format of the output structures of the structure checker
format - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
The format string.
format() - Element in annotation interface chemaxon.checkers.Persistent
Returns the format of the annotated property
format(double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Converts a double into String, applying the maximum number of fractional digits specified.
format(double[][], int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Converts a double[][] 2xN table to a 2-column tab-separated string representation of the table.
format(double, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Converts a double into String, applying the maximum number of fractional digits specified.
format(double, StringBuffer) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Converts a double into String, applying the maximum number of fractional digits specified.
FORMAT_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction
The key of the molecule format parameter of the abstract action.
formula() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
formula() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
formula(int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates a fixed digit sortable molecular formula.
formula(FormulaGenerationRule...) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
formula(Set<FormulaGenerationRule>) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "formula".
FORMULATION - Enum constant in enum class chemaxon.struc.SgroupType
 
fp - Variable in class chemaxon.descriptors.ChemicalFingerprint
storage for the fingerprint
fp - Variable in class chemaxon.descriptors.ECFP
Binary vector storage of the fingerprint
fp - Variable in class chemaxon.descriptors.PharmacophoreFingerprint
storage for the fingerprint
fp - Variable in class chemaxon.descriptors.ReactionFingerprint
storage for the fingerprint
Fr - Static variable in class chemaxon.core.ChemConst
 
FRAG_BASIC - Static variable in class chemaxon.struc.MoleculeGraph
Basic fragmentation, only atom - atom connections (bond) are considered.
FRAG_KEEPING_MULTICENTERS - Static variable in class chemaxon.struc.MoleculeGraph
Fragmentation without breaking multicenter S-groups.
FRAG_KEEPING_SGROUPS - Static variable in class chemaxon.struc.MoleculeGraph
Fragmentation without breaking S-groups.
FRAG_TYPE_COUNT - Static variable in class chemaxon.struc.MoleculeGraph
Number of fragmentation types.
fragmentCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of fragments (disconnected parts) of the molecule.
FRAGMENTER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Fragmenter
freqCount - Variable in class chemaxon.descriptors.MDGenerator
 
from(ProgressObserver) - Static method in interface com.chemaxon.calculations.common.SubProgressObserver
Deprecated.
Creates a delegator to the given ProgressObserver.
fromData(byte[]) - Method in class chemaxon.descriptors.BCUT
Builds a BCUT descriptor from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ChemicalFingerprint
Builds a fingerprint from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.CustomDescriptor
Builds a CustomDescriptor from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ECFP
Builds an ECFP fingerprint from an external data format created by toData().
fromData(byte[]) - Method in class chemaxon.descriptors.MolecularDescriptor
Builds a MolecularDescriptor object from its external (database) representation.
fromData(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Builds a PharmacophoreFingerprint from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ReactionFingerprint
Builds a fingerprint from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ScalarDescriptor
Builds a descriptor from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ShapeDescriptor
 
fromFeatureSet(Set<Integer>) - Method in class chemaxon.descriptors.ECFP
Deprecated, for removal: This API element is subject to removal in a future version.
As of JChem 5.4.1, replaced by fromIdentiferSet().
fromFile(File) - Method in class chemaxon.descriptors.CDParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.CFParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.ECFPParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.PFParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.RFParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.SDParameters
Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.ShapeParameters
Sets parameters from an XML file.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.BCUT
Builds a BCUT descriptor from its float array representation (generated by toFloatArray()).
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ChemicalFingerprint
Builds fingerprint from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.CustomDescriptor
Builds a molecular descriptor from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ECFP
Builds an ECFP fingerprint from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.MolecularDescriptor
Builds a molecular descriptor from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Builds a molecular descriptor from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ReactionFingerprint
Builds fingerprint from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ScalarDescriptor
Builds the descriptor from a float array of one element.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ShapeDescriptor
 
fromFormula(String) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas
 
fromFormula(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Deprecated.
 
fromId(int) - Static method in enum class com.chemaxon.calculations.admet.HergClass
Converts the given integer ID to the appropriate hERG class: 0 to HergClass.SAFE and 1 to HergClass.TOXIC.
fromIdentiferSet(Set<Integer>) - Method in class chemaxon.descriptors.ECFP
Builds an ECFP fingerprint from a set of Integer identifers.
fromIntArray(int[]) - Method in class chemaxon.descriptors.ECFP
Builds an ECFP fingerprint from an array of int identifiers.
fromMethod(AromatizationMethod) - Static method in enum class com.chemaxon.search.transformation.transformers.Aromatizer
Gets the aromatizer-transformer corresponding to the specified aromatization method
fromMolecule(Molecule) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas
 
fromMolecule(Molecule) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Deprecated.
 
fromMolecule(Molecule, boolean) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas
 
fromMolecule(Molecule, boolean) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Deprecated.
 
fromMolecule(Molecule, Set<Integer>, boolean) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas
 
fromMolecule(Molecule, Set<Integer>, boolean) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Deprecated.
 
fromPlainText(Reader) - Static method in class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given text.
fromString(String) - Method in class chemaxon.descriptors.BCUT
Builds a BCUT descriptor from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.BCUTParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.CDParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.CFParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.ChemicalFingerprint
Builds a fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.CustomDescriptor
Builds a descriptor from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.ECFP
Builds an ECFP fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.ECFPParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Builds a molecular descriptor from its string representation.
fromString(String) - Method in class chemaxon.descriptors.PFParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Builds a fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.ReactionFingerprint
Builds a fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.RFParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.ScalarDescriptor
Builds a descriptpr from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.SDParameters
Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.ShapeDescriptor
 
fromString(String) - Method in class chemaxon.descriptors.ShapeParameters
 
fromString(String) - Static method in enum class chemaxon.sss.search.options.HaltOnErrorOption
Gets the halt on error option value for the string representation.
fromString(String) - Static method in enum class chemaxon.sss.search.options.HomologyTranslationOption
 
fromString(String) - Static method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
 
FULL - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Full clean
FULL - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions).
Usage:
 molecule.setValenceCheckOptions(new ValenceCheckOptions(false,true);
             
FULL - Static variable in interface chemaxon.sss.SearchConstants
Full structure search.
FULL_FRAGMENT - Static variable in interface chemaxon.sss.SearchConstants
Full fragment search (formerly called exact fragment).
functionScale - Variable in class chemaxon.calculations.nmr.NMRSpectrum
Scale factor for NMR spectrum function scaling.
fuse(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Adds those atoms and bonds of another molecule to this one that are not already elements.
fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.MoleculeGraph
Adds atoms and bonds of another molecule to this one.
fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.RgMolecule
Add the atoms and bonds of another molecule.
fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.RxnMolecule
Add the atoms and bonds of another molecule.
fuse(RxnMolecule) - Method in class chemaxon.struc.RxnMolecule
Fuse and RxnMolecule to this RxnMolecule.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.Molecule
Adds those atoms and bonds of a molecule graph to this one that are not already elements.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.MoleculeGraph
Adds the atoms and bonds of another molecule to this one.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.RgMolecule
Add those nodes and edges of a graph that are not already elements.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.RxnMolecule
Add those nodes and edges of a graph that are not already elements.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.SelectionMolecule
Adds those atoms and bonds of a graph to this one that are not already elements.
fusedAliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
fusedAliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAliphaticRingCount()
fusedAliphaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of fused aliphatic rings in the molecule (rings s).
fusedAliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAliphaticRingCount(int)
fusedAliphaticRings() - Method in class chemaxon.calculations.Ring
Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
fusedAliphaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAliphaticRings()
fusedAliphaticRings(int) - Method in class chemaxon.calculations.Ring
Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).
fusedAliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAliphaticRings(int)
fusedAromaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
fusedAromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAromaticRingCount()
fusedAromaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of fused aromatic rings in the molecule (rings s).
fusedAromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAromaticRingCount(int)
fusedAromaticRings() - Method in class chemaxon.calculations.Ring
Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
fusedAromaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAromaticRings()
fusedAromaticRings(int) - Method in class chemaxon.calculations.Ring
Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).
fusedAromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedAromaticRings(int)
fusedRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.
fusedRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.fusedRingCount()
fuzzinessFactors - Variable in class chemaxon.descriptors.PFParameters
fuzziness factors of parametrized metrics
fuzzyExp - Variable in class chemaxon.descriptors.PFParameters
fuzzi exponent for the FBPA metric, calculated from the fuzziness factor

G

Ga - Static variable in class chemaxon.core.ChemConst
 
gatherBaseColors() - Static method in class chemaxon.marvin.util.ColorGenerator
Creates a Collection of the base colors.
These colors are:

- black
- white
- red
- green
- blue
- cyan
- magenta
- yellow.
gatherBaseColorsAndBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator
Creates a Collection of the base Molecule RGB colors and base colors.
These colors are the atom label RGB colors of:
- H
- C
- N
- O
- S
- F
- P
- Cl
- Br
- I.
gatherBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator
Creates a Collection of the base Molecule RGB colors.
These colors are the atom label RGB colors of:

- H
- C
- N
- O
- S
- F
- P
- Cl
- Br
- I.


and

- black
- white
gatherBlackAndWhite() - Static method in class chemaxon.marvin.util.ColorGenerator
Creates a Collection of black and white color
GAUSS_44_SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties
 
GAUSS_FAST_EXTENDED_ATOMTYPE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties
 
GAUSS_FAST_EXTENDED_ATOMTYPE_MCS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties
Deprecated.
GAUSS_FAST_PHARMACOPHORE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties
 
GAUSS_FAST_SHAPE_ONLY - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties
 
GAUSS_VOLUME_SIMPLE_44 - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
 
GAUSS_VOLUME_SIMPLE_45 - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
 
GAUSS_VOLUME_SIMPLE_FAST - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
 
GAUSS_VOLUME_SIMPLE_FULL - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
 
GAUSSIAN_CUBE - Static variable in class chemaxon.formats.MFileFormat
Gaussian Cube files.
GAUSSIAN_INPUT - Static variable in class chemaxon.formats.MFileFormat
Gaussian Input Format.
GAUSSIAN_INPUTZ - Static variable in class chemaxon.formats.MFileFormat
Gaussian Input Format: Z-matrix.
GAUSSIAN_OUTPUT - Static variable in class chemaxon.formats.MFileFormat
Gaussian output format.
Gd - Static variable in class chemaxon.core.ChemConst
 
Ge - Static variable in class chemaxon.core.ChemConst
 
gearch - Variable in class chemaxon.struc.MoleculeGraph
 
gearch() - Method in interface chemaxon.struc.Smolecule
Gets graph search algorithms.
GENERAL - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type
General aromatization
GENERAL - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
generate(int, int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
generate(int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
generate(Molecule) - Method in class chemaxon.descriptors.BCUT
Creates the BCUT descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ChemicalFingerprint
Creates the ChemicalFingerprint descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.DescriptorGenerator
Generates descriptor for the given molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ECFP
Creates the ECFP fingerprint for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.MolecularDescriptor
Creates the descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Creates the PharmacophoreFingerprint descriptor from the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ReactionFingerprint
Creates the ReactionFingerprint descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ScalarDescriptor
Creates the ScalarDescriptor descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.HAcc
Calculates the HAcc descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.HBParameters
Calculates the descriptor value for the given molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.HDon
Creates the HDon descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.Heavy
Creates the HeavyAtomCount descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.LDParameters
 
generate(Molecule) - Method in class chemaxon.descriptors.scalars.LogD
Creates the LogD descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.LogP
Creates the LogP descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.Mass
Creates the Mass descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.TPSA
Creates the TPSA descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ShapeDescriptor
 
generate(Molecule, int[]) - Method in class chemaxon.descriptors.DescriptorGenerator
Generates partial descriptor for the given molecule.
generate(Molecule, int[], MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator
Generates the partial chemical fingerprint for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.BCUTGenerator
Generates the BCUT descriptors for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.BCUTParameters
Calls the descriptor generator for the molecule provided and stores result (the descriptor) in the MolecularDescriptor object.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator
Generates the chemical fingerprint for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.CFParameters
Calls CFGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator
Generates the ECFP fingerprint for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPParameters
Calls ECFPGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator
Generates the molecular descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in interface chemaxon.descriptors.MolecularDescriptorGenerator
Deprecated.
Creates a certain type of MolecularDescriptor (depending on the specific ganerator providing this service) for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator
Generates the pharmacophore fingerprint of the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.PFParameters
Calls the corresponding MolecularDescriptorGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator
Generates the reaction fingerprint for the given reaction molecule object.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.RFParameters
Calls RFGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeGenerator
 
generate(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Creates the descriptor for the given Molecule.
generateBracketCoords(Sgroup, int) - Static method in class chemaxon.marvin.util.CleanUtil
Generates brackets with coordinates for a specified S-group.
generateBracketCoords(Sgroup, int, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
Generates brackets with coordinates for a specified S-group.
generateColors(int) - Static method in class chemaxon.marvin.util.ColorGenerator
Generates the specified number of different Colors, with no forbidden colors.
generateColors(int, Collection<Color>) - Static method in class chemaxon.marvin.util.ColorGenerator
Generates the specified number of different Colors, which are different enough from the specified forbidden colors.
generateData(int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
use ShapeData.toData instead.
generateEMFToFile(String, String, String) - Static method in class chemaxon.util.ImageExportUtil
Creates a new .NET based EMF picture and saves it to the given file.
generateRawDisplayList() - Method in class chemaxon.marvin.space.SurfaceComponent
 
generator - Variable in class chemaxon.descriptors.MDParameters
generates MolecularDescriptors
GENERIC - Enum constant in enum class chemaxon.struc.SgroupType
 
GEOMETRY - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
GEOMETRY_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Geometry Plugin Group
GEOMETRY_PROJECTION - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
GeometryPlugin - Class in chemaxon.marvin.calculations
Plugin class for geometric properties calculations.
GeometryPlugin() - Constructor for class chemaxon.marvin.calculations.GeometryPlugin
Constructor.
get(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the content of the specified hitogram bin.
get(int) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Returns the group definition at specified index.
get(int) - Method in class chemaxon.struc.prop.MHashProp
Gets a value.
get(int) - Method in class chemaxon.struc.prop.MListProp
Gets the specified element.
get(int, int, float) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
get(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the histogram bar height of two features ('fa'-'fb') corresponding to the given ditance 'dist'.
get(String) - Method in class chemaxon.struc.MPropertyContainer
Gets a property object.
get(String) - Method in class chemaxon.struc.prop.MHashProp
Gets a value.
GET - Enum constant in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method
mehtod GET
get3DMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the 3D molecule used in 3D surface area calculation.
getAbbreviation() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets the abbreviation of the group.
getAbbreviation(int) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Gets the abbreviation at the provided index
getAbsoluteCellIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
Determines the absolute cell index of a visible cell
getAbsoluteCellIndex(JComponent) - Method in class chemaxon.marvin.beans.MViewPane
Determines in which cell the specified component is located.
getAbsoluteLabelVisible() - Method in class chemaxon.marvin.common.UserSettings
Are Absolute labels visible?
getAbsoluteXY() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
getAbundance(int, int) - Static method in class chemaxon.struc.PeriodicSystem
Natural abundance of the isotope
getAcceptorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the overall acceptor atom count (without multiplicity) in the molecule.
getAcceptorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getAcceptorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getAcceptorSiteCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the overall acceptor count (with multiplicity) in the molecule.
getAcceptorSiteCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the atomic acceptor count corresponding to the specified atom index.
getAccuracyMode() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
 
getAction() - Method in class chemaxon.standardizer.Changes
Gets the base StandardizerAction of the changes
getActionCount() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets the action count of the configuration
getActionIndexes(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets the indexes of actions defined by the provided action string
getActionMap() - Method in class chemaxon.struc.graphics.MTextBox
Returns the ActionMap used to determine what Action to fire for particular KeyStroke binding.
getActionName() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
Gets the name of the original action
getActions() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets all actions of the configuration
getActions(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets actions of a group of the configuration
getActions(String...) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets actions of a group of the configuration
getActionString() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
getActionStringTokens() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Gets the action string token of the checker
getActionStringTokens() - Method in class chemaxon.fixers.StructureFixerDescriptor
Gets the action string token of the fixer
getActionStringTokens() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the action string tokens of the action
getActiveCell() - Method in class chemaxon.marvin.space.GraphicScene
Returns the active cell of the scene.
getActiveCellIndex() - Method in class chemaxon.marvin.space.GraphicScene
Returns the index of the active cell.
getActiveGroups() - Method in class chemaxon.standardizer.Standardizer
getAddedAtoms() - Method in class chemaxon.standardizer.Changes
Gets the list of atoms added during the standardization procedure
getAgent(int) - Method in class chemaxon.struc.RxnMolecule
Gets an agent.
getAgentCount() - Method in class chemaxon.struc.RxnMolecule
Gets the number of agents.
getAgents() - Method in class chemaxon.struc.RxnMolecule
Gets all agents in an array.
getAlias() - Method in class chemaxon.marvin.services.ServiceArgument
Returns the argument alias.
getAliasNames() - Method in class chemaxon.descriptors.BCUT
 
getAliasNames() - Method in class chemaxon.descriptors.ChemicalFingerprint
 
getAliasNames() - Method in class chemaxon.descriptors.ECFP
 
getAliasNames() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getAliasNames() - Method in class chemaxon.descriptors.ReactionFingerprint
 
getAliasNames() - Method in class chemaxon.descriptors.ShapeDescriptor
 
getAliasstr() - Method in class chemaxon.struc.MolAtom
Gets the alias string or pseudo atom type string for pseudo atoms.
getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.Alignment
 
getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
getAlignedMoleculesAsFragments() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.
getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
getAlignedQuery() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
getAlignedQuery() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
getAlignedQuery() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
getAlignedTarget() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
getAlignedTarget() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
getAlignedTarget() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
getAlignedWithNewCoordinates() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
getAlignScaffold() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Gets the scaffold aligning mode
getAliphaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the aliphatic atom count.
getAliphaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the aliphatic bond count.
getAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the aliphatic ring count.
getAliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
getAliphaticRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getAliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the aliphatic rings in the molecule.
getAliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Indentifies aliphatic rings in the molecule having a given size (number of atoms).
getAllAtomCount() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the atom count (including implicit hydrogens).
getAllAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the atom count.
getAllAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the attachment atoms (atoms having attachment point).
getAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
 
getAllFragments() - Method in class chemaxon.struc.RxnMolecule
Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
getAllFromDocument(MDocument) - Static method in class chemaxon.struc.NoStructure
Returns all NoStructure labels from the document.
getAllMolecules() - Method in class chemaxon.struc.MDocument
Gets an array containing all molecule objects.
getAllNonEmptyMolecules() - Method in class chemaxon.struc.MDocument
Gets an array containing all non-empty molecule objects.
getAllObjects() - Method in class chemaxon.struc.MDocument
Gets all objects stored in this document and from the chemical structure of the document.
getAllObjects() - Method in class chemaxon.struc.Molecule
 
getAllObjects() - Method in class chemaxon.struc.RgMolecule
 
getAllObjects() - Method in class chemaxon.struc.RxnMolecule
 
getAllOptionsAsString() - Method in class chemaxon.sss.search.SearchOptions
Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
getAllOptionsAsString(String) - Method in class chemaxon.sss.search.SearchOptions
Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
getAnalysisBoxTerms() - Method in class chemaxon.marvin.common.UserSettings
 
getAngle() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanStep
Represented angle.
getAngle(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the angle of 3 atoms.
getAngle(int, int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the angle of 3 atoms.
getAngleCheckerResult() - Method in class chemaxon.checkers.result.BondAngleCheckerResult
Returns the internal representation of the angle checker result, which contains all information required to fix bond angle errors.
getAnimated() - Method in class chemaxon.marvin.beans.MViewPane
Gets index of animated cells of the table (or simple viewer).
getAnimDelay() - Method in class chemaxon.marvin.beans.MViewPane
Gets the repeat delay for animations.
getAnimFPS() - Method in class chemaxon.marvin.beans.MViewPane
Gets the frames per second for animations.
getAnyBondStyles() - Method in class chemaxon.marvin.MolPrinter
Gets the any bond style.
getAppliedActions() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Gets the list of applied actions
getAppliedActions() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
getAppliedActions() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Gets the list of actions applied in the configuration at the last execution
getAppliedTaskIDs() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Returns the IDs of tasks applied to the last input molecule.
getAppliedTaskIDs() - Method in class chemaxon.standardizer.Standardizer
Returns the IDs of tasks applied to the last input molecule.
getAppliedTaskIndexes() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Returns the indexes of tasks applied to the last input molecule.
getAppliedTaskIndexes() - Method in class chemaxon.standardizer.Standardizer
Returns the indexes of tasks applied to the last input molecule.
getArcAngle() - Method in class chemaxon.struc.graphics.MPolyline
Gets the central angle of the arc.
getArcCenter(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline
Returns the arc center.
getArcHeight() - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
getArcRadius(CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Gets the arc radius.
getArcRadius(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline
 
getArcWidth() - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
getAromataType() - Method in class chemaxon.checkers.result.AromaticityCheckerResult
Returns the type of the aromatization
getAromaticAndAliphaticRings(int, boolean, boolean, int, int) - Method in class chemaxon.struc.MoleculeGraph
Returns the aromatic and or aliphatic ring atom indexes.
Note: This method does not aromatize the already aromatized rings.
getAromaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the aromatic atom count.
getAromaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the aromatic bond count.
getAromaticRingCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the total partial charge of the smallest aromatic ring containing the specified atom.
getAromaticRingCharge(int, int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the partial charge of the smallest aromatic ring containing the specified atom.
getAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the aromatic ring count.
getAromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
getAromaticRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getAromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the aromatic rings in the molecule.
getAromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Indentifies aromatic rings in the molecule having a given size (number of rings).
getAromaticSystemCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the total partial charge of the aromatic system containing the specified atom.
getAromaticSystemCharge(int, int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the partial charge of the aromatic system containing the specified atom.
getAromatizationMethod() - Method in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
getAromatizedStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the enumerated structures in aromatized form.
getAromatizeMethod() - Method in class chemaxon.marvin.common.UserSettings
Gets the aromatize method.
getAromatizer(AromatizationMethod) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns an aromatizer transformer.
getAromType() - Method in class chemaxon.checkers.AromaticityErrorChecker
Returns the aromType
getArrayFlags() - Method in interface chemaxon.struc.Smolecule
Gets info about the used arrays.
getArrowAsProperty() - Method in class chemaxon.struc.RxnMolecule
Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.
getArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline
Gets the arrow flags.
getArrowLength(int) - Method in class chemaxon.struc.graphics.MPolyline
Gets the arrow head length.
getArrowWidth(int) - Method in class chemaxon.struc.graphics.MPolyline
Gets the arrow head width.
getASA() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule.
getASAHydrophobic() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns water accessible surface area of all hydrophobic (|qi|<0.125) atoms.
getASANegative() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0).
getASAPlus() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0).
getASAPolar() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns water accessible surface area of all polar (|qi|>=0.125) atoms.
getAsBitSet() - Method in class chemaxon.descriptors.DescriptorGenerator
Returns the generated descriptor in a BitSet representation if it is available.
getAscent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the ascent of this portion.
getAsFloatArray() - Method in class chemaxon.descriptors.DescriptorGenerator
Returns the generated descriptor in a float array representation if it is available.
getAsIntArray() - Method in class chemaxon.descriptors.DescriptorGenerator
Returns the generated descriptor in an int array representation if it is available.
getAsMolecule() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the found common substructure as a Molecule object.
getAssociatedComponents() - Method in class chemaxon.marvin.space.GraphicComponent
Returns an Iterator that can enumerate the components associated to (depending on) this component.
getAssociatedNonQueryFormat() - Method in class chemaxon.formats.MFileFormat
Gets the associated non-query format.
getAssociatedQueryFormat() - Method in class chemaxon.formats.MFileFormat
Gets the associated query format.
getAsString() - Method in class chemaxon.descriptors.DescriptorGenerator
Returns the generated descriptor in its native string representation.
getAsymmetricAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of asymmetric atoms.
getAsymmetricAtoms() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines the asymmetric atoms.
getAsymmetricEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the asymmetric Euclidean distance.
getAsymmetricEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Calculates the asymmetric Euclidean distance.
getAsymmetricEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP
Calculates the asymmetric Euclidean distance.
getAsymmetricEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getAsymmetricFBPA(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the asymmetric FBPA convolution product based distance of the fingerprint from an other (given as parameter).
getAsymmetryFactor() - Method in class chemaxon.descriptors.MDParameters
Gets the asymmetry factor used in the current parametrized asymmetric metrics.
getAtno() - Method in class chemaxon.struc.MolAtom
Gets the atomic number.
getAtom() - Method in class chemaxon.jep.context.AtomContext
Returns the input atom index.
getAtom() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Gets the atom.
getAtom(int) - Method in class chemaxon.struc.MoleculeGraph
Gets the nth atom.
getAtom(int) - Method in class chemaxon.struc.RgMolecule
Gets a node in the graph union.
getAtom(int) - Method in class chemaxon.struc.RxnMolecule
Gets a node.
getAtom(int) - Method in class chemaxon.struc.Sgroup
Gets an atom in the S-group.
getAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow
Gets the atom at the terminus of an arrow.
getAtom1() - Method in class chemaxon.struc.MolBond
Gets the first endpoint.
getAtom1(int) - Method in interface chemaxon.struc.Smolecule
Gets the index of the first atom of the specified bond.
getAtom1Index() - Method in class chemaxon.marvin.alignment.atrop.BondInfo
Atom index for first end atom.
getAtom2() - Method in class chemaxon.struc.MolBond
Gets the second endpoint.
getAtom2(int) - Method in interface chemaxon.struc.Smolecule
Gets the index of the second atom of the specified bond.
getAtom2Index() - Method in class chemaxon.marvin.alignment.atrop.BondInfo
Atom index for second end atom.
getAtomArray() - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
getAtomArray() - Method in class chemaxon.struc.MoleculeGraph
Creates an array of atoms.
getAtomArray() - Method in class chemaxon.struc.Sgroup
Gets the array of atoms in the S-group.
getAtomCount() - Method in class chemaxon.core.util.BondTable
Returns the number of atoms in the molecule this bond table represents.
getAtomCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getAtomCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the number of atoms in the input molecule.
getAtomCount() - Method in interface chemaxon.struc.Incomplecule
Gets the number of atoms.
getAtomCount() - Method in class chemaxon.struc.MoleculeGraph
Gets the number of atoms.
getAtomCount() - Method in class chemaxon.struc.RgMolecule
Gets the number of nodes in the root structure.
getAtomCount() - Method in class chemaxon.struc.RxnMolecule
Returns the number of nodes in the graph union.
getAtomCount() - Method in class chemaxon.struc.Sgroup
Gets the number of atoms in the S-group.
getAtomCount() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the number of atoms in the found common substructure.
getAtomCount(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the number of atoms in the molecule with arbitrarily enumerating hydrogens.
getAtomCount(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the number of atoms with given atomic number (including its isotopes).
getAtomCount(int) - Method in class chemaxon.struc.MoleculeGraph
Gets the number of atoms with the given atomic number.
getAtomCount(int) - Method in class chemaxon.struc.RgMolecule
Gets the number of atoms with the given atomic number in the root structure.
getAtomCount(int) - Method in class chemaxon.struc.RxnMolecule
Gets the number of atoms with the given atomic number in the unified molecule graph of the reaction.
getAtomCount(int, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the number of atoms with given atomic number in the molecule isotope with the specified mass number.
getAtomFont() - Method in class chemaxon.marvin.common.UserSettings
Gets the atom symbol font name.
getAtomicNumber(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getAtomicNumber(String) - Static method in class chemaxon.struc.MolAtom
Deprecated.
As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String).
The recommended method does not work for symbol not representing a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
getAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem
Returns the atomic number of the element in the periodic system specified by its symbol or -1 if not found.
getAtomicRadius(int) - Static method in class chemaxon.struc.PeriodicSystem
Atomic radius of the element Angstroms.
getAtomicSurfaceAreaIncrement(int) - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the 3D surface area increments.
getAtomIndex() - Method in class chemaxon.calculations.nmr.Shift
Returns the atom index.
getAtomIndex() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
getAtomIndex(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the atom index in the standardized molecule, or the atom index itself if the input molecule has not been standardized.
getAtomIndexes() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the atom indices of the NMR active nuclei.
getAtomIndexMap() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
getAtomIndexMapping() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns an immutable function of the current atom index mapping from the original molecule to standardized one.
getAtomIterator() - Method in class chemaxon.struc.MoleculeGraph
Returns an iterator over the atoms in this molecule in proper sequence.
getAtomIterator() - Method in class chemaxon.struc.RgMolecule
Returns an iterator over the atoms in this molecule in proper sequence.
getAtomIterator() - Method in class chemaxon.struc.RxnMolecule
Returns an iterator over the atoms in this molecule in proper sequence.
getAtomIterator(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the iterator of the atoms of the molecule.
getAtomlogPHIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Increments of implicit H-s are not calculated. Returns the same value as logPPlugin.getAtomlogPIncrement(int)
getAtomlogPIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the logP increment for the specified atom.
getAtomMap() - Method in class chemaxon.struc.MolAtom
Gets the atom-atom mapping number.
getAtomMap(int) - Method in interface chemaxon.struc.Smolecule
Gets the atom-atom mapping number.
getAtomMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the atom mapping of the found common substructure.
getAtomMappingMethod() - Method in class chemaxon.marvin.common.UserSettings
Gets the atom mapping method.
getAtomNumberingType() - Method in class chemaxon.marvin.beans.MarvinPane
Determines the atom numbering.
getAtomNumberingType() - Method in class chemaxon.marvin.common.UserSettings
Gets the atom numbering type.
getAtomNumberingType() - Method in class chemaxon.marvin.MolPrinter
Returns atom numbering type.
getAtomOf(MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
getAtomProperty() - Method in class chemaxon.marvin.space.AtomProperty
 
getAtomProperty() - Method in class chemaxon.marvin.space.MoleculeComponent
See MoleculeIterators.AtomPropertyInterface for details.
getAtomReferenceList() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
getAtomReverseMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the reverse atom mapping of the found common substructure.
getAtoms() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getAtoms() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getAtoms() - Method in class chemaxon.struc.graphics.MAtomSetPoint
Gets the atoms.
getAtoms() - Method in class chemaxon.struc.MDocument.CheckerMark
 
getAtoms(Object) - Static method in class chemaxon.struc.graphics.MEFlow
Gets the atom or atoms at the terminus of an arrow.
getAtomSelections() - Method in class chemaxon.marvin.space.MoleculeComponent
 
getAtomSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane
Gets the color of an atom set.
getAtomSetColor(int) - Method in class chemaxon.struc.MDocument
Gets an atom set color.
getAtomSetColorMode(int) - Method in class chemaxon.struc.MDocument
Gets the atom set coloring mode.
getAtomSetColors() - Method in class chemaxon.descriptors.MolecularDescriptor
Determines the coloring of atoms.
getAtomSetColors() - Method in class chemaxon.descriptors.PFParameters
Gets the coloring of atoms as defined in the XML configuration file.
getAtomSetColors() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Determines the coloring of atoms.
getAtomSetFont(int) - Method in class chemaxon.struc.MDocument
Gets an atom set font.
getAtomSetIndexes(Molecule) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the individual atom color indexes.
getAtomSetIndexes(Molecule) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the individual atom colors by pharmcophore point type.
getAtomSetIndexes(Molecule, PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PFParameters
Gets the individual atom colors by pharmcophore point type.
getAtomSetNames() - Method in class chemaxon.descriptors.MolecularDescriptor
 
getAtomSetNames() - Method in class chemaxon.descriptors.PFParameters
Gets the name of atom sets (pharmacophore point type set), as defined in the configuration file/string.
getAtomSetNames() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getAtomSetRGB(int) - Method in class chemaxon.struc.MDocument
Gets an atom set color.
getAtomSetSize() - Method in class chemaxon.struc.MDocument
Gets the size of the atom set.
getAtomsize() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the atom size.
getAtomsize() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.2, replaced by MolPrinter.getAtomSize().
getAtomSize() - Method in class chemaxon.marvin.common.UserSettings
Gets the atom size in C-C bond length units.
getAtomSize() - Method in class chemaxon.marvin.MolPrinter
Returns the atom size in units of regular bond length.
getAtomStereo(int) - Method in interface chemaxon.struc.Smolecule
Gets atom stereo properties as an integer.
getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.MolAtom
Gets the string representation of the atom symbol.
getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.sgroup.SgroupAtom
Gets the string representation of the atom symbol.
getAtomSymbolListAsString(MolAtom[]) - Static method in class chemaxon.struc.Sgroup
 
getAtomType(int) - Method in interface chemaxon.struc.Smolecule
Gets the type of an atom.
getAtropBonds() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
After the calculate method finished.
getAttach() - Method in class chemaxon.struc.MolAtom
Deprecated.
as of Marvin 6.0 replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom).
If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.
getAttach(MolAtom) - Static method in class chemaxon.struc.Sgroup
Gets the attachment point information from the ExtraAtomProperties
getAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by SuperatomSgroup.getBoundAttachAtoms().
getAttachCount(Integer) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets the attachment point count for the atom specified by the index
getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
getAttachedData() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Gets the attached data.
getAttachedData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
getAttachedDataMatch() - Method in class chemaxon.sss.search.SearchOptions
Returns whether attached data (in data sgroups) should be used when comparing structures.
getAttachedDataPrefixes() - Method in class chemaxon.sss.search.SearchOptions
Returns the prefixes of the names of those data sgroups that will be used during structure comparison or null if all data sgroups should be checked.
getAttachFromExtraAtomProp() - Method in class chemaxon.struc.MolAtom
Gets the attachment information stored in the extra atom properties
getAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the attachment point that's order is given as parameter
getAttachmentPointCount() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the number of the attachment points.
getAttachmentPointOrders() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the orders with which attachment point exists
getAttachmentPointOrders(int) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Returns the attachment point orders of the atom specified by atomIndex.
getAttachmentPointOrders(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the attachment orders of the given attachment atom.
getAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the sorted copy of the attachment point list.
getAttachParentSgroup() - Method in class chemaxon.struc.MolAtom
Gets the smallest containing sgroup which can have the attachment point information of this atom.
getAttrFont(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
Gets the font for the specified attribute object.
getAttribute(String) - Method in class chemaxon.struc.graphics.MBracket
Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MEFlow
 
getAttribute(String) - Method in class chemaxon.struc.graphics.MPolyline
Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MRectangle
Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MRoundedRectangle
Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MTextBox
Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.MObject
Gets the value of an attribute.
getAttributes() - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets the attributes.
getAttributes(int, int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets attributes of the text of len length from start that are supposed to be set even if their values are "default".
getAutoScale() - Method in class chemaxon.marvin.beans.MSketchPane
Returns autoscale property.
getAutoTabScale() - Method in class chemaxon.marvin.beans.MViewPane
Is tab scale automatically changed?
getAvailableCheckers() - Method in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Returns a list of checkers available
getAvailableStandardizerActions() - Method in class chemaxon.standardizer.StandardizerActionFactory
Returns the list of standardizer actions that are available
getAvailableStyles() - Method in class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI
Gets the list of available DocumentStyle names
getAverageNonZeroRatio() - Method in class chemaxon.descriptors.MDGenerator
Gets the average percentage of cells that have non-zero value taken all descriptors generated since the initialization of the generator into account.
getAveragePolarizabilityComponent() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the average polarizability component (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
getAWTFont() - Method in class chemaxon.struc.graphics.MFont
Gets an AWT font instance.
getBackground() - Method in class chemaxon.struc.MObject
Gets the background color of the object.
getBackgroundColor() - Method in class chemaxon.marvin.MolPrinter
Returns the current background color.
getBackgroundColor() - Method in class chemaxon.marvin.space.GraphicScene
Returns the background color of the scene.
getBackgroundColor() - Method in class chemaxon.marvin.space.monitor.Label
Returns the background color of the label.
getBackgroundColorF() - Method in class chemaxon.marvin.space.GraphicScene
 
getBalabanIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
getBallRadius() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the ball radius in units of covalent radius.
getBallRadius() - Method in class chemaxon.marvin.common.UserSettings
Gets the ball radius for ball and stick mode.
getBallRadius() - Method in class chemaxon.marvin.MolPrinter
Gets the ball radius for "ball and stick" mode.
getBaseElectronContainerIndex() - Method in class chemaxon.struc.graphics.MEFlow
 
getBaseElectronIndexInContainer() - Method in class chemaxon.struc.graphics.MEFlow
 
getBaseFont() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the base font.
getBaseFont() - Method in class chemaxon.struc.graphics.MTextBox
Gets the base font.
getBaseFontFamily() - Method in class chemaxon.struc.graphics.MTextBox
Gets the base font family.
getBaseFontStyle() - Method in class chemaxon.struc.graphics.MTextBox
Gets the base font style.
getBestTabScale() - Method in class chemaxon.marvin.beans.MViewPane
Gets the smallest best scale value in the molecule table.
getBestTabScale(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the best scale value for a molecule cell.
getBFactor(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getBFactor(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getBFactorPalette() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the palette that is used when the coloring mode of the component is b-factor coloring.
getBicycloStereo() - Method in class chemaxon.struc.MolAtom
Gets the previously stored bicyclo stereo information of this atom.
getBit(int) - Method in class chemaxon.descriptors.CustomDescriptor
 
getBitCount() - Method in class chemaxon.descriptors.CFParameters
Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.
getBitCount() - Method in class chemaxon.descriptors.RFParameters
Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.
getBitPosition() - Method in class chemaxon.descriptors.ECFPFeature
Gets the generated bit position for this ECFP feature.
getBitPosition(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup
Returns the corresponding bit position for the given integer identifier.
getBitPosition(MolAtom, int) - Method in class chemaxon.descriptors.ECFPFeatureLookup
Returns the corresponding bit position for the given atom neighborhood.
getBoldBondWidth() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the C-C bold bond width in pt units.
getBoldBondWidth() - Method in class chemaxon.marvin.common.UserSettings
Gets the bold bond width in pt.
getBond() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Represented bond info.
getBond(int) - Method in class chemaxon.struc.MolAtom
Gets the i-th bond.
getBond(int) - Method in class chemaxon.struc.MoleculeGraph
Gets the nth bond.
getBond(int) - Method in class chemaxon.struc.RgMolecule
Gets an edge in the graph union.
getBond(int) - Method in class chemaxon.struc.RxnMolecule
Gets an edge.
getBond(int) - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
Returns a bond of a specified index.
getBond(int) - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Returns a bond of a specified index.
getBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow
Gets the bond at the terminus of an arrow.
getBondArray() - Method in class chemaxon.struc.MolAtom
Gets the bonds connected to this atom.
getBondArray() - Method in class chemaxon.struc.MoleculeGraph
Creates an array of bonds.
getBondArray() - Method in class chemaxon.struc.Sgroup
Gets all bonds connecting two atoms that are both in the Sgroup
getBondConnectionInfo() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets a bond triplet which stores the crossing bond and flip information.
getBondCorrespondence() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets four bonds that store the crossing bond and flip information.
getBondCount() - Method in class chemaxon.descriptors.CFParameters
Gets the preset path length (number of adjacent bonds) parameter.
getBondCount() - Method in class chemaxon.descriptors.RFParameters
Gets the preset path length (number of adjacent bonds) parameter.
getBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the bond count.
getBondCount() - Method in interface chemaxon.struc.Incomplecule
Gets the number of bonds
getBondCount() - Method in class chemaxon.struc.MolAtom
Gets the number of bonds/ligands.
getBondCount() - Method in class chemaxon.struc.MoleculeGraph
Gets the number of bonds.
getBondCount() - Method in class chemaxon.struc.RgMolecule
Gets the number of edges in the root structure.
getBondCount() - Method in class chemaxon.struc.RxnMolecule
Gets the number of edges in the graph union.
getBondCount() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the number of bonds in the found common substructure.
getBondCount(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the number of bonds in the molecule with arbitrarily enumerating hydrogens.
getBondFlags() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
getBondFlags(int) - Method in interface chemaxon.struc.Smolecule
Gets the bond descriptor flags.
getBondHashSpacing() - Method in class chemaxon.marvin.common.UserSettings
Gets the bond hash spacing.
getBondHashSpacing() - Method in class chemaxon.marvin.MolPrinter
Returns the bond hash spacing that is the distance hashes in a hashed bond.
getBondIndex() - Method in class chemaxon.marvin.alignment.atrop.BondInfo
Bond index.
getBondIndex(int, int) - Method in class chemaxon.core.util.BondTable
Returns the index of the bond connecting two atoms, or -1 if the two atoms are not connected.
getBondIndex(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the index of the bond connecting two atoms, -1 if the two atoms are not connected by bond.
getBondIndex(int, int) - Method in interface chemaxon.struc.Smolecule
Gets the index of the bond between the specified atoms.
getBondIterator() - Method in class chemaxon.struc.MoleculeGraph
Returns an iterator over the bonds in this molecule in proper sequence.
getBondIterator() - Method in class chemaxon.struc.RgMolecule
Returns an iterator over the bonds in this molecule in proper sequence.
getBondIterator() - Method in class chemaxon.struc.RxnMolecule
Returns an iterator over the bonds in this molecule in proper sequence.
getBondIterator(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the iterator of the atoms of the molecule.
getBondLength() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the C-C bond length in pt units.
getBondLength() - Method in class chemaxon.marvin.common.UserSettings
Gets the bond length in pt.
getBondLength() - Method in class chemaxon.marvin.MolPrinter
Returns the actual bond length in pt.
getBondMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the bond mapping of the found common substructure.
getBondReverseMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the reverse bond mapping of the found common substructure.
getBonds() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getBonds() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getBonds() - Method in class chemaxon.struc.MDocument.CheckerMark
 
getBonds(MolAtom) - Method in class chemaxon.struc.Molecule
Returns the bonds attached to the given atom.
getBonds(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Returns the bonds attached to the given atom in this molecule graph.
getBondSetColor(int) - Method in class chemaxon.struc.MDocument
Gets a bond set color.
getBondSetColorMode(int) - Method in class chemaxon.struc.MDocument
Gets the bond set coloring mode.
getBondSetRGB(int) - Method in class chemaxon.struc.MDocument
Gets a bond set color.
getBondSetSize() - Method in class chemaxon.struc.MDocument
Gets the bond set size.
getBondSetThickness(int) - Method in class chemaxon.struc.MDocument
Gets a bond set thickness.
getBondSpacing() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the bond spacing.
getBondSpacing() - Method in class chemaxon.marvin.common.UserSettings
Gets the double bond spacing.
getBondSpacing() - Method in class chemaxon.marvin.MolPrinter
Returns the double bond spacing that is the distance of the two lines representing a double bond.
getBondTable() - Method in class chemaxon.struc.MoleculeGraph
Gets the bond (edge) table.
getBondTable() - Method in class chemaxon.struc.RgMolecule
Gets the bond table of the root structre.
getBondTable() - Method in class chemaxon.struc.RxnMolecule
Gets the bond table for the graph union.
getBondTo(MolAtom) - Method in class chemaxon.struc.MolAtom
Finds the bond that connects this atom to another atom.
getBondType() - Method in class chemaxon.struc.MolBond
Gets the type of the bond.
getBondType(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines the type of a bond (aromatic bonds are automatically recognized)
getBondType(int) - Method in interface chemaxon.struc.Smolecule
Gets the type of a bond.
getBondType(int, int) - Method in interface chemaxon.struc.Smolecule
Gets the type of a bond between the two specified atoms.
getBondWidth() - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 4.1, replaced by MarvinPane.getBondSpacing()
getBondWidth() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 4.1, replaced by MolPrinter.getBondSpacing()
getBoolean(String) - Static method in class chemaxon.sss.search.SearchOptions
Returns value as a boolean flag.
getBorderColor() - Method in class chemaxon.marvin.space.monitor.Label
Returns the border color of the label.
getBorderWidth() - Method in class chemaxon.marvin.beans.MViewPane
Gets the width of the border between cells.
getBottom() - Method in class chemaxon.marvin.space.GraphicCell
Returns the y coordinate of the bottom of the cell in pixels.
getBoundAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets atoms with attachment point having crossing bond.
getBoundingBox() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the smallest box containing the graphic component.
getBoundingBox() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getBoundingBox() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the BoundingBox that is the smallest container box of the component.
getBoundingBoxAndSetSphereRadius() - Method in class chemaxon.marvin.space.GraphicCell
Computes the radius of the bounding sphere in order to set the z coordinate of the camera properly.
getBoundingCenter() - Method in class chemaxon.marvin.space.BoundingBox
Returns the center of the box as a vector.
getBoundingRadius() - Method in class chemaxon.marvin.space.BoundingBox
Returns the radius of the bounding sphere of the box, which is the distance between the lower-left-front corner and the center.
getBoundingRectangle(MoleculeGraph[]) - Method in class chemaxon.marvin.MolPrinter
Returns the bounding rectangle of the specified molecules using the current scale factor.
getBoundingSphereRadius() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the radius of the bounding sphere of the component.
getBoundRectSize() - Method in class chemaxon.marvin.beans.MSketchPane
Gets the size of the bounding rectangle.
getBracketCount() - Method in class chemaxon.struc.Sgroup
Gets the number of brackets in this S-group.
getBracketOrientation() - Method in class chemaxon.struc.graphics.MBracket
Gets the orientation of the bracket.
getBrackets() - Method in class chemaxon.struc.Sgroup
Gets all graphic brackets from this Sgroup
getBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox
Gets the breaking characters after that the text in the text box can be broken if it doesn't fit into the text box.
getBrightestMolId() - Method in class chemaxon.descriptors.MDGenerator
Gets the id of that molecule which had the maximum number of non-zero cells among all descriptors generated since the initialization of the generator object.
getBrightness() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the brightness of the fingerprint.
getBrightness() - Method in class chemaxon.descriptors.ECFP
Gets the brightness of the fingerprint.
getBrightness() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the brightness of the fingerprint.
getBufferedImage() - Method in class chemaxon.marvin.space.GraphicScene
Returns the Canvas as a BufferedImage with the same size in pixels.
getBuildDate() - Static method in class com.chemaxon.version.VersionInfo
Returns the build date as string (in local time zone).
getBuildTime() - Static method in class com.chemaxon.version.VersionInfo
Returns the build time as string (in local time zone).
getBuildTimestamp() - Static method in class com.chemaxon.version.VersionInfo
Returns the build date and time.
getBuildTimestampStr() - Static method in class com.chemaxon.version.VersionInfo
Returns the build date and time as string in UTC time zone.
getBuildYear() - Static method in class com.chemaxon.version.VersionInfo
Returns the year of the build date as string.
getBuiltInPalette(int) - Static method in class chemaxon.marvin.space.SurfaceColoring
Returns the colors of a built-in palette.
getBuiltInPalette(Object) - Static method in class chemaxon.marvin.space.SurfaceColoring
Returns the colors of a built-in palette.
getBuiltInPalettes() - Static method in class chemaxon.marvin.space.SurfaceColoring
Returns the string identifiers of the built-in palettes.
getC(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the state of a checkbox in a GridBagView table.
getCacheCapacity() - Method in class chemaxon.marvin.view.MDocStorage
Gets the maximum number of cached documents.
getCachedDoc(int, String) - Method in class chemaxon.marvin.view.MDocStorage
Gets the specified document if it is present in the memory.
getCachedDocIndices() - Method in class chemaxon.marvin.view.MDocStorage
Gets the indices of cached records.
getCachedResults(Molecule, boolean) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns cached results, separated from the plugin object, so that no further enqueries needed to the plugin to get the result.
getCacheLock() - Method in class chemaxon.marvin.view.MDocStorage
Gets the synchronization lock for caching operations.
getCalcMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the molecule used in the calculation.
getCameraZ() - Method in class chemaxon.marvin.space.GraphicCell
Returns the z coordinate of the camera.
getCanvasComponent() - Method in class chemaxon.marvin.beans.MSketchPane
Determines canvas component of MarvinSketch.
getCanvasComponent(int) - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.0, replaced by getVisibleCellComponent
getCapacity() - Method in class chemaxon.marvin.view.MDocStorage
Gets the total capacity.
getCarboaliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
getCarboaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
getCarbonVisibility() - Method in class chemaxon.marvin.MolPrinter
Returns the visibility style of the C labels on Carbon atoms.
getCarboRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the carbo ring count.
getCarboRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
getCarboRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
getCarboRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
getCASNumber() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the CAS number via public web service.
getCategory(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCategories
Calculates the solubility category of molecule.
getCell() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the container cell of the component.
getCell(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns the GraphicCell which has the given index.
getCellButtom() - Method in class chemaxon.marvin.space.GraphicScene
Returns the y coordinate of the buttom of the active cell in pixels.
getCellCount() - Method in class chemaxon.marvin.beans.MViewPane
Gets the number of molecule cells in the table.
getCellCount() - Method in class chemaxon.marvin.space.GraphicScene
Returns the number of cells in the scene.
getCellDrawProperty(int, String) - Method in class chemaxon.marvin.space.GraphicScene
Returns the draw property from the given cell or null if not defined.
getCellDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicCell
Returns the value of the cell-range drawing property with the given name.
getCellDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicScene
Returns the draw property from the active cell or null if there is no active cell or the property is not defined in the active cell.
getCellEditorValue() - Method in class chemaxon.marvin.beans.MViewEditor
Returns the edited molecule that is a Molecule instance.
getCellHeight() - Method in class chemaxon.marvin.space.GraphicScene
Returns the height of the cells.
getCellIndex() - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Returns the internal index of the cell either this is a cell id or a component id.
getCellLeft() - Method in class chemaxon.marvin.space.GraphicScene
Returns the x coordinate of the left edge of the active cell.
getCellRight() - Method in class chemaxon.marvin.space.GraphicScene
Returns the x coordinate of the right edge of the active cell.
getCellSize() - Method in class chemaxon.descriptors.MDParameters
Gets the number of bits of an atomic cell in the descriptor.
getCellTop() - Method in class chemaxon.marvin.space.GraphicScene
Returns the y coordinate of the top of the active cell.
getCellWidth() - Method in class chemaxon.marvin.space.GraphicScene
Returns the width of the cells.
getCenter() - Method in class chemaxon.marvin.space.monitor.Control
Returns the center of the transformation.
getCenter(int, int) - Method in class chemaxon.struc.RxnMolecule
Gets the geometrical center of a reaction component.
getCenterAtom() - Method in class chemaxon.descriptors.ECFPFeature
Gets the center atom of the represented substructure.
getCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Gets the central atom of this sgroup.
getChainAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the chain atom count.
getChainBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the chain bond count.
getChangedAtomIndexes() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the indexes of the atoms changed during tautomerization.
getChangeList() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Gets the list of applied changes
getChangeMap() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
The map containing the applied changes for each applied actions
getChanges() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
getChanges() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Gets the list of changes applied on the molecule.
getChangeSupport() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Returns the changeSupport
getCharge() - Method in class chemaxon.struc.MolAtom
Gets the charge.
getCharge() - Method in class chemaxon.struc.sgroup.SgroupAtom
Returns the sum of the charges in the corresponding superatom s-group.
getCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getCharge(int) - Method in interface chemaxon.struc.Smolecule
Gets the charge of an ion.
getCharge(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getChargeAngle() - Method in class chemaxon.struc.MolAtom
 
getChargeCategory() - Method in class chemaxon.marvin.calculations.logDPlugin
 
getChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
getChargeDistribution() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the charge distribution array over pH values.
getChargeFont() - Method in class chemaxon.marvin.MolPrinter
Gets the charge's font.
getChargeFontSize() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
getChargeLocation() - Method in class chemaxon.struc.Sgroup
Returns the charge location attribute of the S-group.
getChargeMatching() - Method in class chemaxon.sss.search.SearchOptions
Get the charge matching option value
getChargePlusMinusDistribution() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the plus and the minus parts of the charge distribution array over pH values.
getChecker(String, Map<String, String>) - Method in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
This method creates a requested (type represented in checkerId) StructureChecker instance with the give parameters
getCheckerConfigFileName() - Method in class chemaxon.marvin.common.UserSettings
Deprecated, for removal: This API element is subject to removal in a future version.
Use UserSettings.getCheckerConfigURL() instead. Deprecated in 5.12.
getCheckerConfiguration() - Method in interface chemaxon.checkers.runner.CheckerRunner
Gets the list of available checkers
getCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings
Returns the URL of configuration for Checkers in marvin sketch.
getCheckerList() - Method in class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
 
getCheckerList() - Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
 
getCheckerList() - Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
 
getCheckerMarks() - Method in class chemaxon.struc.MDocument
Returns the array of checker marks NOTE: checker marks will be reset on any molecule change
getCheckSpHyb() - Method in class chemaxon.sss.search.SearchOptions
Get the sp-hybridization state option
getChemicalHashedFingerprint(int[], int) - Static method in class chemaxon.descriptors.ReactionFingerprint
Creates chemical hashed fingerpint from reaction fingerprint.
getChemTermsFilter() - Method in class chemaxon.sss.search.SearchOptions
Gets the Chemical Terms filtering expression
getChemTermsFilterConfig() - Method in class chemaxon.sss.search.SearchOptions
Gets the configuration string for Chemical Terms filter.
getChemTermsFilterOption() - Method in class chemaxon.sss.search.SearchOptions
FOR INTERNAL USE ONLY.
getChild() - Method in interface chemaxon.common.util.MProgressMonitor
Gets the child of this progress monitor.
getChildSgroup(int) - Method in class chemaxon.struc.Sgroup
Gets a child S-group.
getChildSgroupCount() - Method in class chemaxon.struc.Sgroup
Gets the number of child S-groups.
getChildSgroups() - Method in class chemaxon.struc.Sgroup
Gets the children of this S-group.
getChiralCenterCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of tetrahedral stereogenic centers.
getChiralCenters() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines the chiral center atoms.
getChirality(int) - Method in class chemaxon.struc.MoleculeGraph
Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getChirality(int) - Method in interface chemaxon.struc.Smolecule
Gets the chirality of an atom.
getChiralityOfOriginalLigand() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
getChiralitySupport() - Method in class chemaxon.marvin.beans.MarvinPane
Gets chirality support level.
getChiralitySupport() - Method in class chemaxon.marvin.common.UserSettings
Gets the chirality support parameter.
getChiralitySupport() - Method in class chemaxon.marvin.MolPrinter
Returns the current chirality display mode.
getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
getCIPValue() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Returns the stereo center value.
getCIPValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
getClassName() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
Returns the full class name of the service
getClassName() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Gets the name of the standardizer class
getClean2dOpts() - Method in class chemaxon.marvin.common.UserSettings
Gets the 2D cleaning options.
getClean3dOpts() - Method in class chemaxon.marvin.common.UserSettings
Gets the 3D cleaning options.
getCleanDim() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the number of space dimensions for cleaning.
getCleanRelevantAtoms() - Method in class chemaxon.standardizer.Changes
Gets the list of atoms changed during the standardization procedure, and needs to be cleaned
getClip(CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Gets the clipping rectangle.
getClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the default Toolkit's system clipboard if available, otherwise returns a new singleton clipboard instance.
getClipboardContents() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Inits and return the transferable of the Clipboard for later import.
getClonedValue(String) - Method in class chemaxon.jep.ConstantTable
Returns the value of a constant.
getCoarseReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
Returns the tanimoto distance of the reaction centers.
getCode() - Method in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Gets the MoleculeGraph constant value of the aromatization
getColor() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
getColor() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties
 
getColor() - Method in class chemaxon.marvin.space.ComponentElement
Returns the color that is assigned to the ComponentElement.
getColor() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the constant color of the component.
getColor() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getColor() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the constant color of the surface.
getColor() - Method in class chemaxon.marvin.space.MoleculeComponent
 
getColor() - Method in class chemaxon.marvin.space.monitor.Control
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.monitor.DihedralControl
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.monitor.ResizeControl
Returns the color of the control.
getColor() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Returns the color of the component.
getColor() - Method in class chemaxon.marvin.space.PharmacophorePoint
Returns the color of the PharmacophorePoint.
getColor() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the constant color of the surface.
getColor() - Method in class chemaxon.struc.MDocument.CheckerMark
 
getColor() - Method in class chemaxon.struc.MObject
Gets the color of the object.
getColor3() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the constant color of the surface.
getColor3F() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the constant color of the surface.
getColoredLargestConjugatedSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns a Molecule in which the atoms of largest conjugated system are colored.
getColorF() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getColorF() - Method in class chemaxon.marvin.space.MoleculeComponent
 
getColorF() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the constant color of the surface.
getColoring() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the hit coloring options.
getColoringScheme() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getColors() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getColors() - Method in class chemaxon.marvin.alignment.Pharmacophore3D
 
getColorScheme() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the color scheme.
getColorScheme() - Method in class chemaxon.marvin.MolPrinter
Returns the current color scheme.
getColorType() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getColorType() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the color type of the surface.
getColorType() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the color type of the visualizer.
getColumn(int) - Static method in class chemaxon.core.ChemConst
The column or group of an element in the periodic system.
getColumn(int) - Static method in class chemaxon.struc.MolAtom
The column or group of an element in the periodic system.
getColumnCount() - Method in class chemaxon.marvin.space.GraphicScene
Returns the number of columns in the scene.
getColumnWidth() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the default column width.
getColumnWidth(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the default width of a specified column.
getColumnWidthsString() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets a parameter string containing column widths.
getCommandKeyStroke(int) - Static method in class chemaxon.marvin.util.SwingUtil
Gets the command keystroke preferred on the current platform.
getComment() - Method in class chemaxon.struc.Molecule
Gets the comment.
getComment() - Method in class chemaxon.struc.RgMolecule
Gets the comment of the root molecule.
getCommonActions() - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated. 
getCommonActions() - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated.
at N/A (before 02/12/2015)
getCommonActions() - Method in class chemaxon.marvin.beans.MViewPane
Deprecated.
getCommonBitCount(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
 
getCommonBitCount(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
 
getCompatibleAttributes(MTextAttributes, MFont, MTextAttributes.MFontCreator, int) - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the compatible attributes.
getCompleteHG() - Method in class chemaxon.sss.search.SearchOptions
Deprecated, for removal: This API element is subject to removal in a future version.
This option is no longer supported. This method always returns true.
getComplexValue() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Complex number support will be removed without replacement.
getComponent() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Returns the parameter panel component.
getComponent() - Method in class chemaxon.marvin.space.ComponentElement
Returns the component which contains this ComponentElement.
getComponent() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Returns the molecule whose atoms are monitored.
getComponent() - Method in class chemaxon.marvin.space.monitor.Label
Returns the GraphicComponent of the only selected item.
getComponent() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns the GraphicComponent of the only selected item.
getComponent() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Returns the parameter panel component.
getComponent(int) - Method in class chemaxon.marvin.space.GraphicCell
Returns the component having the given index.
getComponent(int) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns its visualizer with the given index.
getComponent(int, int) - Method in class chemaxon.struc.RxnMolecule
Gets a reactant, product or agent.
getComponent(long) - Method in class chemaxon.struc.RxnMolecule
Gets a reactant, product or agent.
getComponent(Molecule, int) - Method in class chemaxon.checkers.AtomChecker
 
getComponent(Molecule, int) - Method in class chemaxon.checkers.BondChecker
 
getComponent(Molecule, int) - Method in class chemaxon.checkers.ComponentChecker
Gets the component from the molecule with index i.
getComponentCount() - Method in class chemaxon.marvin.space.GraphicCell
Returns the number of components of the cell including monitors, surfaces and so on.
getComponentCount(int) - Method in class chemaxon.struc.RxnMolecule
Gets the number of reactants, products or agents.
getComponentCount(Molecule) - Method in class chemaxon.checkers.AtomChecker
 
getComponentCount(Molecule) - Method in class chemaxon.checkers.BondChecker
 
getComponentCount(Molecule) - Method in class chemaxon.checkers.ComponentChecker
Gets the number of the components in the molecule
getComponentElement() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the previously picked but unprocessed ComponentElement or the whole component as a ComponentElement, if no picking happened.
getComponentElement() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the previously picked but unprocessed ComponentElement or the whole component as a ComponentElement, if no picking happened.
getComponentElement() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the previously picked but unprocessed ComponentElement or the whole component as a ComponentElement, if no picking happened.
getComponentElement(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the visualizer as a ComponentElement.
getComponentFlags(long) - Method in class chemaxon.struc.RxnMolecule
Gets the reaction component type flags from the ID.
getComponentID(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Gets the reaction component ID of an atom.
getComponentID(MolBond) - Method in class chemaxon.struc.RxnMolecule
Gets the reaction component ID of a bond.
getComponentID(Molecule) - Method in class chemaxon.struc.RxnMolecule
Gets the ID of a reaction component.
getComponentIds() - Method in class chemaxon.checkers.result.ReactionCheckerResult
Deprecated.
Returns the List of the ids of the components affected by the problem
getComponentIndex() - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Returns the internal index of the component or -1 if this is a cell id.
getComponentIndex(long) - Method in class chemaxon.struc.RxnMolecule
Gets the reactant, product or agent index from the ID.
getComponentIterator() - Method in class chemaxon.marvin.space.GraphicCell
Returns the iterator of the GraphicComponents of the cell.
getComponentIterator() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the Iterator of its visualizers.
getComponentPartId() - Method in class chemaxon.marvin.space.ComponentElement
In case of complex components the componentPartId identifies a part of the component.
getComponents() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns its visualizers.
getComponents(Molecule) - Static method in class chemaxon.checkers.StructureCheckerUtility
A recursive algorithm collecting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.
getComponents(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction
A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.ExpandAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.MapAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.MapReactionAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.NeutralizeAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RearrangeReactionAction
Every action that needs to do something on a reaction as a whole needs this, otherwise reaction components will be processed one-by-one.
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
getComponents(Molecule) - Method in class chemaxon.standardizer.advancedactions.TransformAction
 
getComponentType(long) - Method in class chemaxon.struc.RxnMolecule
Gets the reaction component type from the ID.
getComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
getConfiguration() - Method in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
 
getConfiguration() - Method in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader
Gets the configuration defined by the pre-set configuration file.
getConfiguration() - Method in class chemaxon.standardizer.configuration.reader.StandardizerXMLReader
 
getConfiguration() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
getConfiguration() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Gets the configuration of the runner
getConfiguration() - Method in class chemaxon.standardizer.Standardizer
Gets the configuration of the standardizer.
getConformer(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns a conformer.
getConformerCount() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the number of different conformers.
getConformers() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns all conformers in a Molecule[] array.
getConformerWithConformerInfoProperty(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Deprecated.
Only intended for internal use.
getConfTryCountLimit() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
 
getConnectedObject(int) - Method in class chemaxon.struc.MDocument
Gets an object from the document or from the chemical structure of the document.
getConnectedObjectCount() - Method in class chemaxon.struc.MDocument
Gets the number of objects in this document and in the chemical structure of this document.
getConnectionAtoms() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets the indexes of atoms connection to any atoms
getConnectivity() - Method in class chemaxon.struc.Sgroup
Gets S-group connectivity.
getContainerMObject(MDocument) - Method in class chemaxon.struc.MObject
 
getContext() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns the evaluation context
getContext() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the context of the data sgroup.
getContextFunctionNames() - Method in interface chemaxon.jep.ChemContext
Deprecated, for removal: This API element is subject to removal in a future version.
This method is the legacy option for specifying the supported context functions. Use the ChemContext.ProvidesFunction annotation instead.
getContextFunctionNames() - Method in class chemaxon.jep.context.AtomContext
Deprecated, for removal: This API element is subject to removal in a future version.
Use the ChemContext.ProvidesFunction annotation instead.
getContextFunctionNames() - Method in class chemaxon.jep.context.MolContext
Deprecated, for removal: This API element is subject to removal in a future version.
Use the ChemContext.ProvidesFunction annotation instead.
getContextFunctionNames() - Method in class chemaxon.jep.context.ReactionContext
Deprecated, for removal: This API element is subject to removal in a future version.
Use the ChemContext.ProvidesFunction annotation instead.
getContextId() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the id of the context of the data sgroup.
getControl() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns the control of this monitor.
getControllableObject(String) - Method in class chemaxon.marvin.space.GraphicCell
Returns a component if there is any which allows itself to be controlled.
getControllableObject(String) - Method in class chemaxon.marvin.space.GraphicScene
Returns a selected component from the active cell what can be controlled by the given tye controller.
getCoordinateBondStyle() - Method in class chemaxon.marvin.common.UserSettings
Gets the "coordinative" bond line style when both atoms are single.
getCoordinateBondStyle() - Method in class chemaxon.marvin.MolPrinter
Gets the coordinate bond line style when both atoms are single.
getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.common.UserSettings
Gets the "coordinative" bond line style when one of the atoms is multicenter.
getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.MolPrinter
Gets the coordinate bond line style.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.ComponentElement
Returns the world coordinates of the ComponentElement.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Gets the coordinates of the previously picked but not yet processed part if there is any in the given preallocated array.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.AngleMonitor
Returns the centroid of the selected elements.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Returns the centroid of the second and third selected elements.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.Label
Returns the coordinates of the selected item as a GeomCalc vector.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Returns the centroid of the selected elements.
getCoordinates(float[]) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns the coordinates of the selected item.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Gets the coordinates of the given ComponentElement in the given preallocated array.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the coordinates of the given ComponentElement in the given array.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the coordinates of the given element in the given preallocated array.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.monitor.Label
Returns the coordinates of the selected item as a GeomCalc vector.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Returns the centroid of the selected elements.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns the coordinates of the selected item.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Gets the position of the component.
getCoordinates(ComponentElement, float[]) - Method in class chemaxon.marvin.space.PharmacophorePoint
Gets the position of the pharmacophore point.
getCoordinatesOfAligned() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
getCoordinatesOfReference() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
getCopyAsFormat() - Method in class chemaxon.marvin.common.UserSettings
Gets the selected format from the Copy As dialog.
getCopyAsTransferableNames() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the format's names that are available in the current environment as transfer types for the Copy As dialog.
getCorrectionLibraryIds() - Static method in class chemaxon.marvin.calculations.pKaPlugin
Returns the id's of available pKa correction libraries.
getCount() - Method in class com.chemaxon.calculations.gui.PluginFactory
Returns the number of plugin records.
getCouplingConstants() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns coupling constants.
getCouplingConstants(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns coupling constants in the given unit.
getCovalentRadius(int) - Static method in class chemaxon.struc.PeriodicSystem
Covalent radius of the element in Angstroms.
getCovalentRadius(int, int) - Static method in class chemaxon.struc.PeriodicSystem
Covalent radius of the element in specific bond type in Angstroms.
getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.Sgroup
Gets the atoms that have crossing bonds.
getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the atoms from the S-group that have crossing bonds.
getCSSR() - Method in class chemaxon.struc.MoleculeGraph
Gets the Complete Set of Smallest Ring atom indexes array.
getCSSRIdxesForAtoms() - Method in class chemaxon.struc.MoleculeGraph
Get the cssr ring indexes in which the atom (specified with it's index) can be located.
getCtab() - Method in class chemaxon.struc.MoleculeGraph
Gets the connection table.
getCtab() - Method in class chemaxon.struc.RgMolecule
Gets the connection table of the root structure.
getCtab() - Method in class chemaxon.struc.RxnMolecule
Gets the connection table for the graph union.
getCTAtom1() - Method in class chemaxon.struc.MolBond
Gets the first atom for cis/trans stereo calculation.
getCTAtom4() - Method in class chemaxon.struc.MolBond
Gets the fourth atom for cis/trans stereo calculation.
getCurrent() - Method in interface chemaxon.checkers.runner.CheckerRunner
 
getCurrent() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
getCurrent() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Gets the current progress percent
getCurrentActionName() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
getCurrentActionName() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Gets which StandardizerAction instance run currently
getCurrentCheckerName() - Method in interface chemaxon.checkers.runner.CheckerRunner
 
getCurrentDefaultFontMetrics() - Method in class chemaxon.struc.graphics.MTextBox
Gets the current default FontMetrics.
getCurrentForeground() - Method in class chemaxon.struc.graphics.MTextBox
Gets the current color.
getCurrentHeight() - Method in class chemaxon.struc.graphics.MTextBox
Gets the current height of the text.
getCurrentMetricIndex() - Method in class chemaxon.descriptors.MDParameters
 
getCurrentScriptCount(int) - Method in class chemaxon.struc.graphics.MTextBox
Gets the number of subscripts or superscripts on the last normal character.
getCurrentSubLevel() - Method in class chemaxon.struc.graphics.MTextBox
Gets the current subscript/superscript level.
getCurrentTextAttributes(int) - Method in class chemaxon.struc.graphics.MTextBox
Gets the common attributes of the selected text or attributes for the next character to be typed.
getCurrentWidth() - Method in class chemaxon.struc.graphics.MTextBox
Gets the current width of the text.
getCursorColumn() - Method in class chemaxon.struc.graphics.MTextBox
Gets the cursor's column number.
getCursorPos() - Method in class chemaxon.struc.graphics.MTextBox
Gets the cursor position.
getCursorRow() - Method in class chemaxon.struc.graphics.MTextBox
Gets the cursor's row number.
getCusromToolBar(JTextPane, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Returns a custom toolbar for textPane instance NOTE: textPane have to be created with this factory
getCustomFuzzyIncrements(int, int) - Method in class chemaxon.descriptors.PFParameters
Gets fuzzy increments for the fuzzy smoothing with a user-defined custom distribution (fuzzy smoothing vector).
getCustomMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets the factory that is used to create the custom matcher.
getCustomName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the customName
getCyclomaticNumber() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the smallest number of graph edges which must be removed such that no circuit remains.
getDarkestMolId() - Method in class chemaxon.descriptors.MDGenerator
Gets the id of that molecule which had the minimum number of non-zero cells among all descriptors generated since the initialization of the generator object.
getData() - Method in class chemaxon.descriptors.MDParameters
Gets the byte array which is used for conversions between internal and external data formats.
getData() - Method in class chemaxon.sss.search.MarkushFeature
Deprecated.
Returns the feature data.
getData() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the data value to be set.
getData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
Gets the data field.
getDataCollectionConsent() - Method in class chemaxon.marvin.common.UserSettings
 
getDataCollectionServer() - Method in class chemaxon.marvin.common.UserSettings
 
getDataFromClipboard(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Returns the Molecule from the Transferable object.
getDataLine(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Gets a line of data.
getDataLineCount() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the number of data lines.
getDataToClipboard(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Returns the clipboard representation of the given Molecule.
getDaviesHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin
Returns the HLB value calculated by Davies method.
getDebug() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the debugging level.
getDecForm() - Method in class chemaxon.descriptors.MDParameters
Gets the formatter object that is capable of formatting fractions with given precision.
getDefault() - Static method in class com.chemaxon.search.mcs.McsSearchOptions
Returns the default search options object.
getDefaultAbbrevgroups() - Static method in class chemaxon.checkers.StructureCheckerHelper
Imports default and user abbreviations and returns them in a AbbrevGroupStorage.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.BCUT
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.CustomDescriptor
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ECFP
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ScalarDescriptor
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ShapeDescriptor
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.BCUTParameters
Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.CDParameters
Gets the XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.CFParameters
Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.ECFPParameters
Get the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.MDParameters
Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.PFParameters
Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.RFParameters
Get the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.ShapeParameters
Get the default XML configuration string.
getDefaultFont() - Method in class chemaxon.struc.graphics.MTextDocument
Gets the default font.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the index of the default metric.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.ECFP
Gets the index of the default metric.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the index of the default metric.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the index of the default metric.
getDefaultProperty(String) - Method in class chemaxon.marvin.common.UserSettings
Gets the value of the given key in the default configuration or null if the key does not exist.
getDefaultSaveFormat() - Method in class chemaxon.marvin.common.UserSettings
Gets the default molecule format in the "Save As" dialog.
getDefaultScale() - Static method in class chemaxon.marvin.beans.MSketchPane
Returns the default scale factor which is equivalent to 100% magnification.
getDefaultServiceDescriptorEditorProvider() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the default ServiceDescriptorEditorProvider instance
getDefaultServiceDescriptorReader() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the default ServiceDescriptorReader instance
getDefaultServiceDescriptorWriter() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the default ServiceDescriptorWriter instance
getDefaultServiceDialogProvider() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the default ServiceDialogProvider instance
getDefaultSize() - Method in class chemaxon.marvin.view.swing.TableSupport
Gets the default size of an MViewPane containing the generated table.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.ECFPParameters
Gets the default configuration of the standardizer.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.MDParameters
Gets the default configuration of the standardizer.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.PFParameters
Gets the default configuration of the standardizer.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.ShapeParameters
Gets the default configuration of the standardizer.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ECFP
Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ReactionFingerprint
Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ScalarDescriptor
Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ShapeDescriptor
Gets a metric dependent default threshold value.
getDefaultValue() - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
getDehydrogenizer() - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a dehydrogenizer transformer.
getDensityCounts() - Method in class chemaxon.descriptors.MDGenerator
Gets the array of bit density.
getDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule
Gets the R-group definition's index which depends on the referenced R-group definition.
getDescent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the descent of this portion.
getDescription() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getDescription() - Method in class chemaxon.checkers.InvalidChecker
 
getDescription() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getDescription() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getDescription() - Method in interface chemaxon.checkers.StructureChecker
 
getDescription() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the description
getDescription() - Method in class chemaxon.fixers.AbstractStructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
getDescription() - Method in interface chemaxon.fixers.StructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
getDescription() - Method in class chemaxon.fixers.StructureFixerDescriptor
Returns the description
getDescription() - Method in class chemaxon.formats.MFileFormat
Gets the format description.
getDescription() - Method in class chemaxon.marvin.space.ComponentElement
Returns the brief description of the ComponentElement, for example type of the atom.
getDescription() - Method in class chemaxon.marvin.space.GraphicComponent
Returs the short description of the component or of the previously picked but not yet processed part if there is any or the description of the whole component.
getDescription() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Returns the measurement as a description.
getDescription() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Returns a descriptive text.
getDescription() - Method in class chemaxon.marvin.space.PharmacophorePoint
Returns textual description.
getDescription() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the description.
getDescription() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the description of the action
getDescription(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Returs the short description of the given part of the component.
getDescription(ComponentElement) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the short description of the given element.
getDescription(ComponentElement) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getDescription(ComponentElement) - Method in class chemaxon.marvin.space.MoleculeComponent
Returs the short description of the given part of the component.
getDescription(ComponentElement) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Returns the measurement as a description.
getDescriptor() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getDescriptor() - Method in class chemaxon.checkers.InvalidChecker
 
getDescriptor() - Method in interface chemaxon.checkers.StructureChecker
Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker
getDescriptor() - Method in class chemaxon.fixers.AbstractStructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
getDescriptor() - Method in interface chemaxon.fixers.StructureFixer
Gets the descriptor object of the fixer.
getDescriptor() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
Returns the ServiceDescriptor represented by editor state or null if the editor is in not valid state
getDescriptor() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
getDescriptor() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
getDescriptor() - Method in interface chemaxon.standardizer.StandardizerAction
Gets the descriptor of the standardizer action.
getDescriptorLongName(String) - Static method in class chemaxon.descriptors.DescriptorGenerator
Returns the long name for the given molecular descriptor type.
getDescriptorTypeName(String) - Static method in class chemaxon.descriptors.MDParameters
Takes the descriptor type name from the root element of the XML configuration.
getDescriptorTypes() - Static method in class chemaxon.descriptors.DescriptorGenerator
Returns the list of the built-in molecular descripor types.
getDescriptorURI() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
Gets the URI of the JSON RPC descriptor file
getDescrType() - Method in class chemaxon.descriptors.CDParameters
Gets the type of the descriptor.
getDesiredLength() - Method in class chemaxon.struc.MolBond
Deprecated, for removal: This API element is subject to removal in a future version.
getDesiredLength(boolean) - Method in class chemaxon.struc.MolBond
Deprecated, for removal: This API element is subject to removal in a future version.
getDesiredLength(int, int, int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int) and MoleculeGraph.getDim().
Usage:
             MolBond.desiredLength(atno1, atno2, type, getDim());
             
getDesiredLength(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int), MolBond.getType() and MoleculeGraph.getDim().
Usage:
             MolBond.desiredLength(atno1, atno2, b.getType, getDim());
             
getDf1() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
 
getDf2() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
 
getDialog(Component, ServiceDescriptor) - Method in interface chemaxon.marvin.services.ServiceDialogProvider
Returns dialog with argument editor and result view
getDiameter() - Method in class chemaxon.descriptors.ECFPFeature
Gets the diameter of the represented substructure.
getDiameter() - Method in class chemaxon.descriptors.ECFPParameters
Gets the preset diameter parameter.
getDihedral(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the dihedral of 4 atoms.
getDihedral(int, int, int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the dihedral of 4 atoms.
getDihedralScanResults() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Get results of executed dihedral scans.
getDim() - Method in class chemaxon.struc.MoleculeGraph
Gets the dimension.
getDipole() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the length of the dipole moment vector.
getDipoleVector() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the dipole moment vector.
getDipoleX() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the x component of the dipole moment vector.
getDipoleY() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the y component of the dipole moment vector.
getDipoleZ() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the z component of the dipole moment vector.
getDirectory() - Method in class chemaxon.marvin.beans.MarvinPane
Sets the working directory.
getDisabledGroupTypes() - Method in class chemaxon.marvin.beans.MSketchPane
 
getDisplay() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
getDisplay(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets a display object, loads it if needed.
getDisplayedChars() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the number of characters to be displayed(1...999 or 0 for all)
getDisplayedLines() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the number of lines to be displayed (0: show all)
getDisplayMolecule() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the molecule object to be used for GUI display.
getDisplayMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the molecule object to be used for GUI display.
getDisplayMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the molecule object to be used for GUI display.
getDisplayQuality() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 6.4 only high quality exists
getDisplayVersion() - Static method in class com.chemaxon.version.VersionInfo
Returns the display version.
getDispopts() - Method in class chemaxon.marvin.beans.MarvinPane
Gets display options.
getDispopts() - Method in class chemaxon.marvin.MolPrinter
Returns the actual display options.
getDispoptsExt() - Method in class chemaxon.marvin.MolPrinter
Returns the actual extended display options.
getDissimilarity() - Method in class com.chemaxon.search.mcs.McsSearchResult
Returns a Tanimoto-like dissimilarity metric score of the input molecules based on the found maximum common substructure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.BCUT
Calculates the dissimilarity ratio between two BCUT objects using the current default metric.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the dissimilarity between two chemical fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFP
Calculates the dissimilarity ratio between two ECFP objects using the current default metric.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.MolecularDescriptor
Calculates the dissimilarity ratio between two MolecularDescriptor objects using the default metric.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ReactionFingerprint
Calculates the dissimilarity between two reaction fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ScalarDescriptor
Calculates the dissimilarity between two scalar descriptor using the default metrics In the present implementation it is always the absolute difference between them.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor
 
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.BCUT
Calculates the dissimilarity between two BCUT objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the dissimilarity between two chemical fingerprints using the specified distance metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.CustomDescriptor
Calculates the dissimilarity between two descriptors using the specified parametrized dissimilarity metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ECFP
Calculates the dissimilarity between two ECFP objects using the specified metric, apart from that it is the same as getDissimilarity(final MolecularDescriptor other).
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.MolecularDescriptor
Calculates the dissimilarity between two MolecularDescriptor objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the dissimilarity between two pharmacophore fingerprints using the specified parametrized distance metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ReactionFingerprint
Calculates the dissimilarity between two reaction fingerprints using the specified distance metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ScalarDescriptor
Calculates the dissimilarity between two scalar descriptor using the specified metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ShapeDescriptor
 
getDissimilarity(T) - Method in class chemaxon.descriptors.SimilarityCalculator
Gets the dissimilarity value according to previously defined metric and its parameters.
getDissimilarityMetricIndex(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the internal index of the given metric.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.BCUT
Gets the dissimilarity metric names introduced for this class of MolecularDescriptor.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the dissimilarity metric names
getDissimilarityMetrics() - Method in class chemaxon.descriptors.CustomDescriptor
Gets the dissimilarity metric names.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ECFP
Gets the dissimilarity metric names introduced for this class of MolecularDescriptor.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the dissimilarity metric names in an array.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the dissimilarity metric names.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the dissimilarity metric names
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ScalarDescriptor
Gets the dissimilarity metric names
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ShapeDescriptor
 
getDissimilarityMetricsParamDefault() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the dissimilarity metric parameter names -> no parameters.
getDissimilarityMetricsParamHelp() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the dissimilarity metric parameter names -> no parameters.
getDissimilarityMetricsParamNames() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the dissimilarity metric parameter names -> no parameters.
getDissimilarityMetricsParamNum() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the dissimilarity metric parameter number -> no parameters.
getDissimilarityMetricsParamRanges() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the dissimilarity metric parameter ranges -> no parameters.
getDistance(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the distance of 2 atoms.
getDistance(int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the distance of 2 atoms.
getDistanceCount(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Counts the given value in a row of the distance matrix.
getDistanceDegree(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
getDoc(int, String) - Method in class chemaxon.marvin.view.MDocStorage
Gets the specified document.
getDoc(int, String, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
Gets the specified document.
getDocLabel(int, MDocument) - Method in class chemaxon.marvin.io.MDocSource
Returns the display label for the given document and document index.
getDocLabel(int, MDocument) - Method in class chemaxon.marvin.view.MDocStorage
Returns the display label for the given document and document index.
getDocSource() - Method in class chemaxon.marvin.view.MDocStorage
Gets the document source.
getDocSourcePosition() - Method in class chemaxon.marvin.view.MDocStorage
Gets the current position in the input.
getDocStorage() - Method in class chemaxon.marvin.beans.MViewPane
Gets the sparse dynamic document storage.
getDocStorage() - Method in class chemaxon.marvin.view.swing.TableSupport
Gets the sparse dynamic document storage.
getDocument() - Method in class chemaxon.marvin.beans.MSketchPane
Gets the document.
getDocument() - Method in class chemaxon.struc.MoleculeGraph
Gets the document object.
getDocument(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the nth document.
getDocument(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns encapsulating document, creates it if needed.
getDocumentForChild(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Gets the parent document for a child molecule graph.
getDocuments() - Method in class chemaxon.marvin.beans.MViewPane
Gets the array of documents.
getDocumentStyleName() - Method in class chemaxon.marvin.common.UserSettings
 
getDomainMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the upper end of the spectrum.
getDomainMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the lower end of the spectrum.
getDominantTautomerDistribution(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the distribution of the dominant tautomer.
getDonorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the overall donor atom count (without multiplicity) in the molecule.
getDonorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getDonorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getDonorSiteCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the overall donor count (with multiplicity) in the molecule.
getDonorSiteCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the atomic donor count corresponding to the specified atom index.
getDotDir() - Static method in class chemaxon.util.DotfileUtil
Gets the directory of the configuration files.
getDotDirName() - Static method in class chemaxon.util.DotfileUtil
Gets the subdirectory name of the configuration files.
getDotDisconnectedFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the dot-disconnected molecular formula of a multifragment molecule with its formal charge.
getDotDisconnectedFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the dot-disconnected molecular formula of a multifragment molecule.
getDotDisconnectedIsotopeFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.
getDotDisconnectedIsotopeFormalChargeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.
getDotDisconnectedIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the dot-disconnected isotope formula of a multifragment molecule.
getDotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the dot-disconnected isotope formula of a multifragment molecule.
getDotFile(String) - Static method in class chemaxon.util.DotfileUtil
Gets a configuration file with the specified relative path.
getDotFileWithEnsuredPath(String) - Static method in class chemaxon.util.DotfileUtil
 
getDoubleArray() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Gets the integer value.
getDoubleBondStereoMatchingMode() - Method in class chemaxon.sss.search.SearchOptions
Get the double bond stereo matching mode.
getDoublePrecision() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the precision.
getDownWedge() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the wedge bond display convention.
getDownWedge() - Method in class chemaxon.marvin.common.UserSettings
Gets the wedge bond display convention.
getDownWedge() - Method in class chemaxon.marvin.MolPrinter
Gets the down wedge orientation.
getDraggedObject() - Method in class chemaxon.struc.MDocument
Gets the dragged object
getDrawProperties() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the set draw properties of the component.
getDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicComponent
Returns the value of a draw property.
getDrawProperty(String) - Method in class chemaxon.marvin.space.GraphicScene
Returns the draw property of the scene or null if the property is not defined.
getDrawProperty(String) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getDrawType() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the drawing type of the molecular surface.
getDrawType() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Returns the name of the drawing type.
getDrawType() - Method in class chemaxon.marvin.space.PharmacophorePoint
Returns the name of the drawing type.
getDrawType() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the actual drawing type.
getDreidingEnergy() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the energy of the conformer.
getDx() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the x shift.
getDy() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the y shift.
getEccentricity(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
getEditable() - Method in class chemaxon.marvin.beans.MViewEditor
Returns the mode that determines if the structure is editable.
getEditable() - Method in class chemaxon.marvin.beans.MViewPane
Returns the mode that determines if the structure is editable.
getEditor() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
Returns the editor component for the ServiceDescriptor
getEditor(Class<T>) - Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider
Returns a ServiceDescriptorEditor instance for specified ServiceDescriptor class
getEditorClassName() - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
getEditorClassName() - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
getEditorClassName() - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
getEditorClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the editorClassName
getEditorClassName() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Returns the editorClassName
getEditorClassName() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Gets the name of the editor of the standardizer class
getEditorComponent() - Method in class chemaxon.marvin.beans.MViewEditor
Returns the editor component.
getEFlowsFromAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
Returns all the EFlow from this atom.
getEFlowsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
Returns all the EFlows that are started from this atom or pointing to this atom.
getEFlowsToAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
Returns all the EFlows to this atom.
getEigenVector() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
getElectronContainersOf(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
getElectronCount() - Method in class chemaxon.struc.MDocument
Returns the number of electrons.
getElectronDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the electron density of an atom calculated with HMO, Double.NaN for no value.
getElectronProp() - Method in class chemaxon.struc.MolAtom
Returns the number of lone pairs on this atom.
getElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
getElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
getElementCount() - Static method in class chemaxon.struc.PeriodicSystem
Number of elements in the periodic system
getElementIndex() - Method in class chemaxon.marvin.space.ComponentElement
Returns the internal index of the ComponentElement in the GraphicComponent.
getElementType() - Method in class chemaxon.marvin.space.ComponentElement
Returns the type of the ComponentElement.
getEnableStandardization() - Method in class chemaxon.descriptors.RFParameters
Shows if standardization should be applied of not.
getEnantiomer(T) - Static method in class chemaxon.calculations.stereo.Stereochemistry
Get the enantiomer pair of the given molecule
getEncapsulatedReader() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the encapsulated record reader if it exists.
getEncapsulatedReader() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the encapsulated record reader if it exists.
getEnclosingCube() - Method in class chemaxon.struc.MoleculeGraph
Gets the cube that encloses the atoms of molecule graph.
getEncoding() - Method in class chemaxon.marvin.io.MolExportModule
Gets the output encoding.
getEncoding() - Method in class chemaxon.marvin.io.MRecord
Gets the encoding.
getEncoding() - Method in class chemaxon.marvin.io.PositionedInputStream
Gets the encoding.
getEncodingFromOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil
Gets the encoding that was explicitly given as an import option.
getEndDx() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the x shift at the end.
getEndLineCount() - Method in class chemaxon.marvin.io.MRecord
Gets the line number at the ending point.
getEndPos() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the position of the last character + 1.
getEndPosition() - Method in class chemaxon.marvin.io.MRecord
Gets the end position in the input file.
getEndPosition() - Method in class chemaxon.struc.MDocument
Gets the end position of this document in the input file.
getEndPosition() - Method in class chemaxon.struc.Molecule
Gets the end position of this molecule in the input file.
getEnegryDifference() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Observed rotational energy barrier.
getEnergy() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanStep
Represented energy.
getEnergy() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the energy of the lowest energy conformer in kcal/mol.
getEnergy(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the energy of the i-th conformer in kcal/mol.
getEnhancedStereo() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
 
getEnhancedStereo() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Returns the enhanced stereo group (optional).
getEnhancedStereoFlags() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Returns the enhanced stereo flags of the molecule.
getEnhancedStereoGroup(String) - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Gets the EnhancedStereoGroup to which the specified flag is mapped.
getEnumCodeNeeded() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Tests whether unique Markush enumeration code should be generated
getErr() - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Get stderr to use.
getError() - Method in class chemaxon.marvin.alignment.MolAligner
Get the error for the best alignment
getError(int) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
getErrorCode() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getErrorCode() - Method in class chemaxon.checkers.ExternalStructureChecker
 
getErrorCode() - Method in class chemaxon.checkers.InvalidChecker
 
getErrorCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
 
getErrorCode() - Method in interface chemaxon.checkers.result.ExternalStructureCheckerResult
This function returns a String which identifies the problems thus this must be unique for each class that implements this interface
getErrorCode() - Method in interface chemaxon.checkers.StructureChecker
Returns the String represented error code of the checker (this error code should be used for external implementation support instead of StructureChecker.getErrorType())
getErrorComponent() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns a component with the appropriate error message.
getErrorCount() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
Return the error count.
getErrorCount() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
getErrorDescription(int) - Method in class chemaxon.checkers.AbstractStructureChecker
Generate the error description depends on erroCount
getErrorDescription(StructureCheckerDescriptor, int) - Static method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getErrorInfo() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
getErrorMessage() - Method in class chemaxon.checkers.InvalidChecker
Gets the error message of the checker instance
getErrorMessage() - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the calculation error information message if ChargePlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
 
getErrorMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the calculation error information message if HBDAPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the calculation error information message if HuckelAnalysisPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the calculation error information message if IonChargePlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the calculation error information message if IsoelectricPointPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
getErrorMessage() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the calculation error information message if logDPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the calculation error information message if logPPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the calculation error information message if MSAPlugin.run() returned false (calculation error).
getErrorMessage() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the calculation error information message if OrbitalElectronegativityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the calculation error information message if pKaPlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the calculation error information message if PolarizabilityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the calculation error information message if RefractivityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the calculation error information message if TPSAPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).
getErrorMessage() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
Gets the error message of the standardizer instance
getErrors() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
getErrorType() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getErrorType() - Method in class chemaxon.checkers.InvalidChecker
 
getErrorType() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getErrorType() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getErrorType() - Method in interface chemaxon.checkers.StructureChecker
 
getErrorType() - Method in class chemaxon.checkers.SubstructureChecker
 
getErrorTypeDefaultFixerMap() - Method in class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
 
getErrorTypeDefaultFixerMap() - Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
 
getErrorTypeDefaultFixerMap() - Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
 
getEstimatedStereoisomerCount() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
Gets the number of stereoisomers, if molecule does not contain pseudo stereocenters.
# of stereoisomer = 2 ^ stereocenter count
getEuclidean(BCUT) - Method in class chemaxon.descriptors.BCUT
Calculates the Euclidean distance.
getEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the Euclidean distance.
getEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Calculates the Euclidean distance.
getEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP
Calculates the Euclidean distance.
getEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the Euclidean distance.
getEuler() - Method in class chemaxon.struc.CTransform3D
Gets the Euler angles from the rotation transformation.
getEventHandler() - Method in class chemaxon.marvin.space.GraphicScene
Returns the event handler of the scene.
getEventHandler() - Method in class chemaxon.marvin.space.MSpaceEasy
Returns the actual event handler of MarvinSpace.
getExactMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
getExactMass() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecular weight of the molecule using the mass of the most frequent natural isotope of the atoms.
getExactSpecialAtomMatching() - Method in class chemaxon.sss.search.SearchOptions
Get the identifiers of those special atoms that should match exactly during structure comparison.
getException() - Method in exception chemaxon.marvin.plugin.PluginException
Returns the wrapped exception.
getExcluded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Gets the excluded abbreviations
getExcluded() - Method in class chemaxon.checkers.AttachedDataChecker
Any attached data that matches this descriptor won't appear as the result of this checker.
getExcluded() - Method in class chemaxon.checkers.PseudoAtomChecker
 
getExcludeString() - Method in class chemaxon.standardizer.actions.ContractSgroupsAction
 
getExcludeString() - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction
 
getExcludeString() - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
getExhaustiveModeLimit() - Method in class chemaxon.sss.search.SearchOptions
Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
getExplicitHcount() - Method in class chemaxon.struc.MolAtom
Gets number of hydrogen connections.
getExplicitHcount() - Method in class chemaxon.struc.MoleculeGraph
Gets the total number of explicit hydrogens attached to the molecule.
getExplicitHcount(int) - Method in interface chemaxon.struc.Smolecule
Gets the number of explicit hydrogen atom neighbors of the given atom.
getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
getExplicitLonePairCount() - Method in class chemaxon.struc.MDocument
Returns the number of Lone Pair electrons set by the user.
getExplicitLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
For internal use only.
getExpression() - Method in class chemaxon.marvin.services.DynamicArgument
Returns the expression used for evaluations
getExtensionList() - Method in class chemaxon.formats.MFileFormat
Gets the extension list.
getExtensions() - Method in class chemaxon.formats.MFileFormat
Deprecated, for removal: This API element is subject to removal in a future version.
getExternalCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings
Returns the URL of the configuration file containing the list of external Checkers in marvin sketch.
getExternalConnections(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the number of bonds of a specified atom where the neighbor atom doesn't belong to the S-group.
getExtraLabel() - Method in class chemaxon.struc.MolAtom
Gets the label string (also called atom value): "result" or "result1|result2".
getExtraLabelColor() - Method in class chemaxon.struc.MolAtom
Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
getExtraLabelColor(int) - Method in class chemaxon.struc.MolAtom
Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue).
getExtraLabelColor(long, int) - Static method in class chemaxon.struc.MolAtom
Gets extra label color from composed color value.
getExtraLabelSetColorMode(int) - Method in class chemaxon.struc.MDocument
Gets the coloring mode of extra label set sequences.
getExtraLabelSetFont(int) - Method in class chemaxon.struc.MDocument
 
getExtraLabelSetRGBs(int) - Method in class chemaxon.struc.MDocument
 
getExtraLabelSetSeq() - Method in class chemaxon.struc.MolAtom
 
getExtraLabelSetSize() - Method in class chemaxon.struc.MDocument
 
getEZStereo(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Gets E/Z stereo information for the given double bond.
getFamily() - Method in class chemaxon.struc.graphics.MFont
Gets the font family name.
getFarClip() - Method in class chemaxon.marvin.space.GraphicCell
Returns the z coordinate of the farther clipping plane which is computed considering all components.
getFavoritesComboBox() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates and returns the favorites combo instance
getFeatureCount() - Method in class chemaxon.descriptors.ECFP
Deprecated, for removal: This API element is subject to removal in a future version.
As of JChem 5.4.1, replaced by ECFP.getIdentiferCount().
getFeaturesFromBitPosition(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup
Returns the substructural features represented by the given bit position.
getFeaturesFromIdentifier(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup
Returns the substructural features represented by the given integer identifier.
getFieldAccessor() - Method in class chemaxon.marvin.view.MDocStorage
Gets the field accessor.
getFieldFont(String) - Method in class chemaxon.marvin.beans.MViewPane
Gets the font of a named field in a table.
getFieldFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the field font size.
getFieldName() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the data field name.
getFields(int, Molecule, String[], MProp[]) - Method in class chemaxon.marvin.io.MFieldAccessor
Extracts properties.
getFieldsShown() - Method in class chemaxon.marvin.view.swing.TableOptions
Are SDfile fields shown in table?
getFieldType() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the field type.
getFile() - Method in class chemaxon.formats.MolImporter
Gets the file object for the input.
getFile() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the current molecule file.
getFileExtensionLC(File) - Static method in class chemaxon.formats.MFileFormatUtil
Gets the file extension in lower case.
getFileExtensionLC(String) - Static method in class chemaxon.formats.MFileFormatUtil
Gets the file extension in lower case.
getFileName() - Method in class chemaxon.formats.MolImporter
Gets the name of the input file
getFilePointer() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Get the file pointer.
getFilePointer() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the current position in the input file.
getFilePointer() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the current position in the input file.
getFilePointer() - Method in class chemaxon.marvin.io.PositionedInputStream
Get the file pointer.
getFinalCause() - Method in exception chemaxon.formats.MolFormatException
Gets the final cause of the exception.
getFingerprint() - Method in class chemaxon.jep.context.MolContext
Returns the input molecule fingerprint.
getFingerprint(Molecule) - Method in interface chemaxon.jep.FingerprintGenerator
Returns the fingerprint of the structure.
getFingerprint(Object) - Method in class chemaxon.jep.context.MolContext
Returns the input molecule fingerprint if argument is the input molecule, null otherwise.
getFiveLongRings() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
This method returns the five long rings in the molecule represented by a List of List of MolAtom
getFixedLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
Gets the fixed location in the polyline.
getFixer(String) - Method in class chemaxon.fixers.StructureFixerFactory
Deprecated.
This method returns a StructureFixer instance identified by fixerId parameters
getFixerClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the fixerClassName
getFixers() - Method in class chemaxon.fixers.StructureFixerFactory
Deprecated.
This method returns all StructureFixer instances available by the current configuration
getFixers(StructureCheckerResult) - Method in interface chemaxon.checkers.runner.CheckerRunner
Returns all the StructureFixer instances which associated with the StructureCheckerErrorType of the result
getFixers(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
 
getFixMode() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the fixMode
getFlags() - Method in class chemaxon.formats.MFileFormat
Gets the format descriptor flags.
getFlags() - Method in class chemaxon.marvin.io.MRecord
Gets the record descriptor flags.
getFlags() - Method in class chemaxon.struc.graphics.MPolyline
Gets the flags.
getFlags() - Method in class chemaxon.struc.MolAtom
Gets flags.
getFlags() - Method in class chemaxon.struc.MolBond
Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits), bond set (5 bits) and reacting center (7 bits) information.
getFlags() - Method in class chemaxon.struc.MoleculeGraph
Gets the dimension and chiral flags.
getFlags() - Method in class chemaxon.struc.RgMolecule
Gets the dimension and chiral flags.
getFlexibilityMode() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
 
getFlexibleRingRotatableBondCount() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
getFlexibleRingSize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
getFloat(int) - Method in class chemaxon.descriptors.CustomDescriptor
 
getFocus() - Method in class chemaxon.struc.MDocument
Gets the focused object
getFogFactor() - Method in class chemaxon.marvin.common.UserSettings
Gets the fog factor.
getFontFamily() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the font family name.
getFontMetrics(Graphics, MFont) - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets and updates the font metrics of a document section.
getFontScale() - Method in class chemaxon.struc.graphics.MTextBox
Gets the font scaling factor.
getFooterAsString() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the footer of the file as a string.
getFooterAsString() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the footer of the file as a string.
getForefather() - Method in class chemaxon.struc.MoleculeGraph
Gets the first parent.
getForeground() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the foreground color.
getForegroundColor() - Method in class chemaxon.marvin.space.monitor.Label
Returns the foreground color of the label.
getFormalCharge() - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the formal charge of the molecule.
getFormalCharge() - Method in class chemaxon.struc.MoleculeGraph
Gets the (total) formal charge of the molecule.
getFormalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the formal charge of a specified atom.
getFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular formula with formal charge.
getFormalChargeFormula(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates a fixed digit sortable molecular formula with formal charge.
getFormat() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
Dipole export format.
getFormat() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Spectrum export format.
getFormat() - Method in class chemaxon.formats.MolExporter
Gets the output file format.
getFormat() - Method in class chemaxon.formats.MolImporter
Get the file format.
getFormat() - Method in class chemaxon.formats.MolInputStream
Get the molecule file format.
getFormat() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the default molecule file format.
getFormat() - Method in class chemaxon.marvin.io.MolExportModule
Returns the output format.
getFormat() - Method in class chemaxon.marvin.io.MRecord
Gets the full format string of the record.
getFormat() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the file format.
getFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
Gets the file format descriptor for the specified codename.
getFormatNamesWithExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil
 
getFormatter() - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
getFormatter() - Method in class chemaxon.calculations.nmr.NMRCalculator
 
getFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
getFormula() - Method in class chemaxon.struc.MoleculeGraph
Gets the molecular formula.
getFormula() - Method in class chemaxon.struc.RgMolecule
Gets the molecular formula in Hill order.
getFormula() - Method in class chemaxon.struc.RxnMolecule
Gets the molecular formula in Hill order.
getFormula(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates a fixed digit sortable molecular formula.
getFovY() - Method in class chemaxon.marvin.space.GraphicCell
Returns the field of view.
getFragCount() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.6, replaced by MoleculeGraph.getFragCount(int) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:
             mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
             
getFragCount(int) - Method in class chemaxon.struc.MoleculeGraph
Returns the number of fragments for the given fragmentation type.
getFragIds(int) - Method in class chemaxon.struc.MoleculeGraph
Gets an array containing the fragment id for each atom for the given fragmentation type.
getFragmentCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of fragments (disconnected parts) of the molecule.
getFragmentCount() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the number of fragments in the found common substructure.
getFreeAtomSetIndex() - Method in class chemaxon.struc.MDocument
Returns the first unused atomset index.
getFreeAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the atoms with free attachment points.
getFreeAttachmentPointCount() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the number of free attachment points.
getFreeAttachmentPointOrders() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the increasingly sorted orders of the free attachment points.
getFreeAttachmentPointOrders(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the sorted free attachment orders of the given attachment atom.
getFreeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getFreeBondSetIndex() - Method in class chemaxon.struc.MDocument
Returns the first unused bondset index.
getFreeLegalAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by SuperatomSgroup.getFreeAttachAtoms().
getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Gets the NMR frequency.
getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator
Returns NMR measurement frequency.
getFrequency() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the NMR measurement frequency in MHz unit.
getFrequencyCounts() - Method in class chemaxon.descriptors.MDGenerator
Gets the absolute frequence count array for all descriptors generated.
getFsp3() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons
getFsp3() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons
getFunction(String) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The function table will become an internal API. No replacement.
getFunctionalGroupDisplayMolTable() - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
getFunctionData() - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
getFunctionData(boolean) - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
getFunctionParameterData() - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
getFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
getFusedAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
getFusedAliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of fused aliphatic rings in the molecule (rings s).
getFusedAliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
getFusedAliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).
getFusedAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
getFusedAromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of fused aromatic rings in the molecule (rings s).
getFusedAromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
getFusedAromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).
getFusedRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.
getFuzzyExponents() - Method in class chemaxon.descriptors.PFParameters
Gets the precalculated fuzzy exponent used in the Fuzzy Bipolar Autocorrelogram (FBPA) metric.
getFuzzyLowerBound() - Method in class chemaxon.descriptors.PFParameters
 
getFuzzySmoothingFactor() - Method in class chemaxon.descriptors.PFParameters
Gets the fuzzy smoothing factor used in the construction of fuzzy fingerprints.
getGaussianFuzzyIncrements() - Method in class chemaxon.descriptors.PFParameters
Gets fuzzy increments for the fuzzy smoothing with a normal distribution.
getGenNameFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the IUPAC name font size.
getGL() - Method in class chemaxon.marvin.space.GraphicScene
Returns the OpenGL2 interface.
getGLAutoDrawable() - Method in class chemaxon.marvin.space.GraphicScene
Returns the GLAutoDrawable object.
getGLCanvas() - Method in class chemaxon.marvin.space.GraphicScene
Returns the GL2 canvas.
getGLInfo(boolean) - Method in class chemaxon.marvin.space.GraphicScene
Returns the OpenGL2 Renderer, Version, and Vendor and Extensions in VERBOSE_LEVEL_DEVEL mode.
getGlobalChecker() - Static method in interface chemaxon.calculator.TaggedCalculator
Returns the global input checker that will be used by all calculators implementing this interface.
getGlobalGUIProperties() - Method in class chemaxon.marvin.view.MDocStorage
Gets the Global GUI properties.
getGlobalProperties() - Method in class chemaxon.formats.MolImporter
Gets the global properties in a container that was retrieved from the input stream, earlier.
getGlobalProperties() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the global properties.
getGrabbedLines() - Method in class chemaxon.marvin.io.PositionedInputStream
Gets the grabbed lines.
getGrabbedMoleculeString() - Method in class chemaxon.formats.MolImporter
Gets the last grabbed molecule string with LF style line endings by default.
getGraphicComponent() - Method in class chemaxon.marvin.space.GraphicComponent
 
getGraphicComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
 
getGraphicComponent(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns the GraphicComponent having the given index in the active cell.
getGraphicComponent(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Returns the GraphicComponent of the given cell.
getGraphicComponent(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Returns the GraphicComponent with the given id.
getGraphicComponentCount() - Method in class chemaxon.marvin.space.GraphicScene
Returns the total number of GraphicComponents in the cells.
getGraphicScene() - Method in class chemaxon.marvin.space.MSpaceEasy
Returns the GraphicScene of MarvinSpace to be able to explicitly set more advanced features.
getGraphUnion() - Method in class chemaxon.struc.MoleculeGraph
Gets a molecule graph containing all the atoms and bonds.
getGraphUnion() - Method in class chemaxon.struc.RgMolecule
Gets a graph containing all the atoms and bonds.
getGraphUnion() - Method in class chemaxon.struc.RxnMolecule
Gets a graph containing all the atoms and bonds.
getGraphUnionAsSelection() - Method in class chemaxon.struc.Molecule
Gets a selection molecule containing all the atoms and bonds.
getGriffinHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin
Returns the HLB value calculated by Griffin method.
getGrinv() - Method in class chemaxon.struc.MoleculeGraph
Gets the graph invariants array.
getGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
Gets the graph invariants (canonical labels).
getGrinv(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 4.0, replaced by MoleculeGraph.getGrinv(int[], int).
Usage:
             getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
             
getGrinv(int[], int) - Method in class chemaxon.struc.MoleculeGraph
Gets the graph invariants (canonical labels).
getGrinvCC() - Method in class chemaxon.struc.MoleculeGraph
Gets the graph invariant change count.
getGrinvCC() - Method in class chemaxon.struc.MProp
Gets the graph invariant change count at the moment of creation.
getGrinvOptions() - Method in class chemaxon.struc.MoleculeGraph
Gets graph invariant calculation options passed to the module.
getGroup() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets the definition of the group.
getGroup(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the menu group for a plugin.
getGroupCount() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Gets the count of the groups of the action
getGroupedDotDisconnectedFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the grouped dot-disconnected molecular formula of a multifragment molecule.
getGroupHit() - Method in class chemaxon.sss.search.SearchHit
Returns the group hit view of the hit object.
getGroupIndices() - Method in class chemaxon.checkers.result.DataSgroupCheckerResult
 
getGroupList() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Gets the list of groups set for the action
getGroupMnemonic(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the group mnemonic for a plugin.
getGroups() - Method in class chemaxon.standardizer.actions.AliasToGroupAction
Gets the abbreviated groups of the action
getGroupsOf(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets the group names associated to an action separated by , character
getGroupsOf(String, List<GroupDefinition>) - Static method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets the group from a list of group definitions, based on the abbreviation.
getGUIPropertyContainer() - Method in class chemaxon.struc.MDocument
 
getHalfWidth() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns NMR half-width.
getHararyIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
getHashCode(Molecule) - Method in class chemaxon.sss.screen.HashCode
Gets hash code with default recursion level.
getHashCode(Molecule, int) - Method in class chemaxon.sss.screen.HashCode
Gets the hash code.
getHashCode(Molecule, int[]) - Method in class chemaxon.sss.screen.HashCode
Gets hash code with default recursion level.
getHashCode(Molecule, int[], int) - Method in class chemaxon.sss.screen.HashCode
Gets the hash code.
getHBond(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns a hydrogen bond.
getHBondCount() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the number of intramolecular hydrogen bonds.
getHcount(int) - Method in interface chemaxon.struc.Smolecule
Gets the total number of hydrogens of an atom.
getHCountMatching() - Method in class chemaxon.sss.search.SearchOptions
Get the interpretation of H count in the query.
getHeadCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets the head crossing bonds.
getHeader() - Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
Returns the table header.
getHeader() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Returns the table header.
getHeader() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the table header.
getHeaderAsString() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the header of the file as a string.
getHeaderAsString() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the header of the file as a string.
getHeaderNewLineCount() - Method in class chemaxon.marvin.io.MRecord
Gets the number of new lines in the molecule header part.
getHeight() - Method in class chemaxon.marvin.space.GraphicCell
Returns the height of the cell.
getHelpText() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getHelpText() - Method in class chemaxon.checkers.InvalidChecker
 
getHelpText() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getHelpText() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getHelpText() - Method in interface chemaxon.checkers.StructureChecker
Gets the help text of the checker
getHelpText() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the help text
getHelpText() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns the help text displayed on empty component
getHelpText() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the help text of the action
getHeteroaliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
getHeteroaliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroaliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
getHeteroaliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the heteroaromatic ring count.
getHeteroaromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroaromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).
getHeteroaromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the hetero ring count.
getHeteroRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
getHeteroRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
getHeteroRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Indentifies hetero rings in the molecule having a given size (number of atoms).
getHidrophobicity() - Method in class chemaxon.marvin.calculations.logDPlugin
 
getHighestEigenvalue(int, int) - Method in class chemaxon.descriptors.BCUT
Gets the specified highest eigenvalue.
getHighestEigenvaluesCount(int) - Method in class chemaxon.descriptors.BCUTParameters
Gets the number of highest eigenvalues calculated.
getHistogramSimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor
Deprecated, for removal: This API element is subject to removal in a future version.
getHitIndexType() - Method in class chemaxon.sss.search.MolSearchOptions
Returns the representation on which the hit indexes are given in case of Markush search.
getHitOrdering() - Method in class chemaxon.sss.search.SearchOptions
Returns the hit ordering type.
getHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin
Returns the HLB value.
getHMOChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
getHMOEigenVector() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the eigenvector.
getHMOElectronDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the electron density of an atom calculated with HMO, Double.NaN for no value.
getHMOElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
getHMOElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the electrophilic order of an atom, -1 for no value.
getHMOHuckelOrbitalCoefficients() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the huckel orbital coefficients.
getHMONucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
getHMONucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the nucleophilic order of an atom, -1 for no value.
getHMORealEigenValue() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the real part of the eigenvalue.
getHMOTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the total pi energy of the input molecule.
getHomologyBroadTranslation() - Method in class chemaxon.sss.search.SearchOptions
Get target-side homology matching option.
getHomologyNarrowTranslation() - Method in class chemaxon.sss.search.SearchOptions
Get query-side homology matching option, which homology atoms can match specific atoms.
getHorizontalAlignment() - Method in class chemaxon.struc.graphics.MTextBox
Gets the horizontal alignment.
getHPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the sum of the implicit H atom polarizability values around the given heavy atom.
getHResult(int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns the sum result of the H neighbours of the given atom.
getHuckelOrbitalCoefficients() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
getHybridizationState() - Method in class chemaxon.struc.MolAtom
Gets the hybridization state.
getHybridizationState(int) - Method in interface chemaxon.struc.Smolecule
Gets the hybridization state of an atom.
getHydrogen() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
getHyperWienerIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the hyper Wiener index of the molecule.
getIcon() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getIcon() - Method in class chemaxon.checkers.InvalidChecker
 
getIcon() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getIcon() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getIcon() - Method in interface chemaxon.checkers.StructureChecker
Gets the Icon of the current checker
getIcon() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the Icon related to iconPath property
getIcon() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
 
getIcon() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
 
getIcon() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Returns the Icon related to iconPath property
getIcon(int) - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo
Returns a MarvinSketch icon in 16x16 or 32x32 size.
getIcon(int) - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo
Returns a MarvinView icon in 16x16 or 32x32 size.
getIconPath() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the icon path
getIconPath() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the path of icon associated to the action
getId() - Method in class chemaxon.marvin.space.GraphicCell
Returns the cell id as a UOID.
getId() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the id of the component.
getId() - Method in class chemaxon.marvin.space.MoleculeComponent
 
getId() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the id of the action
getId() - Method in class chemaxon.struc.Molecule
 
getId() - Method in class chemaxon.struc.Sgroup
 
getId(String) - Static method in class chemaxon.marvin.services.json.JsonServiceDescriptor
Gets an ID for a method name, to make sure the client can identify the answer for the request.
getID() - Method in class chemaxon.standardizer.AbstractStandardizerAction
Gets the identifier string of the standardizer action.
getID() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
getID() - Method in interface chemaxon.standardizer.StandardizerAction
Gets the identifier of the standardizer task
getID() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Gets the id of the standardizer class
getIDBackgroundRGBA(int) - Method in class chemaxon.marvin.view.MDocStorage
Gets the background color's RGBA value in a record.
getIdentiferCount() - Method in class chemaxon.descriptors.ECFP
Gets the number of integer identifers generated for the fingerprint.
getIdentifier() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the checker identifier
getIdentifier() - Method in class chemaxon.descriptors.ECFPFeature
Gets the generated integer identifier for this ECFP feature.
getIdentifier() - Method in class chemaxon.fixers.StructureFixerDescriptor
Returns the fixer identifier
getIdentifier(MolAtom, int) - Method in class chemaxon.descriptors.ECFPFeatureLookup
Returns the corresponding integer identifier for the given atom neighborhood.
getIdentityTransformer() - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns an identity transformer.
getIDForegroundRGBA(int) - Method in class chemaxon.marvin.view.MDocStorage
Gets the foreground color's RGBA value in a record.
getIgnoreRotatableBonds() - Method in class chemaxon.descriptors.PFParameters
 
getImage(double) - Method in class chemaxon.marvin.beans.MSketchPane
Gets the canvas contents as an image using a scale factor.
Examples:
To get an image with a scale factor equivalent to 100% magnification: getImage(getDefaultScale());
To get an image with the actual scale factor: getImage(getScale());
getImage(Dimension) - Method in class chemaxon.marvin.beans.MSketchPane
Gets the canvas contents as an image scaled to fit in the specified rectangle.
getImageExportParameterStringForStyle(String) - Method in class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI
Creates a string used for Image Export, without format.
getImageImportServiceURL() - Method in class chemaxon.marvin.common.UserSettings
 
getImageMolecule() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the molecule to be used for legend image.
getImplicitH() - Method in class chemaxon.marvin.beans.MarvinPane
Query the display method of implicit hydrogens.
getImplicitH() - Method in class chemaxon.marvin.MolPrinter
Returns the display method of implicit hydrogens.
getImplicitHcount() - Method in class chemaxon.struc.MolAtom
Gets the number of implicit hydrogens attached.
getImplicitHcount() - Method in class chemaxon.struc.MoleculeGraph
Gets the total number of implicit hydrogens attached to the molecule.
getImplicitHcount() - Method in interface chemaxon.struc.Smolecule
Gets the total number of implicit Hydrogens.
getImplicitHcount(int) - Method in interface chemaxon.struc.Smolecule
Gets the number of implicit Hydrogens of an atom.
getImplicitHCount(boolean) - Method in class chemaxon.struc.MolAtom
Gets the implicit Hydrogen count of the atom.
getImplicitHCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getImplicitHMatching() - Method in class chemaxon.sss.search.SearchOptions
Get option for matching implicit and explicit hydrogens
getImplicitizableHList(Molecule, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Gets which atom is an implicitizable hydrogen.
getImplicitizeFlag() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
Returns the flag which can used to identify which hydrogens should be implicitize.
getIn() - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Get stdin to use.
getIndex() - Method in class chemaxon.marvin.space.GraphicCell
Returns the internal index of the cell.
getIndex() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Returns the index of the actual action of the configuration
getIndexOfOriginalLigand() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
getInnerPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
getInputCount() - Method in class chemaxon.formats.MolConverter.Builder
Gets the number of input files/streams.
getInputCount() - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
getInputFormat() - Method in class chemaxon.marvin.io.MRecord
Gets the input format.
getInputFormat() - Method in class chemaxon.struc.MDocument
Gets the input file format.
getInputFormat() - Method in class chemaxon.struc.Molecule
Gets the input file format.
getInputMolDim() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the input molecule dimension.
getInputMolecule() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Returns the input molecule (the molecule before standardization).
getInputMolecule() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Gets the input molecule.
getInputPriority() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Priority of the MTransferable object when importing from clipboard.
getInputStream(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
Creates an InputStream from the given String.
getInputStreamFromClipboard() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Gets an InputStream from the clipboard data if the format is supported by this MTransferable
getInstance() - Static method in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Returns the default factory instance.
getInstance(String, String) - Static method in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Returns the factory instance for specified paths.
getInt(int) - Method in class chemaxon.descriptors.CustomDescriptor
 
getIntArray() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Gets the integer value.
getIntegralValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the value of the NMR integral function at a given x point.
getInternalMetricIndex() - Method in class chemaxon.descriptors.MDParameters
Gets the MolecularDescriptor specific metric index of the current parametrized metric.
getInternalSize() - Method in class chemaxon.descriptors.MDParameters
Gets the required memory size to store the descriptor according to the specified parameters.
getInternalVersionId() - Static method in class com.chemaxon.version.VersionInfo
Returns the internal version identifier.
getIntValue() - Method in enum class chemaxon.struc.AtomProperty.Radical
Gets the integer representation of the radical.
getInverseName() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the inverse option name.
getInvisibleSets() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the visibility of the specified atom sets.
getIonizerErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Returns the calculation error information message or the empty string if there is no error.
getIonizerErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the calculation error information message or the empty string if there is no error.
getIsotope(int, int) - Static method in class chemaxon.struc.PeriodicSystem
Retrieves an isotope of the element
getIsotopeComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the molecular composition (w/w%).
getIsotopeComposition(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the molecular composition (w/w%).
getIsotopeCount() - Static method in class chemaxon.struc.PeriodicSystem
Number of isotopes in the periodic system
getIsotopeCount(int) - Static method in class chemaxon.struc.PeriodicSystem
Number of isotopes of the element
getIsotopeDistribution() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the isotopic distributions for the molecule.
getIsotopeFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular formula (isotopes are separated).
getIsotopeFormalChargeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular formula with formal charge (isotopes are separated).
getIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular formula (isotopes are separated).
getIsotopeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular formula (isotopes are separated).
getIsotopeMatching() - Method in class chemaxon.sss.search.SearchOptions
Get option for matching isotopes
getIterator() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
Returns an iterator that iterates through all molecules in the file/stream.
getItsArrow() - Method in class chemaxon.struc.RxnMolecule
Gets the reaction arrow of this reaction.
getJar() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Gets the jar containing the standardizer class
getJavaVersionStr() - Static method in class com.chemaxon.version.VersionInfo
Returns the Java VM version information as string.
getJChemTableVersion() - Static method in class com.chemaxon.version.VersionInfo
Returns the internal version number of JChem database tables.
getKeepCounts() - Method in class chemaxon.descriptors.ECFPParameters
Gets the counts (multiplicity) parameter.
getKey() - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Returns the plugin key.
getKey(int) - Method in class chemaxon.struc.MPropertyContainer
Gets a property key.
getKey(int) - Method in class chemaxon.struc.prop.MHashProp
Gets a key.
getKey(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the menu key for a plugin.
getKeys() - Method in class chemaxon.struc.MPropertyContainer
Returns the property keys.
getKeys(int, Molecule) - Method in class chemaxon.marvin.io.MFieldAccessor
Gets the keys in a record.
getKnownExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil
Returns the file extension if it is a known extension.
getL(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets a label.
getL(int, int) - Method in class chemaxon.marvin.view.MDocStorage
Gets a text label in a record.
getLabel() - Method in class chemaxon.struc.NoStructure
The label for the noStructure.
getLabel(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getLabel(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getLabelCenter() - Method in class chemaxon.struc.sgroup.SgroupAtom
Gets the index of the character in the label the bonds should point to.
getLabelInformation(String) - Method in class chemaxon.marvin.space.GraphicComponent
 
getLabelInformation(String) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Collects the label information of the visualizers.
getLabelInformation(String) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getLabelInformation(String) - Method in class chemaxon.marvin.space.MoleculeComponent
 
getLabelInformation(String, boolean) - Method in class chemaxon.marvin.space.GraphicComponent
Labels will be created associated to this GraphicComponent if the component supports the given labeltype, and returns arbitrary numbers of ComponentElements with correct coordinates and description to create a label.
getLabelInformation(String, boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
Labels will be created associated to this MoleculeComponent if the labeltype is "atom", "extraatomlabel" or "molecule".
getLabels() - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
use isAtomSymbolsVisible() instead
getLabels(double[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns formatted array.
getLargestConjugatedSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the largest conjugated system in the molecule.
getLargestConjugatedSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the largest conjugated system size (number of pi electron pairs).
getLargestRing() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the atoms of the largest ring (number of atoms) in the molecule.
getLargestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the largest ring size.
getLargestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the size of largest ring containing the specified atom.
getLargestRingSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the atoms of the largest ring system (number of rings) in the molecule.
getLargestRingSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the size of the largest ring system (number of rings) in the molecule.
getLastEOL() - Method in class chemaxon.marvin.io.PositionedInputStream
 
getLastIndexOfAction(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets the last index of an action defined by the provided action string
getLastLicense() - Method in class chemaxon.marvin.common.UserSettings
 
getLastProcessedLineNum() - Method in class chemaxon.formats.recognizer.Recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 2014.07.21.0 not used
getLastSketchFrameSize() - Method in class chemaxon.marvin.common.UserSettings
 
getLastViewFrameSize() - Method in class chemaxon.marvin.common.UserSettings
 
getLeft() - Method in class chemaxon.marvin.space.GraphicCell
Returns the x coordinate of the left edge of the active cell.
getLeftBracket(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
 
getLeftName() - Method in class chemaxon.struc.sgroup.SgroupAtom
Gets the string that will be shown at the left side of the molecule.
getLegalAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by SuperatomSgroup.getAllAttachAtoms().
getLength() - Method in class chemaxon.descriptors.MDParameters
Returns the number of cells forming the descriptor.
getLength() - Method in class chemaxon.struc.MolBond
Gets the actual length of the bond.
getLevel() - Method in interface chemaxon.common.util.MProgressMonitor
Gets the level of this progress monitor.
getLevelCount() - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Gets the number of levels.
getLibrarySizeString() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the display string representation of the Markush library size (number of all enumerated structures).
getLicenseEnvironment() - Method in class chemaxon.standardizer.Standardizer
Gets the license environment of the standardizer
getLicenseExceptionMessage() - Static method in class chemaxon.license.LicenseManager
Returns the common message used at license problems.
getLicenseExceptionPanel(LicenseException) - Static method in class chemaxon.license.LicenseManager
Returns the common swing component used to indicate missing license.
getLicenseExceptionPanel(String) - Static method in class chemaxon.license.LicenseManager
Returns the common swing component used to indicate missing license.
getLigand(int) - Method in class chemaxon.struc.MolAtom
Gets the i-th ligand of this atom.
getLigand(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
getLigandAtno(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
getLigandBondType(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
getLigandCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getLigandIndex(MolAtom) - Method in class chemaxon.struc.MolAtom
Returns the index of the specified ligand in this atom.
getLigandOrder(MolAtom) - Method in class chemaxon.struc.MolAtom
Gets the order of a specified ligand.
getLigandOrderVisibility() - Method in class chemaxon.marvin.MolPrinter
Gets the ligand order visibility setting.
getLigands() - Method in class chemaxon.struc.MolAtom
Returns the atoms connected to this atom by a bond.
getLigands() - Method in class chemaxon.struc.StereoActivePart
Get the ligands of the stereo active atom which take part in the stereo description.
getLigands(Integer) - Method in class chemaxon.struc.SelectionMolecule
 
getLimitedStructureCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the number of structures to be generated.
getLine(int) - Method in class chemaxon.struc.graphics.MTextBox
Gets a line.
getLineColor() - Method in class chemaxon.struc.MObject
Gets the line color of the object.
getLineCount() - Method in class chemaxon.formats.MolImporter
Gets the current line number.
getLineCount() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Get the current line number.
getLineCount() - Method in class chemaxon.marvin.io.MolImportModule
Returns the line count in the molecule input stream.
getLineCount() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the current line number in the input file.
getLineCount() - Method in interface chemaxon.marvin.io.MRecordReader
Get the current line number.
getLineCount() - Method in class chemaxon.marvin.io.PositionedInputStream
Gets the current line number.
getLineCount() - Method in class chemaxon.struc.graphics.MTextBox
Gets the number of lines.
getLineMiddlePoint(DPoint3, DPoint3) - Static method in class chemaxon.struc.graphics.MPolyline
 
getLineNumber() - Method in class chemaxon.marvin.io.MRecordReader.Position
Gets the line number.
getLineNumberInFile() - Method in exception chemaxon.formats.MolFormatException
Gets the line number relative to the first line of the file.
getLineNumberInRecord() - Method in exception chemaxon.formats.MolFormatException
Gets the line number relative to the first line of the record.
getLineNumberMap() - Method in class chemaxon.marvin.io.MRecord
Gets the line number to original line number mapping.
getLineOnScreen(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Returns the i-th row of the data sgroup label, as displayed on the screen (with tag, query operator, units etc.)
getLinkNodeOuterAtom(int) - Method in class chemaxon.struc.MolAtom
Gets the index of one of the link node's outer neighbor atoms.
getList() - Method in class chemaxon.struc.MolAtom
Gets the atom list.
getList() - Method in class chemaxon.struc.prop.MListProp
Gets the array.
getListeners() - Method in class chemaxon.marvin.view.MDocStorage
 
getLoadSaveLocation() - Method in class chemaxon.marvin.common.UserSettings
Gets the load/save filechooser working directory selection method names, based on the preferences dialog.
getLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
Gets the filechooser's default working directory, if it is set, and the filechooser working directory selection method is saveCustomLocation.
getLocalMaximumPlaces() - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
getLocalMenuName() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getLocalMenuName() - Method in class chemaxon.checkers.InvalidChecker
 
getLocalMenuName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getLocalMenuName() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getLocalMenuName() - Method in interface chemaxon.checkers.StructureChecker
Gets the local menu name of the checker
getLocalMenuName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the local menu name
getLocalParity(int) - Method in class chemaxon.struc.MoleculeGraph
Computes the local parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getLocalParity(int) - Method in class chemaxon.struc.RgMolecule
Computes the local parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getLocalParity(int) - Method in class chemaxon.struc.RxnMolecule
Computes the local parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getLocation() - Method in class chemaxon.struc.MolAtom
Gets the coordinates.
getLocation() - Method in class chemaxon.struc.MoleculeGraph
Gets the origin of the molecule.
getLocation() - Method in class chemaxon.struc.MPoint
Gets the point's location.
getLocation() - Method in class chemaxon.struc.NoStructure
Returns the clone of the location of the NoStructure.
getLocation(CTransform3D) - Method in class chemaxon.struc.MPoint
Gets the point's location.
getLocation(DPoint3) - Method in class chemaxon.struc.MolAtom
Gets the coordinates.
getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Gets the location.
getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Gets the location.
getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
Gets the location.
getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
Gets the location.
getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
Gets the location.
getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
Gets the point's location.
getLock() - Method in class chemaxon.struc.MolAtom
Get lock object for synchronization.
getLock() - Method in class chemaxon.struc.MolBond
Gets lock object for synchronization.
getLock() - Method in class chemaxon.struc.MoleculeGraph
Gets the lock object for synchronization.
getlogD() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the logD value for the pH specified in logDPlugin.setpH(double).
getlogDpI() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the logD value at pI.
getlogDs() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the logD array.
getLogger() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
Returns the dipole calculator logger.
getLogger() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Gets the calculator logger.
getLogger() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
Returns the current logger.
getLogicalValue(Object) - Static method in class chemaxon.jep.ChemJEP
Returns the logical correspondent of the specified result object: ChemJEP.TRUE, ChemJEP.FALSE or ChemJEP.UNDECIDED.
getLogPercentageLimit() - Method in class chemaxon.marvin.calculations.pKaPlugin
 
getlogPMicro() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the micro logP value.
getlogPNonionic() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the logP value for the non-ionic form.
getLogPTrainingIds() - Static method in class chemaxon.marvin.calculations.logDPlugin
Returns the id's of available logP trainings.
getlogPTrue() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the most typical logP among logD at pI, micro logP and nonionic logP.
getLonePairCount() - Method in class chemaxon.struc.MDocument
Returns the number of Lone Pair electrons.
getLonePairCount() - Method in class chemaxon.struc.MolAtom
Returns the automatically calculated lone pair count of this atom.
getLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
getLonePairCount(int) - Method in class chemaxon.struc.RgMolecule
Gets the number of lone pairs.
getLonePairsVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Tests whether lone pairs are visible.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.MolecularDescriptor
Calculates an estimate for the minimum value of the distance using the default distance metric.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the lower bound estimate of the dissimilarity from the given fingerprint.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.ReactionFingerprint
Calculates the lower bound estimate of the dissimilarity from the given fingerprint.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.ScalarDescriptor
Calculates the lower bound estimate of the dissimilarity from the given descriptor.
getLowerBound(Object) - Method in class chemaxon.descriptors.ChemicalFingerprint
Deprecated, for removal: This API element is subject to removal in a future version.
getLowestEigenvalue(int, int) - Method in class chemaxon.descriptors.BCUT
Gets the specified lowest eigenvalue.
getLowestEigenvaluesCount(int) - Method in class chemaxon.descriptors.BCUTParameters
Gets the number of lowest eigenvalues calculated.
getLowestEnergyConformer() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the calculated lowest energy conformer.
getLowestEnergyConformer() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the lowest energy conformer of the molecule.
getM(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the nth molecule in memory.
getM(int, String) - Method in class chemaxon.marvin.beans.MViewPane
Gets the nth molecule in a text format.
getMacroDistributions() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the macrospecies distribution arrays for all macro pKa values: the i-th row is the disrtibution vector of the i-th ionization state as function of the pH.
getMacroDistributions(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the i-th macrospecies distribution as function of the pH
getMacroMolecule() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the MacroMolecule this component visualizes.
getMacroMoleculeComponent() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getMacroMoleculeComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the macromolecule visualizer if this MoleculeComponent visualizes a ligand in a complex.
getMacropKaValues(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Calculates the acidic pKa values in ascending order or the basic pKa values in descending order.
getMacropKaValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin
Calculates the least acidic pKa values in ascending order or the biggest basic pKa values in descending order.
getMacroSpeciesCharge(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the formal charges of a given macrospecies.
getMacroSpeciesCount() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the number of macrospecies count.
getMag() - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 2.8.1, replaced by getScale()
getMainDoc(int) - Method in class chemaxon.marvin.view.MDocStorage
Gets the document at the specified position.
getMainDoc(int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
Gets the document at the specified position.
getMainMolecule(int, Molecule) - Method in class chemaxon.marvin.io.MFieldAccessor
Gets the main molecule object in a record.
getMainMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getMainMoleculeGraph() - Method in class chemaxon.struc.MDocument
Gets the main molecule graph.
getMainMolFieldness() - Method in class chemaxon.marvin.view.swing.TableOptions
Tests whether the main molecule is a field.
getMajorMicrospecies() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the major microspecies at the pH set in MajorMicrospeciesPlugin.setpH(double).
getMap() - Method in class chemaxon.struc.prop.MHashProp
Gets the map.
getMap(MoleculeGraph) - Method in class chemaxon.struc.prop.MHCoords3DProp
Gets a map containing MolAtom objects as keys and DPoint3 arrays as values.
getMappingStyle() - Method in class chemaxon.standardizer.actions.MapAction
Returns the mapping style of the underlying mapper.
getMappingStyle() - Method in class chemaxon.standardizer.actions.MapReactionAction
Returns the mapping style of the underlying mapper.
getMappingStyle() - Method in class com.chemaxon.mapper.AutoMapper
Returns the mapping style of the mapper.
getMappingStyle() - Method in class com.chemaxon.mapper.AutoMapper.Options
 
getMarginSize() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the documents margin size.
getMarginSize() - Method in class chemaxon.marvin.common.UserSettings
Gets the documents margin size.
getMarkushAromHandling() - Method in class chemaxon.sss.search.SearchOptions
Gets the Markush aromatic search behavior.
getMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.MolAtom
Gets the atomic weight.
getMass() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.RgMolecule
Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.RxnMolecule
Calculates the molecular weight of the molecule.
getMass(int) - Static method in class chemaxon.struc.PeriodicSystem
Atomic weight of the element based on the natural abundance of its isotopes
getMass(int, int) - Static method in class chemaxon.struc.PeriodicSystem
Atomic weight of an isotope
getMassno() - Method in class chemaxon.struc.MolAtom
Gets the mass number.
getMassno(int) - Method in interface chemaxon.struc.Smolecule
Gets the mass number of an atom.
getMassPrecision(int) - Static method in class chemaxon.struc.PeriodicSystem
The precision of an elemental mass is the number of measured digits after the decimal separator.
getMassPrecision(int, int) - Static method in class chemaxon.struc.PeriodicSystem
The precision of an isotopic mass is the number of measured digits after the decimal separator.
getMatchCount() - Method in class chemaxon.sss.search.Search
The number of times the query molecule appears in the target molecule.
getMatchedQueryAtoms() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the indices of the query atoms that are part of the found common substructure.
getMatchedQueryBonds() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the indices of the query bonds that are part of the found common substructure.
getMatchedTargetAtoms() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the indices of the target atoms that are part of the found common substructure.
getMatchedTargetBonds() - Method in class com.chemaxon.search.mcs.McsSearchResult
Gets the indices of the target bonds that are part of the found common substructure.
getMaxAttachmentPointOrder(int) - Method in class chemaxon.struc.RgMolecule
Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.
getMaxCols() - Method in class chemaxon.marvin.view.swing.TableOptions
Get maximum value of columns in the table.
getMaxConsideredRingSize() - Method in class com.chemaxon.search.mcs.McsSearchOptions
Gets the maximum size of rings considered during search for the specified ring handling mode.
getMaxDimCached() - Method in class chemaxon.marvin.view.MDocStorage
Gets the maximum molecule dimension.
getMaxDist() - Method in class chemaxon.descriptors.PFParameters
Gets the miximum distance of pharmacophore points that is considered.
getMaxDist() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getMaxEnergy() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Observed largest energy.
getMaxGradLimit() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
getMaximalProjectionArea() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the maximal projection area in Angstrom^2.
getMaximalProjectionRadius() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the radius of the circle surrounding the maximal projection in Angstrom.
getMaximum() - Method in interface chemaxon.common.util.MProgressMonitor
Gets the maximum value.
getMaximumBitRatio() - Method in class chemaxon.descriptors.MDGenerator
Gets the maximum percentage of non-zero cells in descriptors generated.
getMaximumMappedValue() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the maximum value of the mapped property on this surface.
getMaximumValue() - Method in class chemaxon.marvin.space.SurfaceColoring
Returns the greatest property value of the surface vertices.
getMaxRepetitions() - Method in class chemaxon.struc.MolAtom
Gets the maximum number of repetitions for a link atom.
getMaxRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MoleculeGraph
Returns the maximal attachment point order of R-group attachment point atoms in this molecule graph.
getMaxRows() - Method in class chemaxon.marvin.view.swing.TableOptions
Get maximum value of rows in the table
getMaxSize() - Method in class chemaxon.marvin.view.swing.TableOptions
Get the maximum number of molecules displayed in the table.
getMaxThreadCount() - Method in class com.chemaxon.mapper.AutoMapper.Options
 
getMaxX() - Method in class chemaxon.marvin.space.BoundingBox
Returns the maximum x coordinate of the box.
getMaxY() - Method in class chemaxon.marvin.space.BoundingBox
Returns the maximum y coordinate of the box.
getMaxZ() - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
getMaxZ() - Method in class chemaxon.marvin.space.BoundingBox
Returns the maximum z coordinate of the box.
getMChemicalStruct() - Method in class chemaxon.struc.MDocument
 
getMcsSimilarityLimit() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties
 
getMDocumentStream() - Method in class chemaxon.formats.MolImporter
Creates an MDocument Stream with the iterator of the importer.
getMDocumentStream() - Method in class chemaxon.marvin.io.MDocSource
 
getMeaningfulFrequencies() - Static method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the array of meaningful NMR measurement frequencies in MHz.
getMeasure() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
Gets the measure of the action
getMediumReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
Returns the tanimoto distance of the reaction centers and their neighbouring atoms and bonds.
getMElectron() - Method in class chemaxon.struc.graphics.MEFlow
 
getMElectronContainer() - Method in class chemaxon.struc.graphics.MEFlow
 
getMElectronContainerIndexInAtom(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
getMElectronContainerOf(MElectron) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
getMElectronRef() - Method in class chemaxon.struc.graphics.MEFlow
 
getMenu(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the menu string for a plugin.
getMergedst() - Method in class chemaxon.marvin.beans.MSketchPane
Gets the merge distance.
getMessage() - Method in interface chemaxon.calculator.CalculatorError
Returns the message that describes this error.
getMessage() - Method in exception chemaxon.sss.search.SearchException
Returns the detailed message string of this exception, plus all the causes concatenated.
getMessage() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
Returns an error message.
getMetalAtoms() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
This method returns the metallocene relevant metal atoms represented by a List of MolAtom.
getMethod() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
Gets the method of the action
getMethod() - Method in class chemaxon.standardizer.actions.TautomerizeAction
 
getMetricIndex(String) - Method in class chemaxon.descriptors.MDParameters
Gets the index of the given parametrized metric.
getMetricIndex(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the index of the given parameterized metric.
getMetricName() - Method in class chemaxon.descriptors.MDParameters
Gets the user defined symbolic name of the current parametrized metric.
getMetricName() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the name of the current parameterized metric.
getMetricName(int) - Method in class chemaxon.descriptors.MDParameters
Gets the user defined symbolic name of the specified parametrized metric.
getMetricName(int) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the name of a metric specified parameterized metric by its index.
getMicrospecies(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the microspecies molecule.
getMicrospeciesCount() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the number of microspecies
getMidPointLocation(int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Gets the middle point of the arc.
getMIMEType() - Method in class chemaxon.formats.MFileFormat
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 2014.07.21.0 not used
getMinDist() - Method in class chemaxon.descriptors.PFParameters
Gets the minimum distance of pharmacophore points that is considered.
getMinDist() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getMinEnergy() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Observed lowest energy.
getMinFragmentSize() - Method in class com.chemaxon.search.mcs.McsSearchOptions
Gets the minimum required size of the fragments of the common substructures.
getMinimalProjectionArea() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the minimal projection area in Angstrom^2.
getMinimalProjectionRadius() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the radius of the circle surrounding the minimal projection in Angstrom.
getMinimumBitRatio() - Method in class chemaxon.descriptors.MDGenerator
Gets the minimum percentage of non-zero cells in descriptors generated.
getMinimumHeight() - Method in class chemaxon.struc.graphics.MTextBox
Gets the minimum height of the text.
getMinimumMappedValue() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the minimum value of the mapped property on this surface.
getMinimumValue() - Method in class chemaxon.marvin.space.SurfaceColoring
Returns the lowest property value of the surface vertices.
getMinRepetitions() - Method in class chemaxon.struc.MolAtom
Gets the minimum number of repetitions for a link node.
getMinX() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum x coordinate of the box.
getMinY() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum y coordinate of the box.
getMinZ() - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
getMinZ() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum z coordinate of the box.
getMirroredArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline
Mirror transformation for arrow heads.
getMMFF94Energy() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the MMFF94 energy of the structure (default: kcal/mol).
getMnemonic(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the menu mnemonic for a plugin.
getMode() - Method in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
 
getModifiedAtoms() - Method in class chemaxon.standardizer.Changes
Gets the list of modified atoms during the standardization procedure
getMol() - Method in class chemaxon.marvin.beans.MSketchPane
Returns the clone of the current molecule being on the canvas.
getMol(String) - Method in class chemaxon.marvin.beans.MSketchPane
Gets the molecule in a text format.
getMolbg() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the molecule background color.
getMolBytes() - Method in class chemaxon.marvin.io.MRecord
Gets the molecule bytes, with preprended header and appended footer if appropriate.
getMolCenter(int, String) - Method in class chemaxon.marvin.view.MDocStorage
Gets a molecule center.
getMolCrd() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getMolecule() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the input molecule of the dipole moment computation.
getMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the molecule under examination.
getMolecule() - Method in class chemaxon.calculations.Ring
Retrieves the input molecule
getMolecule() - Method in class chemaxon.calculations.stereo.Stereochemistry
Retrieves the input molecule
getMolecule() - Method in class chemaxon.calculations.TopologyAnalyser
Retrieves the input molecule
getMolecule() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getMolecule() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getMolecule() - Method in class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
 
getMolecule() - Method in class chemaxon.jep.context.MolContext
Returns the input molecule.
getMolecule() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the Molecule representation of the MacroMolecule.
getMolecule() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getMolecule() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the Molecule of the MoleculeComponent.
getMolecule() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Returns the target molecule
getMolecule() - Method in class chemaxon.struc.prop.MMoleculeProp
Gets the molecule.
getMolecule() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
Returns the input molecule.
getMolecule(int) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Gets the molecule at the provided index
getMolecule(int) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Gets the molecule at the provided index
getMolecule(int) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Gets the molecule at the provided index
getMolecule1Aligned() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
 
getMolecule2Aligned() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
 
getMoleculeCount() - Method in class chemaxon.descriptors.MDGenerator
Gets the number of molecules processed (that is, the number of descriptors generated) since the initialization of the object.
getMoleculeGraph() - Method in class chemaxon.struc.graphics.MChemicalStruct
Gets the stored molecule graph.
getMoleculeIterator() - Method in class chemaxon.marvin.io.MDocSource
Gets a molecule iterator for this document source.
getMoleculeIterator(MolImporter) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Gets a molecule iterator from the importer.
getMoleculeIterators(MolImporter[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Gets molecule iterators from the importers in an array.
getMoleculeMovie() - Method in class chemaxon.struc.MDocument
Gets the molecule movie.
getMoleculeName() - Method in class chemaxon.marvin.io.MRecord
Returns the name of the molecule in the record.
getMoleculeOrig() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
Gets back a clone of the unmodified input structure.
getMolecules() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
getMoleculeString() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the last molecule as a string.
getMoleculeWithAlignedCoordinates(int) - Method in class chemaxon.marvin.alignment.Alignment
After the alignment result molecule can be obtained.
getMolfileExtensions() - Static method in class chemaxon.formats.MFileFormatUtil
Gets the array of known molecule file extensions.
getMolfileFormats() - Static method in class chemaxon.formats.MFileFormatUtil
Gets the array of known molecule file formats.
getMolfileVersion() - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Gets the molfile version.
getMolfileVersion() - Method in class chemaxon.marvin.io.formats.mdl.MolImport
Gets the molfile version.
getMolID() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getMolImportModule() - Method in class chemaxon.formats.MolImporter
 
getMolImportModule() - Method in class chemaxon.marvin.io.MRecordImporter
 
getMolIndex() - Method in exception chemaxon.marvin.io.MolExportException
Returns the molecule index.
getMolInputStream() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the molecule input stream.
getMolInputStream() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the molecule input stream.
getMolInputStream(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
Creates a MolInputStream from the given String to be able to manually add molecules to the event handler.
getMolNameFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the molecule name font size.
getMolObject(int) - Method in class chemaxon.struc.graphics.MEFlow
Gets the electron source or sink.
getMolPainter(int, String) - Method in class chemaxon.marvin.view.MDocStorage
Gets a molecule painter.
getMolPanel() - Method in class chemaxon.marvin.beans.MarvinPane
Returns the underlying panel.
getMolPanel() - Method in class chemaxon.marvin.beans.MSketchPane
 
getMolPanel() - Method in class chemaxon.marvin.beans.MViewPane
 
getMolPolarizability() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the molecular polarizability value.
getMolStream() - Method in class chemaxon.formats.MolImporter
Creates a Molecule Stream with the iterator of the importer.
getMolStream() - Method in class chemaxon.marvin.io.MDocSource
 
getMolString() - Method in class chemaxon.marvin.io.MRecord
Gets the molecule string, with preprended header and appended footer if appropriate.
getMonitorColor() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Returns the color of the control if it exists.
getMonitorColor() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
 
getMoreErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the more error message
getMostFrequentNaturalIsotope(int) - Static method in class chemaxon.struc.PeriodicSystem
Returns the mass number of the most frequent natural isotope of the element
getMostLikelyMolFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
Gets the most likey molecule file format from the file name extension.
getMostSimplifiedMolecule() - Method in class chemaxon.struc.Molecule
Gets the simplified molecule object even if there is a parent document with other objects.
getMostSimplifiedMolecule() - Method in class chemaxon.struc.RgMolecule
Gets the simplified molecule object even if there is a parent document with other objects.
getMProp() - Method in class chemaxon.struc.MDocument
Gets the document as a property.
getMrvWithSettings() - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
getMsAcceptorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the average acceptor counts over the microspecies distribution for different pH-s.
getMsCount() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the number of microspecies and/or distributions.
getMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the microspecies distribution array.
getMsDistributions() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the microspecies distribution arrays for all microspecies: the i-th element is the disrtibution array of the i-th microspecies.
getMsDonorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the average donor counts over the microspecies distribution for different pH-s.
getMSketchPane() - Method in class chemaxon.marvin.beans.MSketch
 
getMSLogic() - Method in class chemaxon.struc.RxnMolecule
Deprecated, for removal: This API element is subject to removal in a future version.
Multi-step reactions not supported. Method performs no operations.
getMsMolecule(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the microspecies molecule.
getMultiplets() - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
getMultiplier() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets the multiplier.
getMViewPane() - Method in class chemaxon.marvin.beans.MView
 
getMViewParam() - Method in class chemaxon.marvin.beans.MViewParams
Generates the parameter string that can be set to MViewPane.
getName() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the name of the NMR spectrum.
getName() - Method in class chemaxon.checkers.AbstractStructureChecker
 
getName() - Method in class chemaxon.checkers.InvalidChecker
 
getName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getName() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getName() - Method in interface chemaxon.checkers.StructureChecker
Gets the name of the checker
getName() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the checker name
getName() - Method in class chemaxon.descriptors.BCUT
Gets the name of the BCUT descriptor object.
getName() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the name of the ChemicalFingerprint object.
getName() - Method in class chemaxon.descriptors.CustomDescriptor
Gets the name of the CustomDescriptor object.
getName() - Method in class chemaxon.descriptors.ECFP
Gets the name of the ECFP fingerprint object.
getName() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the name of the descriptor.
getName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the name of the PharmacophoreFingerprint object.
getName() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the nice name of the ReactionFingerprint descriptor object.
getName() - Method in class chemaxon.descriptors.ScalarDescriptor
Gets the name of the ScalarDescriptor object.
getName() - Method in class chemaxon.descriptors.scalars.HAcc
Gets the name of the HAcc descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.HDon
Gets the name of the HDon descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.Heavy
Gets the name of the HeavyAtomCount descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.LogD
Gets the name of the LogD descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.LogP
Gets the name of the LogP descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.Mass
Gets the name of the Mass descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.TPSA
Gets the name of the TPSA descriptor object.
getName() - Method in class chemaxon.descriptors.ShapeDescriptor
Gets the name of the ShapeDescriptor fingerprint object.
getName() - Method in class chemaxon.fixers.AbstractStructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
getName() - Method in interface chemaxon.fixers.StructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
getName() - Method in class chemaxon.fixers.StructureFixerDescriptor
Returns the fixer name
getName() - Method in class chemaxon.formats.MFileFormat
Gets the codename of the format.
getName() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Gets the name of the represented MTransferable.
getName() - Method in class chemaxon.marvin.services.ServiceArgument
Returns the name of the argument
getName() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the name of the component.
getName() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getName() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
getName() - Method in class chemaxon.marvin.space.PharmacophorePoint
 
getName() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the option name.
getName() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the name of the action
getName() - Method in interface chemaxon.struc.Incomplecule
Gets the molecule title/name.
getName() - Method in class chemaxon.struc.Molecule
Gets the molecule name/title that was set by Molecule.setName(String).
getName() - Method in class chemaxon.struc.MoleculeGraph
Gets the molecule title/name.
getName() - Method in class chemaxon.struc.RgMolecule
Gets the name of the root molecule.
getName() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
Gets the name.
getName(int) - Static method in class chemaxon.struc.PeriodicSystem
Name of the element
getNameIOServiceURL() - Method in class chemaxon.marvin.common.UserSettings
 
getNameList() - Method in class chemaxon.formats.MFileFormat
Gets all the codenames of the format.
getNames() - Method in class chemaxon.formats.MFileFormat
Deprecated, for removal: This API element is subject to removal in a future version.
getNameSpace() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Returns the namespace
getNavmode() - Method in class chemaxon.marvin.beans.MViewPane
Gets the mouse drag action.
getNDists() - Method in class chemaxon.descriptors.PFParameters
Gets the number of histograms bars, that is that number of distance values disguished.
getNearClip() - Method in class chemaxon.marvin.space.GraphicCell
Returns the z coordinate of the nearer clipping plane which is computed considering all components.
getNeighbor(int, int) - Method in interface chemaxon.struc.Smolecule
Gets the index of a neighbor of an atom.
getNeighborCount(int) - Method in interface chemaxon.struc.Smolecule
Gets the number of neighbors of an atom.
getNewOldIndexMap() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
getNewToOld() - Method in class chemaxon.standardizer.Standardizer
Returns the new -> old atom index mapping.
getNewToOldMap() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Returns the new -> old atom index mapping.
getNext() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
Returns the next input molecule.
getNextAromatizedStructure() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the next enumerated structure.
getNextStructure() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the next enumerated structure, or null if no more structures.
getNodeColor() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
getNodeCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getNodes() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getNodeType() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
getNoErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the no error message of the concerning checker
getNominalMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
getNonQueryImplicitHcount() - Method in class chemaxon.struc.MolAtom
Gets the number of implicit hydrogens attached.
getNormal(int) - Method in class chemaxon.marvin.space.SurfaceComponent
Warning: for internal use only.
getNotAbsoluteRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets the not absolute (contains non-"and" enhanced) (R) or (S) chiral centers
getNotAbsoluteRSChiralCenters(List<MolAtom>) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets the not absolute (contains non-"and" enhanced) (R) or (S) chiral centers
getNotSpec() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties
 
getNucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
getNucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Gets the nucleus type.
getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator
Returns the NMR active nucleus.
getNucleusString() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the nucleus type string.
getNucleusType() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the type of the nucleus under examination.
getNumber() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Number of type.
getNumberFactory() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This feature will be removed without replacement.
getNumberFormat() - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
 
getNumberOfFeatures() - Method in class chemaxon.descriptors.PFParameters
The number of pharmacophore features (aka types, properties) used in the fingerprints.
getNumberOfFeatures() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getNumberOfMetrics() - Method in class chemaxon.descriptors.MDParameters
Gets the total number of parametrized metrics available in the present configuration.
getNumberOfMetrics() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the number of parameterized metrics available for the particular descriptor.
getNumberOfMetrics() - Method in class chemaxon.descriptors.SDParameters
Gets the total number of parametrized metrics available in the present configuration.
getNumberOfNMRActiveNuclei() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns number of the NMR active nuclei.
getNumberOfWeights() - Method in class chemaxon.descriptors.MDParameters
Gets the number of weights the current parametrized metric takes.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.BCUTParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.CDParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.CFParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.ECFPParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.MDParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.PFParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.RFParameters
Gets the number of weight factors used by the specified metric.
getNumberOfWeights(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the number of weight factors used by the specified metric.
getNumElectrons() - Method in class chemaxon.struc.graphics.MEFlow
Gets the number of electrons the arrow represents.
getObject(int) - Method in class chemaxon.struc.MDocument
Gets an object from the document.
getObject(String) - Method in class chemaxon.struc.MPropertyContainer
Gets a property object.
getObjectAtPointer() - Method in class chemaxon.marvin.beans.MSketchPane
Get the object at the mouse pointer.
getObjectContainingSelection() - Method in class chemaxon.struc.MDocument
Gets the object that contains the selection.
getObjectCount() - Method in class chemaxon.struc.MDocument
Gets the number of objects in this document.
getObjectCount() - Method in class chemaxon.struc.Molecule
 
getObjectCount() - Method in class chemaxon.struc.RgMolecule
 
getObjectCount() - Method in class chemaxon.struc.RxnMolecule
 
getObjectFromClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the current content of the clipboard if the data can be imported in any of data formats supported by MolImporter.
getObjectFromClipboard(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the current content of the clipboard if the data can be imported in any of data formats supported by MolImporter.
getObjectFromTransferable(Transferable) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the content of Transferable if the data can be imported in any of data formats supported by MolImporter.
getObjectFromTransferable(Transferable, String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the content of Transferable if the data can be imported in any of data formats supported by MolImporter.
getObjectsMiddle(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup
Calculates the middle point of the coordinates of objects this sgroup is associated to.
getOccurredException() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Gets the exception occurred during standardization process
getOffset() - Method in class chemaxon.marvin.view.MDocStorage
Gets the offset in the document source.
getOldNewIndexMap() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
getOldToNew() - Method in class chemaxon.standardizer.Standardizer
Returns the old -> new atom index mapping.
getOldToNewMap() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Returns the old -> new atom index mapping.
getOneErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the one error message
getOperatorToolBar(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Returns the operator toolbar for textPane instance NOTE: textPane have to be created with this factory
getOption(String) - Method in class chemaxon.sss.search.SearchOptions
Returns option value in string format.
getOptionDescriptors(String) - Method in class chemaxon.marvin.io.MolExportModule
Gets an array of option descriptors for the specified format.
getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Gets the option descriptors.
getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.marvin.io.MolExportModule
Gets an array of option descriptors.
getOptionDescriptors(ResourceBundle, String, String, List<OptionDescriptor>) - Static method in class chemaxon.marvin.io.MolExportModule
Gets an array of option descriptors.
getOptionNames() - Method in class chemaxon.sss.search.SearchOptions
Returns the name of all available options which can be used to set/get option values with SearchOptions.setOption(String, String) and SearchOptions.getOption(String) methods.
getOptions() - Method in class chemaxon.formats.MolImporter
Gets the import options.
getOptions() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the import options.
getOptions() - Method in class chemaxon.marvin.io.MolExportModule
Returns the output options.
getOptions() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the options for the import module.
getOptions() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the import options.
getOptionSign() - Method in class chemaxon.marvin.io.MolExportModule
Gets the sign of the options.
getOptionsPane() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
getOptionsPane(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the options pane for a plugin, loads it if needed.
getOptionsToDeselect() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the options that must be deselected if this option is selected.
getOptionsToDisable() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the options that must be switched off if this option is selected.
getOptionsToEnable() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the options that must be switched off if this option is selected.
getOptionString() - Method in enum class chemaxon.sss.search.options.HaltOnErrorOption
 
getOptionString() - Method in enum class chemaxon.sss.search.options.HomologyTranslationOption
 
getOptionString() - Method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
 
getOptionString() - Method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
 
getOptionString() - Method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
getOrCreateUUID() - Method in class chemaxon.marvin.common.UserSettings
 
getOrientation() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties
 
getOrientationType() - Method in class chemaxon.marvin.alignment.Alignment
 
getOriginal() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets the original molecule of the group.
getOriginal() - Method in class chemaxon.standardizer.Changes
Gets the original molecule of the standardization process.
getOriginal() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Gets the original molecule
getOriginalMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
getOrigQueryAtom(int) - Method in class chemaxon.sss.search.MolComparator
Converts search internal atom index (in the query) to the original atom index in the query molecule.
getOrigQueryAtom1(int) - Method in class chemaxon.sss.search.MolComparator
Returns the index of the first atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).
getOrigQueryAtom2(int) - Method in class chemaxon.sss.search.MolComparator
Returns the index of the second atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).
getOrigQueryBond(int) - Method in class chemaxon.sss.search.MolComparator
Returns bond index in the query molecule for the given query bond (search internal bond index in the query).
getOrigQueryNeighbour(int) - Method in class chemaxon.sss.search.MolComparator
For a search internal atom index (in the query), returns a neighbour atom index (original atom index in the query molecule).
getOrigTargetAtom(int) - Method in class chemaxon.sss.search.MolComparator
Converts search internal atom index (in the target) to the original atom index in the target molecule.
getOrigTargetAtom1(int) - Method in class chemaxon.sss.search.MolComparator
Returns the index of the first atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).
getOrigTargetAtom2(int) - Method in class chemaxon.sss.search.MolComparator
Returns the index of the second atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).
getOrigTargetBond(int) - Method in class chemaxon.sss.search.MolComparator
Returns bond index in the target molecule for the given target bond (search internal bond index in the target).
getOrigTargetNeighbour(int) - Method in class chemaxon.sss.search.MolComparator
For a search internal atom index (in the target), returns a neighbour atom index (original atom index in the target molecule).
getOsVersionStr() - Static method in class com.chemaxon.version.VersionInfo
Returns the OS version information as string.
getOtherAtom(MolAtom) - Method in class chemaxon.struc.MolBond
Gets the other end of the bond.
getOtherCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets the other bond if a bond is a crossing bond in a ladder-type polimer bracket.
getOtherEnd() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Gets the atom at the other end point.
getOut() - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Get stdout to use.
getOwnerCount() - Method in class chemaxon.marvin.common.UserSettings
Gets the current number of owners.
getPageFormat(String) - Method in class chemaxon.marvin.common.UserSettings
Gets the specified PageFormat
getPageSettings() - Method in class chemaxon.struc.MDocument
Gets the page settings of multipage molecular document.
getPalette() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the used built-in palette.
getPaletteString() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the string identifier of the used built-in palette.
getParameter(String) - Method in class chemaxon.marvin.beans.MarvinPane
Gets a parameter.
getParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns the parameter panel.
getParameterPanel() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
getParameterPanel(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets the parameter panel for a plugin, loads it if needed.
getParameters() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the parameters associated with the object.
getParameters() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
Gets the parameter map of the action
getParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Returns the parameters set by the user.
getParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Returns the plugin parameters.
getParameters(Properties) - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Returns the plugin parameters.
getParametersClassName() - Method in class chemaxon.descriptors.BCUT
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.CustomDescriptor
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ECFP
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the name of the parameters class corresponding to the descriptor (prefixed with the package name as getClass().getName() would return).
getParametersClassName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ScalarDescriptor
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.HAcc
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.HDon
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.Heavy
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.LogD
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.LogP
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.Mass
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.TPSA
Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ShapeDescriptor
Gets the name of the parameters class corresponding to the descriptor.
getParams() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the parameter string.
getParent() - Method in class chemaxon.struc.MolAtom
Return the molecule graph that contains this atom.
getParent() - Method in class chemaxon.struc.MolBond
Gets the parent graph.
getParent() - Method in class chemaxon.struc.MoleculeGraph
Gets the parent graph that contains this substructure.
getParentDocument() - Method in class chemaxon.struc.MoleculeGraph
Gets the document or the document of the parent graph.
getParentLine() - Method in class chemaxon.struc.graphics.MMidPoint
Gets the parent line.
getParentMolecule() - Method in class chemaxon.struc.Sgroup
Gets the parent molecule.
getParentRect() - Method in class chemaxon.struc.graphics.MRectanglePoint
Gets the parent rectangle.
getParentSgroup() - Method in class chemaxon.struc.Sgroup
Gets the parent S-group.
getParentSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated.
as of Marvin 6.2, intended for internal use, similar functionality can be reached by SuperatomSgroup.getSgroupGraph()
getParity(int) - Method in class chemaxon.struc.MoleculeGraph
Computes the parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getParity(int) - Method in class chemaxon.struc.RgMolecule
Computes the parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getParity(int) - Method in class chemaxon.struc.RxnMolecule
Computes the parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getParity(int) - Method in interface chemaxon.struc.Smolecule
Gets the parity of an atom.
getParityType(int) - Method in class chemaxon.struc.MoleculeGraph
Gets parity type.
getPartialAtomCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getPartialAtomCharge(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getPath() - Method in class chemaxon.formats.MolInputStream
Gets the path or URL of the file.
getPeptideDisplayType() - Method in class chemaxon.marvin.common.UserSettings
Gets the current peptide display type
getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Returns the pH where the major microspecies should be taken.
getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the pH where the major microspecies should be taken.
getpH() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the pH where the major microspecies should be taken.
getPharmacophore() - Method in class chemaxon.marvin.alignment.Pharmacophore3D
 
getpHs() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the pH array.
getpHs() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the pH array.
getpHs() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the pH array.
getpHs() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the pH array.
getpI() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the isoelectric point.
getPiCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the pi charge of a specified atom.
getPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane
Gets the current molecule piece in the specified format.
getPiOEN(int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the pi orbital electronegativity of a specified atom.
getpKa(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the most significant pKa value for the given atom index.
getpKa(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin
getpKaConc(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the so called concentration ionization constant.
getpKaMixed(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the so called mixed ionization constant
getpKaOfpI() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the pKa values of the calculated isoelectric point.
getpKaPrefixType() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the pKa prefix type.
getpKaType(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the pKa type: pKaPlugin.ACIDIC, pKaPlugin.BASIC or 0 if there is no pKa value for the given atom.
getpKaValues(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the pKa values for the given atom index and pKa type.
getPlaceholderText() - Method in class chemaxon.marvin.services.DynamicArgument
Returns the value placeholder text.
getPlacementOrigin(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup
If isAbsolutePlacement is false it calculates the middle point of the coordinates of atoms this S-group is associated to.
getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument
Gets the document as plain text.
getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the selected text as a plain text string.
getPlattIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
getPlugin() - Method in class chemaxon.marvin.plugin.CalculatorPluginService
Returns the calculator plugin object.
getPlugin() - Method in exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
Returns the plugin object.
getPlugin() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
 
getPlugin() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
 
getPlugin() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
getPlugin(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets a plugin, loads it if needed.
getPluginIDs() - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
getPluginIndex(String) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets a plugin index from record key.
getPluginList() - Static method in class chemaxon.license.LicenseManager
Returns the list of the plugin identifiers known by the license manager.
getPluginParameters() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the plugin parameter table (this should be set in the plugin).
getPluginResource(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the plugin JAR as resource URL, given the JAR file path relatively to the "plugins" directory.
getPMap(Molecule, PSymbols) - Method in class chemaxon.descriptors.PFGenerator
Gets pharmacophore map of the input molecule.
getPMAPTagName() - Method in class chemaxon.descriptors.PFGenerator
Gets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.
getPoint(int) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Gets the point.
getPoint(int) - Method in class chemaxon.struc.graphics.MChemicalStruct
Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.graphics.MEFlow
Gets a point of the line.
getPoint(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Gets the point.
getPoint(int) - Method in class chemaxon.struc.graphics.MPolyline
Gets the clone of a point of the line.
getPoint(int) - Method in class chemaxon.struc.MObject
Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.MPoint
Gets the point.
getPointCount() - Method in class chemaxon.struc.graphics.MChemicalStruct
Gets the number of points (atoms).
getPointCount() - Method in class chemaxon.struc.graphics.MPolyline
Gets the number of points.
getPointCount() - Method in class chemaxon.struc.MObject
Gets the number of points.
getPointCount() - Method in class chemaxon.struc.MPoint
Gets the number of points.
getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Gets a reference to a point or midpoint in the polyline.
getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Gets an internal selectable point of the rectangle.
getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
Gets an internal selectable point of the rectangle.
getPointRef(int, CTransform3D) - Method in class chemaxon.struc.MObject
Gets a reference to a point of the object.
getPointRef(int, CTransform3D) - Method in class chemaxon.struc.MPoint
Gets a point of the line.
getPointRefCount() - Method in class chemaxon.struc.graphics.MEFlow
Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MPolyline
Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MRectangle
Gets the number of internal selectable point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MRoundedRectangle
Gets the number of internal selectable point references.
getPointRefCount() - Method in class chemaxon.struc.MObject
Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.MPoint
Gets the number of point references.
getPoints() - Method in class chemaxon.struc.graphics.MPolyline
Gets the points.
getPoints() - Method in class chemaxon.struc.MoleculeGraph
Gets an array containing the atom coordinates.
getPoints(int) - Method in class chemaxon.struc.prop.MHCoords3DProp
Gets the Hydrogen locations for an atom.
getPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the atom polarizability value.
getPopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Are popup menus enabled?
getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a portion of the document.
getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets a portion of the text relative to this portion.
getPortName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Returns the port name
getPos() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the data display DASP position (0...9).
getPosition() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the current position.
getPosition() - Method in exception chemaxon.marvin.io.MRecordParseException
Gets the position of the error.
getPosition() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns the monitor's position.
getPosition() - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets the position in the document.
getPositionInPolyline() - Method in class chemaxon.struc.graphics.MMidPoint
Gets the position in the polyline.
getPositionInRect() - Method in class chemaxon.struc.graphics.MRectanglePoint
Gets the position in the rectangle.
getPossibleAtomCenteredStereoAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.stereo.Stereochemistry
Returns the indexes of atom-centered stereoactive atoms.
getPossibleAtomCenteredStereoAtomsWithNoParity(MoleculeGraph) - Static method in class chemaxon.calculations.stereo.Stereochemistry
Returns the indexes of atoms that have the possibility to have tetrahedral stereo and have no exact parity set on them.
getPossibleAttachmentPoints(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom) and MolAtom.getAttachParentSgroup().
Usage:
 SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup());
 List&ltInteger&gt orders = group.getAttachmentPointOrders(molAtom);
             
getPossibleRotatableBondCount() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Rotatable bond count before the atrop isomer calculation.
getPreBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox
Gets the breaking characters before that the text in the text box can be broken if it doesn't fit into the text box.
getPreferredIUPACName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the preferred IUPAC name.
getPreferredLabelDir(CTransform3D, int) - Method in class chemaxon.struc.MolAtom
Gets the preferred direction for an additional label.
getPreferredSize() - Method in class chemaxon.marvin.beans.MViewPane
Gets the preferred size of the component.
getPreferredView() - Method in class chemaxon.marvin.io.MolImportModule
Specifies which view style is preferred (for instance in MarvinView) for this format.
getPrefix() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns the code assist invoke prefix
getPrefix() - Method in exception chemaxon.naming.NameFormatException
The part of the input name that was recognized, or null.
getPreviousNormalTextSectionIndex() - Method in class chemaxon.struc.graphics.MTextBox
Gets the index of the last `normal' text section before the current subscript/superscript section.
getPrimaryIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Gets the primary indexes.
getPrimaryMolecule() - Method in class chemaxon.struc.MDocument
Gets the primary molecule object.
getPrimaryMolecules() - Method in class chemaxon.struc.MDocument
Gets an array containing the primary molecule objects.
getPrimitives() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the primitives (for example triangles) of the surface.
getPrincipalPolarizabilityComponents() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the principal components a(xx), a(yy), a(zz) of polarizability tensor (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
getPriority() - Method in class chemaxon.fixers.StructureFixerDescriptor
Returns the fixer priority.
getPriority() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Gets the priority of the MTransferable object by exporting to clipboard.
getPriority(String) - Method in class chemaxon.formats.MFileFormat
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 2014.07.21.0 use MFileFormat.getSubFormatPriority(String) instead
getProbeRadius() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the probe radius the surface computing will use.
getProduct() - Method in exception chemaxon.license.LicenseException
 
getProduct(int) - Method in class chemaxon.struc.RxnMolecule
Gets a product.
getProductCount() - Method in class chemaxon.struc.RxnMolecule
Gets the number of products.
getProductList(boolean) - Static method in class chemaxon.license.LicenseManager
Returns the list of the product identifiers known by the license manager.
getProductName() - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
getProductName() - Method in class chemaxon.calculations.nmr.NMRCalculator
 
getProductName() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
getProductName() - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
 
getProductName() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.ResonancePlugin
 
getProductName() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
getProductName() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProductName() - Method in class chemaxon.marvin.calculations.TPSAPlugin
 
getProductName() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the product identifier of the plugin as given by LicenseManager.
getProducts() - Method in class chemaxon.struc.RxnMolecule
Gets all products in an array.
getProductTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
Returns the tanimoto distance of the product sides.
getProgessLength() - Method in interface chemaxon.checkers.runner.CheckerRunner
 
getProgessLength() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
getProgessLength() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Gets the length of the standardization process
getProgress() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Estimates the progress.
getProgressBar() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
getProgressMonitor(Component) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates a progress observer object to be used in CalculatorPlugin.setProgressMonitor(chemaxon.common.util.MProgressMonitor).
getPropArraySize() - Method in class chemaxon.struc.MDocument.Prop
Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.MProp
Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MHashProp
Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MListProp
Gets the array size.
getProperties() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
Returns the flag which can used to identify which properties should be fixed.
getProperty(String) - Method in class chemaxon.marvin.common.UserSettings
Returns the value for the given key.
getProperty(String) - Method in class chemaxon.struc.MolAtom
Returns the property value to which the specified property key is mapped at this atom, or null if this atom has no mapping for this property key.
getProperty(String) - Method in class chemaxon.struc.MolBond
Returns the property value to which the specified property key is mapped at this bond, or null if this bond has no mapping for this property key.
getProperty(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, this method is deprecated. Replaced by MPropHandler.getPropertyString(MoleculeGraph, String).
Usage:
String property = MPropHandler.getPropertyString(mol, key);
getPropertyChangeSupport() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
Returns the PropertyChangeSupport associated with this editor
getPropertyContainer() - Method in class chemaxon.marvin.io.MRecord
Gets the properties.
getPropertyCount() - Method in class chemaxon.struc.Molecule
Gets the total number of RDfile/SDfile properties.
getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo
Returns the property descriptor array.
getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo
Returns the property descriptor array.
getPropertyDescriptors(Class<?>, Vector<PropertyDescriptor>) - Method in class chemaxon.marvin.beans.MarvinPaneBeanInfo
Puts the descriptors of the common Marvin bean properties into the specified Vector.
getPropertyKey(int) - Method in class chemaxon.struc.Molecule
Gets an RDfile/SDfile property key.
getPropertyKeys() - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 4.1, replaced by properties().getKeys() and properties().getKeyEnumeration().
One-to-one replacement is method getKeyEnumeration() but method getKeys() is simpler to use.
getPropertyMap() - Method in class chemaxon.marvin.common.UserSettings
Shortcut to getPropertyMap(UserSettings.PROPERTY_TYPE_ALL)
getPropertyMap(String) - Method in class chemaxon.marvin.common.UserSettings
Returns a map of properties from the given type.
getPropertyObject(MoleculeGraph, String) - Static method in class chemaxon.marvin.io.MPropHandler
Returns the property object associated with the given key in the given molecule.
getPropertyObject(String) - Method in class chemaxon.struc.Molecule
Gets an RDfile/SDfile property object.
getPropertyString(MoleculeGraph, String) - Static method in class chemaxon.marvin.io.MPropHandler
Converts the property object associated with the given key in the given molecule to string.
getPropertyText(Molecule) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns molecule properties is text form.
getPropList() - Method in class chemaxon.struc.MPropertyContainer
Gets the list of basic properties.
getPropType() - Method in class chemaxon.struc.MDocument.Prop
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.MProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MBooleanProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MDoubleProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MHashProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MHCoords3DProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MIntegerProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MListProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MMoleculeProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MObjectProp
Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MStringProp
Gets the type name of the property.
getPropValue() - Method in class chemaxon.struc.MDocument.Prop
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.MProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MBooleanProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MDoubleProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MHashProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MHCoords3DProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MIntegerProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MListProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MMoleculeProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MObjectProp
Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MStringProp
Gets the property value as an object.
getPropXSDType() - Method in class chemaxon.struc.MDocument.Prop
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.MProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MBooleanProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MCollectionProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MHCoords3DProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MMoleculeProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MObjectProp
Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MStringProp
Gets the XSD type name of the property.
getPSymbols() - Method in class chemaxon.descriptors.PFParameters
Gets the pharmacophore type symbols used in the current configuration.
getQProp(String) - Method in class chemaxon.struc.MolAtom
Gets a query property.
getQPropAsInt(int, String) - Method in interface chemaxon.struc.Smolecule
Gets a query property as an integer.
getQPropAsInt(String) - Method in class chemaxon.struc.MolAtom
Gets a query property as an integer.
getQPropMinMax(String) - Method in class chemaxon.struc.MolAtom
Gets the minimum and maximum possible values of a query property.
getQPropNames() - Method in class chemaxon.struc.MolAtom
Gets the names of query properties with non-null values.
getQPropNameSet() - Method in class chemaxon.struc.MolAtom
Gets the names of query properties with non-null values, or null if no query properties are set.
getQuery() - Method in class chemaxon.sss.search.MolSearch
 
getQuery() - Method in class chemaxon.sss.search.Search
Retrieves the query structure.
getQuery() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Gets the query structure.
getQueryAromaticity() - Method in class chemaxon.struc.MolAtom
Gets the aromatic/aliphatic query property.
getQueryAsString(Molecule) - Static method in class chemaxon.sss.search.Search
For internal purposes only.
getQueryAtom() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Gets the atom to be searched for by the action (the query atom)
getQueryCode() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the program code of the query option.
getQueryLabel() - Method in class chemaxon.struc.MolAtom
Gets the string representation of the query atom
getQueryMode() - Method in class chemaxon.formats.MolImporter
Gets query mode.
getQueryMode() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the query mode.
getQueryMoleculeErrorMessage(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
 
getQueryOp() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the data query operator.
getQuerystr() - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.7, replaced by MolAtom.getQueryString()
getQuerystr() - Method in class chemaxon.struc.MolBond
Gets the query properties.
getQuerystr() - Method in class chemaxon.struc.QueryBond
Gets the query properties.
getQueryString() - Method in class chemaxon.struc.MolAtom
Returns s the query string assigned to this atom.
getQueryToPrint() - Method in class chemaxon.sss.search.Search
For internal purposes only.
getRadical() - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.2. use MolAtom.getRadicalValue() instead
getRadical(int) - Method in interface chemaxon.struc.Smolecule
Deprecated, for removal: This API element is subject to removal in a future version.
getRadicalCount() - Method in class chemaxon.struc.MDocument
Returns the number of Radical electrons.
getRadicalCount() - Method in class chemaxon.struc.MolAtom
Gets the number of free electrons.
getRadicalCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getRadicalMatching() - Method in class chemaxon.sss.search.SearchOptions
Get option for radical matching behaviour.
getRadicalValue() - Method in class chemaxon.struc.MolAtom
Gets the AtomProperty.Radical enum value that represents the radical of the atom.
getRadicalValue(int) - Method in interface chemaxon.struc.Smolecule
Gets the radical value of an atom.
getRadius() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Returns the radius of the arrow.
getRadius() - Method in class chemaxon.marvin.space.PharmacophorePoint
Returns the radius of the PharmacophorePoint in angstroms.
getRainbowPalette() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the color palette that is used when the coloring mode of the component is rainbow coloring.
getRandicIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
getRandomSeed() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Gets the random seed value.
getRangeMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Maximal y value of the NMR spectrum function.
getRangeMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Minimal y value of the NMR spectrum function.
getRawValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the value of the unscaled NMR spectrum function at a given x point.
getRCSBLink(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
Returns the URL of the RCSB database
getRCSBLink(String, boolean) - Static method in class chemaxon.marvin.space.MSpaceEasy
Returns the URL of the RCSB database
getReactant(int) - Method in class chemaxon.struc.RxnMolecule
Gets a reactant.
getReactantCount() - Method in class chemaxon.struc.RxnMolecule
Gets the number of reactants.
getReactants() - Method in class chemaxon.struc.RxnMolecule
Gets all reactants in an array.
getReactantTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
Returns the tanimoto distance of the reactant sides.
getReaction() - Method in class chemaxon.jep.context.ReactionContext
Returns the reaction.
getReaction(MoleculeGraph) - Static method in class chemaxon.struc.RxnMolecule
Returns the reaction represented by the given molecule if exists, otherwise null.
getReactionArrow() - Method in class chemaxon.struc.RxnMolecule
Gets a two-element array containing the endpoints of the reaction arrow.
getReactionArrow(boolean) - Method in class chemaxon.struc.RxnMolecule
Gets the reaction arrow of this reaction with the possibility to generate an arrow if the arrow is not yet set.
getReactionArrowList() - Method in class chemaxon.struc.RxnMolecule
Gets the list of the reaction arrows of this reaction.
getReactionArrowType() - Method in class chemaxon.struc.RxnMolecule
Gets the reaction arrow type.
getReactionArrowTypeName() - Method in class chemaxon.struc.RxnMolecule
Gets the reaction arrow type name.
getReactionSmarts() - Method in class chemaxon.checkers.result.SubstructureCheckerResult
Returns the reactionSmarts
getReactionSmarts() - Method in class chemaxon.checkers.SubstructureChecker
Returns the reactionSmarts
getReactionStereo() - Method in class chemaxon.struc.MolAtom
Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
getReactionSupport() - Method in class chemaxon.marvin.beans.MSketchPane
Is reaction drawing supported?
getReadGlobalGUIProperties() - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.1 when this and the MarvinPane.getSaveGlobalGUIProperties() function have been merged.
getRealBondCount() - Method in class chemaxon.struc.MolAtom
Gets the number of bonds connected to "real" atoms.
getRealEigenValue() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
getRealRotatableBondCount() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Rotatable bond count (atrop bonds excluded)
getRecognizedFormat() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Gets the recognized file format.
getRecognizedFormat() - Method in interface chemaxon.marvin.io.MRecordReader
Gets the recognized file format.
getRecognizer(int, int) - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Gets an element of the recognizer list at the specified level.
getRecordCount() - Method in class chemaxon.formats.MolImporter
Gets the current record number.
getRecordCount() - Method in class chemaxon.marvin.io.ArrayMDocSource
Gets the current record number.
getRecordCount() - Method in class chemaxon.marvin.io.MDocSource
Gets the current record number.
getRecordCountMax() - Method in class chemaxon.formats.MolImporter
Gets the total number of records read.
getRecordCountMax() - Method in class chemaxon.marvin.io.ArrayMDocSource
Gets the total number of records.
getRecordCountMax() - Method in class chemaxon.marvin.io.MDocSource
Gets the total number of records.
getRecordIDBackground(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the highlight color of a record.
getRecordIDForeground(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the foreground color of a record.
getRecordIndex() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
Gets the requested, unavailable record index.
getRecordIndexMax() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
Gets the maximum available record index.
getRecordIndexMin() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
Gets the minimum available record index.
getRecordNumber() - Method in class chemaxon.marvin.io.MRecordReader.Position
Gets the record number.
getRecordReader() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the record reader.
getReferenceAndRotatedFused() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
before getRotatedMolecule the AlignRigidEasy.align() method must be called
getReferenceMolecule() - Method in interface chemaxon.marvin.alignment.MCSAlignment
Reference molecule.
getReferenceWithNewCoordinates() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
getReflogDs() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the reference logD array.
getRefpHs() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the reference pH array.
getRefractivity() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the refractivity value.
getRefractivityHIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the refractivity increment on the H atoms attached to a given atom.
getRefractivityIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the refractivity increment for a given atom.
getRelativeNegativity() - Method in class chemaxon.struc.MolAtom
Check negativity compared to the neighbors.
getRemark() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.
getRemark() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns a warning message in case of arithmetical overflow (the number of enumerated structures exceeds Long.MAX_VALUE), null otherwise.
getRemark() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns a warning message if there are no resonants, null otherwise.
getRemark() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns a warning message if there are no tautomers, null otherwise.
getRemark() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.
getRemark() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the calculation remark.
getRemark() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the calculation remark.
getRemark() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns the calculation remark.
getRemovedAtoms() - Method in class chemaxon.standardizer.Changes
Gets the list of atoms removed during the standardization procedure
getRendering() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the rendering style.
getRendering() - Method in class chemaxon.marvin.MolPrinter
Returns the rendering style of atoms and bonds.
getRenderingQuality() - Method in class chemaxon.marvin.space.GraphicComponent
Returns the actual rendering quality of the component.
getRepeatingUnitAtom(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets a paradigmatic repeating unit atom.
getRepeatingUnitAtomCount() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets the number of atoms in the pararadigmatic repeating unit.
getRepeatingUnitAtoms() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets the repeating unit atoms.
getReplaceAtom() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Gets the atom to replaced with by the action
getReporter() - Method in class chemaxon.checkers.StructureCheck
Gets the reporter used by the check procedure.
getRepresentationClass() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Gets the name of the representation class of the MTransferable.
getRequestMethod() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
Gets the HTTP method of the request.
getRequiredHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin
Returns the Required HLB value calculated by chemaxon method.
getResidueAtomId() - Method in class chemaxon.struc.MolAtom
Gets the residue atom identifier.
getResidueSeq() - Method in class chemaxon.struc.MolAtom
Gets the residue sequence number.
getResidueType() - Method in class chemaxon.struc.MolAtom
Gets the residue type.
getResidueTypeId(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getResidueTypeId(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getResolution() - Method in class chemaxon.descriptors.PFParameters
Gets the resolution of histograms.
getResolution() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getResourceBundle(String) - Static method in class chemaxon.marvin.beans.MarvinPane
Utility method to get a resource bundle.
getResult() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
getResult() - Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
Returns the cached results.
getResult() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Returns the calculation result after the plugin has been CalculatorPlugin.run().
getResult() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Returns the plugin object itself.
getResult() - Method in class chemaxon.standardizer.Changes
Gets the result molecule of the standardization process
getResult(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the result item for the specified type and index.
getResult(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the result string for the given molecule.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the microsepcies if pH is different from Double.NaN, otherwise returns the input molecule itself.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
getResult(Object, int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the result item for the specified type and index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call ElementalAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call ElementalAnalyserPlugin.getResult(Object, int) with a 0 index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call GeometryPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call GeometryPlugin.getResult(Object, int) with a 0 index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call IsoelectricPointPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call IsoelectricPointPlugin.getResult(Object, int) with a 0 index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call MarkushEnumerationPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call MarkushEnumerationPlugin.getResult(Object, int) with a 0 index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.pKaPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call pKaPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call pKaPlugin.getResult(Object, int) with a 0 index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call TopologyAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call TopologyAnalyserPlugin.getResult(Object, int) with a 0 index.
getResult(Object, String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call CalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call CalculatorPlugin.getResult(Object, int) with a 0 index.
getResult(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call CalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call CalculatorPlugin.getResult(Object, int) with a 0 index.
getResultantImplicitHCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the implicit H charge around a central atom
getResultAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue): RED for acidic pKa, BLUE for basic pKa.
getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result in String format for the first result type.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the specified result molecule in SMILES format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result in String format.
getResultComponent() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns the result component for display.
getResultCount() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
getResultCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the number of result items for the first result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the number of result items: 1.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the number of result items for the given result key.
getResultDomain() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
getResultDomain() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the domain for the first result type.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the calculation domain CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the calculation domain CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULE in case of increments .
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the calculation domain CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
getResultList() - Method in interface chemaxon.checkers.runner.CheckerRunner
 
getResultMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the plugin calculation error message, error or warning.
getResultMessage() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the plugin calculation error message, error or warning.
getResultMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
getResultMolecule() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
The result molecule will be 3D and aromatized version of the input molecules.
getResultMolecule() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
getResultMolecule() - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
getResultMolecule() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the major microspecies for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Get result structure
getResultMolecule() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the result molecule for display.
getResultMolecule(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the decorated result molecule for the given target molecule.
getResultMolecules() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
getResultMolecules() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
getResultMolecules() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the result molecule array for display.
getResultMolecules(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the result molecules for the given target molecule.
getResults(Object) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns result items for the given result type.
getResultsAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result with possible subresults.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the specified result in GUI-specific String format: A for acceptor, D for donor.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the specified results in String format.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the specified result with possible subresults (both pKa values instead of the most significant pKa) in String format.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the specified result with possible subresults.
getResultSource() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the result as a document source object.
getResultSource() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the result as a document source object.
getResultSource() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the result as a document source object.
getResultSource() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the result as a document source object.
getResultSource() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the result as a document source object.
getResultSource() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the result as a document source object.
getResultSource() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the result as a document source object.
getResultTypeList() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the result types (possible types: "sigma", "pi", "total").
getResultTypes() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns the string IDs of the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.IonChargePlugin
Returns the result types (possible type: "charge").
getResultTypes() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the result types (possible types: "majority-ms").
getResultTypes() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the result types (possible types: "sigma", "pi").
getResultTypes() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the result types (possible types: pKa, acidic, basic, msdistr).
getResultTypes() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns the result types (possible types: sigma, pi, total).
getResultTypes() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
getResultTypes() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the result types.
getReturnTypes() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Returns the array of return types
getRgroup() - Method in class chemaxon.struc.MolAtom
Gets the R-group ID.
getRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MolAtom
Gets the attachment point order of an R-group attachment point.
getRgroupBridgeCount() - Method in class chemaxon.struc.RgMolecule
Returns the number of R-group bridges defined in this structure.
getRgroupBridgeIds() - Method in class chemaxon.struc.RgMolecule
Returns the list of R-group bridge IDs defined in this structure.
getRgroupBridgeMember(RgroupBridgeId, int) - Method in class chemaxon.struc.RgMolecule
Returns a definition member of the given R-group bridge.
getRgroupBridgeMemberCount(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule
Returns the number of definition members of the given R-group bridge.
getRgroupCount() - Method in class chemaxon.struc.RgMolecule
Gets the number of R-groups.
getRgroupDisplayLabel(int) - Method in class chemaxon.struc.RgMolecule
 
getRgroupId(int) - Method in class chemaxon.struc.RgMolecule
Gets the ID of an R-group.
getRgroupId(int) - Method in interface chemaxon.struc.Smolecule
Gets the R-group identifier of an atom.
getRgroupId(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule
 
getRgroupIds() - Method in class chemaxon.checkers.result.RgroupCheckerResult
Returns the list of affected R-group IDs.
getRgroupIndex(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule
Returns the index of the ordinary R-group that actually represents the given R-group bridge.
getRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule
Gets an R-group member.
getRgroupMemberCount(int) - Method in class chemaxon.struc.RgMolecule
Gets the number of R-group members.
getRgroupMemberG(int, int) - Method in class chemaxon.struc.RgMolecule
Gets an R-group member.
getRgroupMemberId(MolAtom) - Method in class chemaxon.struc.RgMolecule
Gets the unique identifier of the R-group member that contains the specified atom.
getRight() - Method in class chemaxon.marvin.space.GraphicCell
Returns the x coordinate of the right edge of the cell.
getRightBracket(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
 
getRightName() - Method in class chemaxon.struc.sgroup.SgroupAtom
Set the string that will be shown at the right side of the molecule.
getRingAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the ring atom count.
getRingBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the ring bond count.
getRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the ring count.
getRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
getRingCountOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
getRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getRingHandlingMode() - Method in class com.chemaxon.search.mcs.McsSearchOptions
Gets the ring handling mode specified.
getRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the rings in the molecule.
getRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies rings in the molecule having a given size.
getRingSystemCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of ring systems.
getRingSystemCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the number of ring systems having a given size (number of rings) in the molecule.
getRingSystemCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getRingSystems() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the ring systems in the molecule.
getRingSystems(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Indentifies the ring systems in the molecule having a given size (number of rings).
getRLigandEqualityCheck() - Method in class chemaxon.sss.search.SearchOptions
Returns true if undefined R-atoms with the same R-group ID should match the same structure.
getRlogic(int) - Method in class chemaxon.struc.RgMolecule
Gets R-logic flags.
getRlogicRange(int) - Method in class chemaxon.struc.RgMolecule
Gets R-logic occurrence range.
getRLogicVisible() - Method in class chemaxon.marvin.common.UserSettings
Tells whether the R-logic is visible if exists
getRmsd() - Method in class chemaxon.marvin.alignment.Alignment
 
getRmsd() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
getRmsd() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
 
getRoot() - Method in class chemaxon.struc.RgMolecule
Gets the root structure.
getRootG() - Method in class chemaxon.struc.RgMolecule
Gets the root structure.
getRootSgroups() - Method in class chemaxon.struc.Molecule
Gets root s-groups (groups that are not embedded into another s-group).
getRotatableBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the rotatable bond count.
getRotatedCoordinates() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
before getRotatedCoordinates the AlignRigidEasy.align() method must be called
getRotatedMolecule() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
before getRotatedMolecule the AlignRigidEasy.align() method must be called
getRotateMatrix() - Method in class chemaxon.marvin.space.GraphicCell
Returns the matrix of rotation.
getRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the rotation part of the transformation matrix.
getRotBondCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getRow(int) - Static method in class chemaxon.struc.MolAtom
The row or or period of an element in the periodic system.
getRow(int) - Static method in class chemaxon.struc.PeriodicSystem
The row or or period of an element in the periodic system.
getRowCount() - Method in class chemaxon.marvin.space.GraphicScene
Returns the number of rows in the scene.
getRowHeight() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the row height.
getrsChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets the (r) and (s) stereo centers of the molecule
getRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets the (R) and (S) chiral centers of the molecule
getSaltCount() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Gets the count of the salts of the action
getSaltID(int) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Gets the salt ID at the provided index
getSaltList() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Gets the custom salt list of the action
getSaveGlobalGUIProperties() - Method in class chemaxon.marvin.beans.MarvinPane
Checks whether we have to read GUI properties from a .MRV file
getSaveGUIPropertiesInMRV() - Method in class chemaxon.marvin.common.UserSettings
 
getSaveLoadZoomFactorToMRV() - Method in class chemaxon.marvin.common.UserSettings
Tells if marvin save the zoom factor to mrv or not.
getScale() - Method in class chemaxon.marvin.beans.MSketchPane
Returns the scale factor of the current magnification.
getScale() - Method in class chemaxon.marvin.MolPrinter
Returns the scale factor in units of regular bond length.
getScale() - Method in class chemaxon.struc.CTransform3D
Gets the scale factor.
getScale() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the relative size of the font compared to the base font.
getScaledAWTFont(Float) - Method in class chemaxon.struc.graphics.MFont
Gets an AWT font instance after scaling.
getScaledTanimoto(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Gets the Tanimoto dissimilarity coefficient.
getScaledTanimoto(PharmacophoreFingerprint, PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the scaled Tanimoto metric (adapted to hystograms).
getScaleFactor() - Method in class chemaxon.descriptors.MDParameters
Gets the scale factor used in the current parametrized scalable metrics.
getScalingHypothesis() - Method in class chemaxon.descriptors.MDParameters
Gets the scaling hypothesis used in scaled metrics.
getScreeningConfigurationString(String, String, String) - Method in class chemaxon.descriptors.MDParameters
Returns parts of the parameter values in string.
getScriptCount(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets the number of subscripts or superscripts on the last normal character.
getSearcher() - Method in class chemaxon.sss.search.MolSearch
 
getSearchMode() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Gets the current search mode.
getSearchOptions() - Method in class chemaxon.sss.search.Search
Returns the SearchOptions object associated with this Search object.
getSearchOptions() - Method in class chemaxon.standardizer.advancedactions.TransformAction
Gets the search options of the action
getSearchOptions() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Returns the search options used by this instance.
getSearchType() - Method in class chemaxon.sss.search.SearchOptions
Returns the currently set global search operation mode.
getSearchType(String) - Static method in class chemaxon.sss.search.SearchOptions
Decodes the string representation of the search type and returns the predefined constant value defined in SearchConstants.
getSecondaryIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Gets the secondary indexes.
getSecondaryStructureType(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
Gets the type of the secondary structure element which the current atom belongs to.
getSecondaryStructureType(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getSection(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a section of the document.
getSectionCount() - Method in class chemaxon.struc.graphics.MTextDocument
Gets the number of sections in the document.
getSectionIndexOfCharAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets the section index of a character.
getSectionShiftY(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets the y shift of a section.
getSelectedAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
 
getSelectedAtoms(int, String) - Method in class chemaxon.marvin.view.MDocStorage
Gets the selected atom indices.
getSelectedDocument() - Method in class chemaxon.struc.graphics.MTextBox
 
getSelectedElements() - Method in class chemaxon.marvin.space.monitor.Monitor
Returns the set of the monitored items.
getSelectedFieldCount() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the number of selected fields.
getSelectedFields() - Method in class chemaxon.marvin.view.swing.TableOptions
Get selected fields array which are selected in Table Options dialog box
getSelectedFieldTypes() - Method in class chemaxon.marvin.view.swing.TableOptions
Get type array of selected field types.
getSelectedIndex() - Method in class chemaxon.marvin.beans.MViewPane
Gets the index of the molecule that is selected by the user.
getSelectedItem() - Method in class chemaxon.marvin.space.monitor.Label
 
getSelectedString() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selected substring.
getSelection() - Method in class chemaxon.marvin.beans.MSketchPane
Gets a clone of the selection.
getSelection() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
Returns the selection of atoms.
getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
getSelection() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Gets a selection which contains index of center atom and indexes of ligands.
getSelection() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
getSelectionEndColumn() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selection's end column number.
getSelectionEndPos() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selection's end position.
getSelectionEndRow() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selection's end row number.
getSelectionStartColumn() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selection's start column number.
getSelectionStartPos() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selection's start position.
getSelectionStartRow() - Method in class chemaxon.struc.graphics.MTextBox
Gets the selection's start row number.
getSeparator(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Gets if a separator is required after the plugin menuitem in the Tools menu.
getServiceDescriptorConfigurationAsStream() - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns an InputStream with service configuration.
getServiceDescriptorConfigurationAsStream(ServicesConfigURLProvider) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns an InputStream with service configuration.
getServiceDescriptorConfigurationAsStream(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the service descriptor configuration stream from path, or null.
getServiceDescriptorEditorProvider(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the ServiceDescriptorEditorProvider instance if available, or null
getServiceDescriptorReader(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the ServiceDescriptorReader instance if available, or null
getServiceDescriptorWriter(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the ServiceDescriptorWriter instance if available, or null
getServiceDialogProvider(String) - Static method in class chemaxon.marvin.services.ServiceDescriptorTools
Returns the ServiceDialogProvider instance if available, or null
getServicesConfigurationPath() - Method in class chemaxon.jep.Evaluator
Returns the custom services configuration path.
getServicesConfigURL() - Method in class chemaxon.marvin.common.UserSettings
Returns the URL of configuration for Services in marvin sketch
getSet() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the set of attributes used.
getSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3, replaced by getAtomSetColor
getSetSeq() - Method in class chemaxon.struc.MolAtom
Gets the atom set sequence number.
getSetSeq() - Method in class chemaxon.struc.MolBond
Gets the bond set.
getSeverity() - Method in class chemaxon.checkers.StructureCheckerDescriptor
Returns the severity
getSgroup() - Method in class chemaxon.struc.sgroup.SgroupAtom
Gets the S-group corresponding to this superatom.
getSgroup(int) - Method in class chemaxon.struc.Molecule
Gets an S-group.
getSgroupArray() - Method in class chemaxon.struc.Molecule
Gets the array of S-groups.
getSgroupCount() - Method in class chemaxon.struc.Molecule
Gets the number of S-groups.
getSgroupGraph() - Method in class chemaxon.struc.Sgroup
Gets a COPY of the molecule graph.
getSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the molecule graph as a selection.
getSgroupIterator() - Method in class chemaxon.struc.Molecule
Returns an iterator over the s-groups in this molecule in proper sequence.
getSgroupLigands() - Method in class chemaxon.struc.Molecule
Gets the S-group's ligands if the structure represents an S-group.
getSgroups() - Method in class chemaxon.checkers.result.SgroupCheckerResult
Returns a List which contains the affected groups of the problem
getSgroupType() - Method in class chemaxon.struc.Sgroup
Gets the S-group type.
getSgroupType(String) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Gets the S-group type.
getShapes(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
 
getShapeScore() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
 
getShapeSimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor
 
getShapeTanimoto() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
 
getShapeTanimoto() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
getShapeTanimoto() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
getShapeTanimoto() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
getShift() - Method in class chemaxon.calculations.nmr.Shift
Returns the chemical shift.
getShiftError() - Method in class chemaxon.calculations.nmr.Shift
Returns the error (confidence interval radius) of the shift.
getShiftErrorClassification() - Method in class chemaxon.calculations.nmr.Shift
Returns the error classification of the stored chemical shift.
getShifts() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns chemical shifts.
getShiftX() - Method in class chemaxon.marvin.space.GraphicCell
Returns the shifting value of the x direction.
getShiftX(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns corrected shifting value of the given cell.
getShiftY() - Method in class chemaxon.marvin.space.GraphicCell
Returns the shifting value of the y direction.
getShiftY(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns corrected shifting value of the given cell.
getShortestPath(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the shortest topological path (number of bonds) between two atoms.
getShortName() - Method in class chemaxon.descriptors.BCUT
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ChemicalFingerprint
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.CustomDescriptor
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ECFP
Gets the short name of the fingerprint.
getShortName() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ReactionFingerprint
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ScalarDescriptor
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.HAcc
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.HDon
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.Heavy
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.LogD
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.LogP
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.Mass
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.TPSA
Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ShapeDescriptor
Gets the short name of the fingerprint.
getShortName() - Method in enum class chemaxon.struc.SgroupType
 
getShowLogPercentage() - Method in class chemaxon.marvin.calculations.pKaPlugin
 
getSigmaCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the sigma charge of a specified atom.
getSigmaOEN(int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns the sigma orbital electronegativity of a specified atom.
getSimilarity() - Method in class com.chemaxon.search.mcs.McsSearchResult
Returns a Tanimoto-like similarity score of the input molecules based on the found maximum common substructure.
getSimilarity(T) - Method in class chemaxon.descriptors.SimilarityCalculator
Gets the similarity value according to previously defined metric and its parameters.
getSimpleName() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
 
getSimpleName() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
 
getSimpleName() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
 
getSimpleName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
 
getSimpleName() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
 
getSimpleParamString() - Method in enum class chemaxon.descriptors.MetricsType
 
getSimplifiedMolecule() - Method in class chemaxon.struc.Molecule
Gets the simplified molecule object.
getSimpView() - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.5, replaced by MSketchPane.isBondDraggedAlong()
getSingleHit() - Method in class chemaxon.sss.search.SearchHit
Returns the single hit view of the hit object.
getSingleMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the microspecies distribution at the specified pH value set in pKaPlugin.setpH(double).
getSink() - Method in class chemaxon.struc.graphics.MEFlow
Gets the destination of the electron-flow arrow (MolAtom, MolBond, or MolAtom[2] for incipient bond).
getSinkAtom() - Method in class chemaxon.struc.graphics.MEFlow
Gets the atom at the sink of this arrow.
getSinkAtoms() - Method in class chemaxon.struc.graphics.MEFlow
Gets the atom or atoms at the arrow sink.
getSinkBond() - Method in class chemaxon.struc.graphics.MEFlow
Gets the bond at the sink of this arrow.
getSize() - Method in class chemaxon.marvin.view.MDocStorage
Gets the total number of entries.
getSizeDouble() - Method in class chemaxon.struc.graphics.MFont
Gets the font size.
getSketchAnyBond() - Method in class chemaxon.marvin.common.UserSettings
Gets the default any bond drawing style in the sketcher.
getSketchArrowHeadLength() - Method in class chemaxon.marvin.common.UserSettings
Gets the current arrow head length.
getSketchArrowHeadWidth() - Method in class chemaxon.marvin.common.UserSettings
Gets the current arrow head width.
getSketchArrowTailLength() - Method in class chemaxon.marvin.common.UserSettings
Gets the current arrow tail length.
getSketchArrowTailWidth() - Method in class chemaxon.marvin.common.UserSettings
Gets the current arrow tail width.
getSketchCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings
Gets the default carbon displaying style in the sketcher.
getSketchColorScheme() - Method in class chemaxon.marvin.common.UserSettings
Gets the sketcher's default color scheme.
getSketchImplicitH() - Method in class chemaxon.marvin.common.UserSettings
Gets the display method of implicit hydrogens for the sketcher.
getSketchLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings
Gets the default ligand order displaying style in the sketcher.
getSketchLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
Based on the preferences this funtion returns the proper working directory for the MarvinSketch application's load filechooser.
getSketchMode() - Method in class chemaxon.marvin.beans.MSketchPane
Gets the sketching mode.
getSketchMolbg2d() - Method in class chemaxon.marvin.common.UserSettings
Gets the sketcher's default 2D molecule background color.
getSketchMolbg3d() - Method in class chemaxon.marvin.common.UserSettings
Gets the sketcher's default 3D molecule background color.
getSketchRecentFileList() - Method in class chemaxon.marvin.common.UserSettings
Gets the recent files' list at marvinsketch, the last item is the most recent.
getSketchRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings
Gets the recent file list requested size, based on a preferences setting
getSketchRendering2d() - Method in class chemaxon.marvin.common.UserSettings
Gets the rendering style for the 2D sketcher.
getSketchRendering3d() - Method in class chemaxon.marvin.common.UserSettings
Gets the rendering style for the 3D sketcher.
getSketchSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
Not implemented yet don't use it.
getSkip(int) - Method in class chemaxon.struc.graphics.MPolyline
Gets the distance of the (visible) head or tail from the corresponding line end point.
getSmallestRing() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the smallest ring (number of stoms) in the molecule.
getSmallestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the smallest ring size.
getSmallestRingSizeForIdx() - Method in class chemaxon.struc.MoleculeGraph
Get the smallest ring size in which the atom (specified with it's index) can be located.
getSmallestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the size of smallest ring containing the specified atom.
getSmallestRingSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Identifies the smallest ring system (number of rings) in the molecule.
getSmallestRingSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns the size of the smallest ring system (number of rings) in the molecule.
getSMILESFontSize() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the SMILES font size.
getSmolecule() - Method in class chemaxon.calculations.ElementalAnalyser
Retrieves the input molecule
getSmoleculeAtomProperty() - Method in class chemaxon.marvin.space.AtomProperty
 
getSolubility() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
Returns the solubility value.
getSolubility(SolubilityUnit) - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
Returns the solubility value.
getSolubilityCategory() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
Returns the solubility category.
getSolubilityCategory(SolubilityCategories) - Method in interface com.chemaxon.calculations.solubility.SolubilityResult
Returns the solubility category.
getSolventCount() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Gets the count of the solvents of the action
getSolventID(int) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Gets the solvent ID at the provided index
getSolventList() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Gets the custom solvent list of the action
getSortedMicrospecies(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the microspecies molecule, sorted by descreasing distribution at the given pH.
getSortedMsDistribution(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the microspecies distribution, sorted by descreasing distribution at the given pH.
getSortedSgroups() - Method in class chemaxon.struc.Molecule
Gets the sorted S-groups in parent-child order.
getSortedValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
getSource() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
getSource() - Method in interface chemaxon.checkers.result.StructureCheckerResult
 
getSource() - Method in class chemaxon.struc.graphics.MEFlow
Gets the origin of the electron-flow arrow (MolAtom or MolBond).
getSourceAtom() - Method in class chemaxon.struc.graphics.MEFlow
Gets the atom at the source of this arrow.
getSourceAtoms() - Method in class chemaxon.struc.graphics.MEFlow
Gets the atom or atoms at the arrow source.
getSourceBond() - Method in class chemaxon.struc.graphics.MEFlow
Gets the bond at the source of this arrow.
getSpecResult(Molecule, String) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Deprecated, for removal: This API element is subject to removal in a future version.
This method depends on the now deprecated CalculatorPlugin.getResult(Object, String) method, so this is deprecated as well and will be removed.
getSSRType() - Method in class chemaxon.sss.search.SearchOptions
Gets the type of the set of smallest rings to use
getSSSR() - Method in class chemaxon.struc.MoleculeGraph
Gets the Smallest Set of Smallest Ring atom indexes array.
getSSSRBonds() - Method in class chemaxon.struc.MoleculeGraph
Gets the Smallest Set of Smallest Ring bond indexes array.
getSSSRBondsAsBitSet() - Method in class chemaxon.struc.MoleculeGraph
Gets the Smallest Set of Smallest Ring edges as an array of BitSets, one BitSet for each ring.
getSSSRBondSet() - Method in class chemaxon.struc.MoleculeGraph
Get SSSR bond index bitset.
getSSSRBondSetInLong() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of 15.09.2014, use MoleculeGraph.getSSSRBondSet() instead
getSSSRIdxesForAtoms() - Method in class chemaxon.struc.MoleculeGraph
Get the sssr ring indexes in which the atom (specified with it's index) can be located.
getStandardError(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin
 
getStandardized() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Gets the standardized molecule
getStandardizerAction(String, Map<String, String>) - Method in class chemaxon.standardizer.StandardizerActionFactory
This method creates a requested (type represented in actionId) StandardizerAction instance with the give parameters
getStartAt() - Method in class chemaxon.marvin.view.swing.TableOptions
Get the index number of the molecule that is the first to be displayed.
getStartLineCount() - Method in class chemaxon.marvin.io.MRecord
Gets the line number at the starting point.
getStartPos() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the position of the first character.
getStartPosition() - Method in class chemaxon.marvin.io.MRecord
Gets the start position in the input file.
getStartPosition() - Method in class chemaxon.struc.MDocument
Gets the starting position of this document in the input file.
getStartPosition() - Method in class chemaxon.struc.Molecule
Gets the starting position of this molecule in the input file.
getStatus() - Method in class chemaxon.marvin.alignment.Alignment
 
getStepLimit() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
getSteps() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Represented scan steps.
getSteps() - Method in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
 
getStereo(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates absolute stereo configuration of the given atom.
getStereo(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates absolute stereo configuration of the given double bond.
getStereo1(MolAtom) - Method in class chemaxon.struc.MolBond
Gets wedge bond type relative to the specified chiral atom.
getStereo2(int, int, int, int) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans (Z/E) stereo information for the given bond.
getStereo2(MolBond, MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, int, int, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.RgMolecule
 
getStereoActiveAtom() - Method in class chemaxon.struc.StereoActivePart
Get the active atom index.
getStereoActiveParts() - Method in interface chemaxon.struc.CIPStereoDescriptorIface
 
getStereoActiveRef() - Method in class chemaxon.struc.StereoActivePart
 
getStereoCare() - Method in class chemaxon.struc.MolAtom
Reports double bond stereo care information on the connected bonds.
getStereoCenter() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
Returns an optional of stereo centers.
getStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
 
getStereoDoubleBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the number of stereo double bonds.
getStereoFontRatio() - Method in class chemaxon.marvin.MolPrinter
Returns the current ratio of the font size of the stereo label compared to the normal atom label size.
getStereoGroupNumber() - Method in class chemaxon.struc.MolAtom
Gets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
getStereoGroupType() - Method in class chemaxon.struc.MolAtom
Gets the stereochemical group type for the enhanced stereo representation.
getStereoisomer(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns a stereoisomer.
getStereoisomerCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the number of different stereoisomers.
getStereoisomerCount() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
Returns the number of stereoisomers.
getStereoisomers() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns the stereoisomers in a Molecule[] array.
getStereoisomers() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
Returns the list of generated stereoisomers.
getStereoModel() - Method in class chemaxon.sss.search.SearchOptions
Get the stereo model option.
getStereoSearchType() - Method in class chemaxon.sss.search.SearchOptions
Get the stereo search type option.
getStereoValue() - Method in interface chemaxon.struc.CIPStereoDescriptorIface
 
getStericEffectIndex(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.
getStericHindrance(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Calculates hindrance of an atom from covalent radii values and distances.
getStickdst() - Method in class chemaxon.marvin.beans.MSketchPane
Gets the sticking distance.
getStickThickness() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the stick thickness.
getStickThickness() - Method in class chemaxon.marvin.common.UserSettings
Gets the stick diameter for ball and stick mode.
getStickThickness() - Method in class chemaxon.marvin.MolPrinter
Gets the 3D stick's diameter.
getStoichiometry() - Method in class chemaxon.standardizer.actions.ExpandAction
Gets the stoichiometry value of the action
getStoredParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Returns the stored parameters.
getStoredParameters(Properties) - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Returns the stored parameters.
getStrategy() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Returns the strategy to use.
getStrictMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
getStrictReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms and bonds, and the neighbours' neighbouring atoms and bonds.
getString() - Method in class chemaxon.marvin.io.MRecord
Gets the record text as string.
getString() - Method in class chemaxon.struc.graphics.MFont
Gets the string representation.
getString() - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets the text string.
getString(String) - Method in class chemaxon.struc.MPropertyContainer
Deprecated, for removal: This API element is subject to removal in a future version.
getStringFromClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns the String data from the clipboard contents, if the clipboard contains a Transferable that provides support to DataFlavor.stringFlavor
getStructurallogPIncrement() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the structural logP increment.
getStructure() - Method in class chemaxon.standardizer.advancedactions.TransformAction
Deprecated, for removal: This API element is subject to removal in a future version.
getStructure(int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns a structure.
getStructure(int) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns a resonant structure.
getStructure(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns a tautomer.
getStructureCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the number of all enumerated structures, -1 in case of arithmetical overflow (if the number would exceed Long.MAX_VALUE).
getStructureCount() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns the number of different structures.
getStructureCount() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns the number of different resonant structures.
getStructureCount() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the number of different tautomers.
getStructureID() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the structure ID used in Markush code (enumeration ID) generation.
getStructures() - Method in class chemaxon.checkers.result.SubstructureCheckerResult
Returns the structures
getStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the enumerated structures.
getStructures() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns all structures.
getStructures() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns resonant structures in Molecule[] array.
getStructures() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 5.9 replaced by TautomerizationPlugin.getStructure(int)
getStyle() - Method in class chemaxon.struc.graphics.MFont
Gets the font style.
getSubDocument(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
 
getSubFormatPriority(String) - Static method in class chemaxon.formats.MFileFormat
Gets the priority of the specified subformat name.
getSubGraphCount() - Method in class chemaxon.struc.MoleculeGraph
Gets the number of all "submolecules".
getSubGraphCount() - Method in class chemaxon.struc.RgMolecule
Gets the number of all "submolecules".
getSubGraphCount() - Method in class chemaxon.struc.RxnMolecule
Gets the number of all "submolecules".
getSubGraphs() - Method in class chemaxon.struc.MoleculeGraph
Gets all "submolecules".
getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.MoleculeGraph
Gets all "submolecules".
getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RgMolecule
Gets all "submolecules".
getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RxnMolecule
Gets all "submolecules".
getSubLevel() - Method in class chemaxon.struc.graphics.MTextAttributes
Gets the subscript/superscript level.
getSubscript() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the subscript for non-superatom S-groups.
getSubscript() - Method in class chemaxon.struc.Sgroup
Gets the subscript for non-superatom S-groups.
getSubscript() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets the subscript.
getSubstructure() - Method in class chemaxon.descriptors.ECFPFeature
Gets the corresponding substructure as a Molecule object.
getSubType() - Method in class chemaxon.struc.Sgroup
Gets polymer S-group subtype.
getSuperAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the superatom.
getSuperscript() - Method in class chemaxon.struc.Sgroup
Gets the superscript for non-superatom S-groups.
getSuperscript() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets the superscript for Sru S-groups.
getSupportedDescriptors() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider
Returns a set of supported ServiceDescriptor classes.
getSurface() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the surface.
getSurfaceArea() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns the surface area, calculation type is previously set in MSAPlugin.setSurfaceAreaType(int).
getSurfaceArea() - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns the surface area.
getSurfacePrecision() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the grid resolution from which the surface is computed.
getSurfaceSimplificationEnabled() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns true if Surface Simplification is enabled.
getSurfaceSmoothnessFactor() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Surfaces can be smoothed by the following algorithm: Paul Bourke: Surface Relaxation and Smoothing http://astronomy.swin.edu.au/~pbourke/modelling/relax/ This algorithm has a smoothness factor.
getSurfaceThreshold() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the isovalue/threshold of the surface.
getSurfaceType() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns the type of the surface.
getSurfaceType(String) - Static method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
getSurfaceTypeString(int) - Static method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
getSymbol() - Method in class chemaxon.struc.MolAtom
Gets the element symbol.
getSymbol() - Method in class chemaxon.struc.sgroup.SgroupAtom
Gets the abbreviated group symbol.
getSymbol(int) - Method in class chemaxon.descriptors.PFParameters
Gets the symbol associated with the specified Pharmacophore.
getSymbol(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
 
getSymbol(int) - Static method in class chemaxon.struc.PeriodicSystem
Symbol of the element
getSymbolIndex(String) - Method in class chemaxon.descriptors.PFParameters
Gets the index associated with the specified Pharmacophore symbol.
getSymbolTable() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
getSymbolTable() - Method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
getSymmetricFBPA(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the symmetric FBPA convolution product based distasnce of the fingerprint from an other (given as parameter).
getSzegedIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Szeged index of the molecule.
getT(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets a text field value in a GridBagView table.
getT(int, int) - Method in class chemaxon.marvin.view.MDocStorage
Gets a text field in a record.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor
Sets up the editor component.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer
The implementation of this method sets up the rendering component to display the passed-in molecule, and then returns the component.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer
The implementation of this method sets up the rendering component to display the passed-in molecule, and then returns the component.
getTableOptions() - Method in class chemaxon.marvin.view.swing.TableSupport
Gets the table options component.
getTableSupport() - Method in class chemaxon.marvin.beans.MViewPane
Gets an object that helps to build and use a viewer table.
getTableText(String, String[], double[][]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns table in string form.
getTabScale() - Method in class chemaxon.marvin.beans.MViewPane
Gets the magnification in the molecule cells.
getTabScale(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the magnification for a molecule cell.
getTag() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the tag character for footnote display (or space if blank).
getTags() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the tags associated to the action
getTailCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets the tail crossing bonds.
getTanimoto(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the Tanimoto metric.
getTanimoto(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Gets the Tanimoto dissimilarity coefficient.
getTanimoto(ECFP) - Method in class chemaxon.descriptors.ECFP
Calculates the Tanimoto distance.
getTanimoto(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the Tanimoto metric (adapted to hystograms)
getTarget() - Method in class chemaxon.sss.search.MolSearch
 
getTarget() - Method in class chemaxon.sss.search.Search
Retrieves the target molecule.
getTarget() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Gets the target structure.
getTargetAsString(Molecule) - Static method in class chemaxon.sss.search.Search
For internal purposes only.
getTargetGroups() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Gets the target action groups of the standardizer
getTargetHomologyMatchingMode() - Method in class chemaxon.sss.search.SearchOptions
Returns the target homology matching mode.
getTargetToPrint() - Method in class chemaxon.sss.search.Search
For internal purposes only.
getTautomerEqualityMode() - Method in class chemaxon.sss.search.MolSearchOptions
Internal use only.
getTautomerSearch() - Method in class chemaxon.sss.search.SearchOptions
Indicates if tautomers of the query should be enumerated for search.
getTCenter() - Method in class chemaxon.struc.graphics.MRectangle
Gets the transformed point.
getTemplates() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
Gets the template molecules of the clean action
getTemporaryObject(String) - Method in class chemaxon.struc.MolAtom
Gets a temporary object.
getTerminalBondDeletionStyle() - Method in class chemaxon.marvin.common.UserSettings
Gets the terminal bon deletion style.
getText() - Method in class chemaxon.marvin.space.monitor.Label
Returns the explicit text of the label, or null if there is no explicit label set.
getText() - Method in class chemaxon.struc.graphics.MTextBox
Gets the text stored.
getTextAttributesAtCursor() - Method in class chemaxon.struc.graphics.MTextBox
Gets the common attributes of the text on the cursor.
getTextDocument() - Method in class chemaxon.struc.graphics.MTextBox
Gets the text document.
getThickness() - Method in class chemaxon.struc.graphics.MPolyline
Gets the line thickness.
getThreshold() - Method in class chemaxon.descriptors.MDParameters
Gets the threshold value being set for the current parametrized version.
getThreshold() - Method in class chemaxon.descriptors.MolecularDescriptor
Gets threshold value of the current parameterized metric.
getThreshold(int) - Method in class chemaxon.descriptors.MDParameters
Gets a metric dependent threshold value.
getThreshold(int) - Method in class chemaxon.descriptors.MolecularDescriptor
Gets a metric dependent default threshold value.
getThrowable() - Method in interface chemaxon.util.iterator.MoleculeIterator
Deprecated, for removal: This API element is subject to removal in a future version.
Not used. MoleculeIterator.next() throws NoSuchElementException in case of error.
getThrowable() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns the throwable object.
getTimeLimit() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
getTimeLimit() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Gets the maximum allowed MCS search time in milliseconds.
getTimeoutLimitMilliseconds() - Method in class chemaxon.sss.search.SearchOptions
The search on a single target timeouts reaching this amount of time.
getTitle() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns the frame title.
getTitle() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns the frame title.
getToolBar(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Returns the default toolbar for textPane instance NOTE: textPane have to be created with this factory
getToolbarConfigPath() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns the toolbar configuration path
getTop() - Method in class chemaxon.marvin.space.GraphicCell
Returns the y coordinate of the top of the cell.
getTopLeftIndex() - Method in class chemaxon.marvin.beans.MViewPane
Gets the index of the top left cell.
getTopLevelContainer() - Method in class chemaxon.marvin.beans.MarvinPane
 
getTopNode() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This method returns an internal representation which will be hidden in the future. No replacement.
getTopologyConstraint() - Method in class com.chemaxon.search.mcs.buildup.BuildupMcs
Gets the the maximum difference in topology the mapped part of the molecules can have.
getTOption() - Method in class chemaxon.struc.graphics.MRectangle
Gets the transformation options.
getTotalCharge() - Method in class chemaxon.struc.MoleculeGraph
Gets the total (formal) charge of the molecule.
getTotalCharge() - Method in class chemaxon.struc.Sgroup
Calculates the sum of the charge values on the atoms in this S-group.
getTotalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns the total charge of a specified atom.
getTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
getTPSA() - Method in class chemaxon.marvin.calculations.TPSAPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 4.1, replaced by TPSAPlugin.getSurfaceArea()
getTraditionalName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns the traditional IUPAC name.
getTrainingIds() - Static method in class chemaxon.marvin.calculations.logPPlugin
Returns the id's of available logP trainings.
getTransferableFor(Molecule, Properties) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Creates a MTransferable object to the given Molecule with the given properties.
getTransferableFor(Molecule, Properties, String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Creates a MTransferable to the given Molecule with the given properties in the given format.
getTransferData(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Returns the result of the transfer operation.
getTransferDataFlavors() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Returns the DataFlavors supported by the actual implementation.
getTransform() - Method in class chemaxon.standardizer.advancedactions.TransformAction
Gets the transformation molecule of the action
getTransformationCenter() - Method in class chemaxon.marvin.space.GraphicCell
Returns the transformation center.
getTransformationCenter() - Method in class chemaxon.marvin.space.GraphicScene
Returns the center of transformation of the active cell or null if there is no active cell.
getTversky(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the Tversky !!DISSIMILARITY!! index: (1-(commonly used tversky))
getTversky(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the Tversky !!DISSIMILARITY!! index
getTverskyAlpha() - Method in class chemaxon.descriptors.MDParameters
Gets Tversky alpha value for the given parametrized metric.
getTverskyBeta() - Method in class chemaxon.descriptors.MDParameters
Gets Tversky beta value for the given parametrized metric.
getType() - Method in class chemaxon.checkers.AromaticityErrorChecker
Returns the type of the aromatization
getType() - Method in class chemaxon.descriptors.SDParameters
 
getType() - Method in class chemaxon.marvin.services.ServiceArgument
Returns the argument type
getType() - Method in class chemaxon.marvin.util.OptionDescriptor
Gets the option type.
getType() - Method in class chemaxon.sss.search.MarkushFeature
Deprecated.
Returns the feature type.
getType() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
Gets the type of absolute stereo action
getType() - Method in class chemaxon.standardizer.actions.AromatizeAction
Gets the type of aromatization
getType() - Method in class chemaxon.standardizer.actions.ClearStereoAction
Gets the type of the action as string.
getType() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
Gets the type of action
getType() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Gets the type value of the action
getType() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
Gets the type of action
getType() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
Gets the type of action
getType() - Method in class chemaxon.standardizer.advancedactions.TransformAction
Gets the type of transformation
getType() - Method in interface chemaxon.struc.CIPStereoDescriptorIface
 
getType() - Method in class chemaxon.struc.graphics.MBracket
Gets the bracket type.
getType() - Method in class chemaxon.struc.MolBond
Gets the bond type.
getType() - Method in class chemaxon.struc.Sgroup
Gets S-group type.
getType() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Gets the type of enhanced stereo flag.
getType(int) - Method in class chemaxon.descriptors.BCUTParameters
Gets the type of the BCUT descriptor.
getType(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getType(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getType(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Checks whether the atoms in the selection are all in reactants, products or agents.
getType(String) - Static method in enum class chemaxon.struc.SgroupType
Returns an SgroupType for the given short name.
getTypeCount() - Method in class chemaxon.descriptors.BCUTParameters
Gets the count of descriptor types.
getTypes() - Method in class chemaxon.checkers.AtomTypeChecker
Returns the checked atom types
getTypeString(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
getTypeString(Object) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns a string representation of the given type.
getUndefinedRAtom() - Method in class chemaxon.sss.search.SearchOptions
Returns undefined R atom matching behaviour mode.
getUndefinedrsChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets the undefined (r) and (s) stereo centers of the molecule
getUndefinedRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets the undefined (R) and (S) chiral centers of the molecule
getUndo() - Method in class chemaxon.marvin.beans.MSketchPane
Gets the maximum undo depth.
getUnguessableFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
Gets the file format from the file name extension for formats that are not guessable from the file content.
getUnit() - Method in class chemaxon.calculations.dipole.DipoleResult
Returns the dipole moment unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Gets the NMR unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator
Returns NMR spectrum unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the unit type.
getUnits() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the unit of this data field.
getUpperLimit() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
 
getUpperLimit() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
 
getUpperLimit() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
The upper limit of category.
getUsableObject(UOID) - Method in class chemaxon.marvin.space.GraphicComponent
Returns the component that the given UOID identifies.
getUsableObject(UOID) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
 
getUsableObjectId(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
 
getUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Returns the user defined comparators.
getUserSettings() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the user settings object.
getUserTypes() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the user defined result types.
getVagueBondLevel() - Method in class chemaxon.sss.search.SearchOptions
Getter for vague bond level.
getValence() - Method in class chemaxon.struc.MolAtom
Gets the valence.
getValence(int) - Method in interface chemaxon.struc.Smolecule
Gets the valence.
getValenceCheckOptions() - Method in class chemaxon.struc.MoleculeGraph
Returns the options for valence checking.
getValenceCheckOptions() - Method in class chemaxon.struc.RgMolecule
 
getValenceCheckState() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by MoleculeGraph.getValenceCheckOptions() and MoleculeGraph.isValenceCheckEnabled().
Usage:
 // Same as getValenceCheckState() == ValenceCheckState.OFF:
 isValenceCheckEnabled() == true;
 // Same as getValenceCheckState() == ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED:
 getValenceCheckOptions.isLocalAromatic() == true;
 // Same as getValenceCheckState() == ValenceCheckState.FULL:
 getValenceCheckOptions.isLocalAromatic() == false;
             
getValenceProp() - Method in class chemaxon.struc.MolAtom
Gets the valence property.
getValenceProperty(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
getValencePropMinMax() - Method in class chemaxon.struc.MolAtom
Gets the minimum and maximum possible values of the valence property.
getValidationResultLabel(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Returns a JLabel instance, dinamically showing validation result of textPane NOTE: will validate against Molecular Context.
getValidationResultLabel(JTextPane, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Returns a JLabel instance, dinamically showing validation result of textPane NOTE: textPane have to be created with this factory
getValidationResultLabelForReactionContext(JTextPane) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Returns a JLabel instance, dinamically showing validation result of textPane NOTE: will validate against Reaction Context.
getValidSinkAtomPairsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom) .
getValidSinkAtomPairsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond) .
getValidSinkAtomsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom) .
getValidSinkAtomsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond) .
getValidSinkBondsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom) .
getValidSinkBondsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond) .
getValidSourceAtomPairsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtomPairs(Molecule) .
getValidSourceAtomsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtoms(Molecule) .
getValidSourceBondsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceBonds(Molecule) .
getValue() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
getValue() - Method in class chemaxon.marvin.services.ServiceArgument
Returns the argument value
getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 14.9.15, replaced by AtropStereoCenter.getCIPValue().
getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 14.9.15, replaced by AxialStereoCenter.getCIPValue().
getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 14.9.15, replaced by CisTransStereoCenter.getCIPValue().
getValue() - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 14.9.15, replaced by StereoCenter.getCIPValue().
getValue() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 14.9.15, replaced by TetrahedralStereoCenter.getCIPValue().
getValueAsObject() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
getValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns the value of the NMR spectrum function at a given x point.
getVanDerWaalsRadius(int) - Static method in class chemaxon.struc.PeriodicSystem
Van der Waals radius of the element in Angstroms.
getVariable(String) - Method in interface chemaxon.jep.ChemContext
Returns the value of a variable.
getVDWSA() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns van der Waals surface area.
getVerboseLevel() - Method in class chemaxon.marvin.space.GraphicCell
Gets the verbose level.
getVerboseLevel() - Method in class chemaxon.marvin.space.GraphicScene
Gets the verbose level.
getVersion() - Static method in class com.chemaxon.version.VersionInfo
Returns the product version.
getVertexCount() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the number of allocated vertices in the SurfaceComponent.
getVertexX(int) - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the x coordinate of the ith vertex.
getVertexY(int) - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the y coordinate of the ith vertex.
getVertexZ(int) - Method in class chemaxon.marvin.space.SurfaceComponent
Returns the z coordinate of the ith vertex.
getVerticalAlignment() - Method in class chemaxon.struc.graphics.MTextBox
Gets the vertical alignment.
getViewAnyBond() - Method in class chemaxon.marvin.common.UserSettings
Gets the default any bond drawing style in the viewer.
getViewCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings
Gets the default carbon displaying style in the viewer.
getViewColorScheme() - Method in class chemaxon.marvin.common.UserSettings
Gets the viewer's default color scheme.
getViewHandlerType() - Method in class chemaxon.marvin.view.swing.TableOptions
Gets the view handler type.
getViewImplicitH() - Method in class chemaxon.marvin.common.UserSettings
Gets the display method of implicit hydrogens for the viewer.
getViewLayout() - Method in class chemaxon.marvin.common.UserSettings
Gets the table layout of the Viewer.
getViewLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings
Gets the default ligand order displaying style in the viewer.
getViewLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
Based on the preferences this funtion returns the proper working directory for the MarvinView application's load filechooser.
getViewMolbg2d() - Method in class chemaxon.marvin.common.UserSettings
Gets the viewer's default molecule background color for 2D.
getViewMolbg3d() - Method in class chemaxon.marvin.common.UserSettings
Gets the viewer's default molecule background color for 3D.
getViewNavmode2d() - Method in class chemaxon.marvin.common.UserSettings
Gets the navigation mode for the 2D viewer.
getViewNavmode3d() - Method in class chemaxon.marvin.common.UserSettings
Gets the navigation mode for the 3D viewer.
getViewportHeight() - Method in class chemaxon.marvin.space.GraphicScene
Returns the phisical height of the viewport.
getViewportWidth() - Method in class chemaxon.marvin.space.GraphicScene
Returns the phisical width of the viewport.
getViewRecentFileList() - Method in class chemaxon.marvin.common.UserSettings
Gets the recent files' list in MarvinView, the last item is the most recent.
getViewRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings
Gets the recent file list requested size, based on a preferences setting
getViewRendering2d() - Method in class chemaxon.marvin.common.UserSettings
Gets the rendering style for the 2D viewer.
getViewRendering3d() - Method in class chemaxon.marvin.common.UserSettings
Gets the rendering style for the 3D viewer.
getViewSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings
Not implemented yet, don't use it.
getVisibleAtomCount() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
getVisibleAtomCount() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the number of atoms currently visible.
getVisibleButtonB(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the i-th button in the visible area of the viewer.
getVisibleButtonC(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the i-th checkbox in the visible area of the viewer.
getVisibleCellComponent(int) - Method in class chemaxon.marvin.beans.MViewPane
Gets the canvas of the specified cell in a GridBag layout based table.
getVisibleCellCount() - Method in class chemaxon.marvin.beans.MViewPane
Gets the number of the visible cells in a GridBag layout based table.
getVisibleCellIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
Determines the visible cell index of a cell
getVisibleCoords(MolAtom) - Method in class chemaxon.struc.Molecule
Returns the coordinates of the given atom (contained in the molecule).
getVisibleCoords(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Returns the coordinates of the given atom (contained in the molecule).
getVisiblePointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
Gets an internal selectable point of the rectangle.that is visible when highlighting.
getVisiblePointRefCount() - Method in class chemaxon.struc.graphics.MBracket
Gets the number of internal selectable point references that are visible when highlighting.
getVisualizable() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getVolume() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
getVolume() - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
getVolumeScore() - Method in class chemaxon.marvin.alignment.Alignment
Calculates the volume score between the current orientation and conformation of the two molecules.
getVolumeTanimoto() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
getWarningMessage() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns a warning message if there are no conformers, null otherwise.
getWarningMessage() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns a warning message if lowest energy conformer calculation was unsuccessful or aborted by user, null otherwise.
getWarningMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns the calculation warning information message if no H-bond donor/acceptor atoms found, returns the empty string otherwise.
getWarningMessage() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns the calculation warning information message if no isoelectric point exists, returns the empty string otherwise.
getWarningMessage() - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the calculation warning message.
getWarningMessage() - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the calculation warning message.
getWarningMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns a warning message if there are no stereoisomers, null otherwise.
getWarningMessage() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
getWarningMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the calculation warning information message.
getWebServiceName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Returns the service name
getWeightedAsymmetricEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the weighted asymmetric Euclidean distance.
getWeightedAsymmetricEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Calculates the weighted asymmetric Euclidean distance.
getWeightedAsymmetricEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP
Calculates the weighted asymmetric Euclidean distance.
getWeightedAsymmetricEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the weighted asymmetric Euclidean distance.
getWeightedEuclidean(BCUT) - Method in class chemaxon.descriptors.BCUT
Calculates the weighted Euclidean distance.
getWeightedEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Calculates the weighted Euclidean distance.
getWeightedEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor
Calculates the weighted Euclidean distance.
getWeightedEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP
Calculates the weighted Euclidean distance.
getWeightedEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the weighted Euclidean distance.
getWeights() - Method in class chemaxon.descriptors.MDParameters
Gets all weights for the given parametrized metric.
getWeights() - Method in class chemaxon.struc.graphics.MAtomSetPoint
Gets the atom weights used in average location calculation.
getWidth() - Method in class chemaxon.marvin.space.GraphicCell
Returns the width of the cell.
getWienerIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
getWienerPolarity() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.
getWinScale() - Method in class chemaxon.marvin.beans.MViewPane
Gets the magnification in the zoom windows.
getWireThickness() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the line thickness for wireframe mode.
getWireThickness() - Method in class chemaxon.marvin.common.UserSettings
Gets the bond thickness in wireframe mode.
getWireThickness() - Method in class chemaxon.marvin.MolPrinter
Gets the line thickness for wireframe mode.
getWord(ByteBuffer, int) - Method in class chemaxon.marvin.io.PositionedInputStream
 
getWorkOnBackGround() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns whether the subsystem works on the current thread or on a background thread.
getWrapperException(Exception) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Returns a wrapper exception to be returned.
getWrapperException(Exception) - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Returns a wrapper exception to be returned.
getWrongLengthBonds() - Method in class chemaxon.checkers.result.BondLengthCheckerResult
Returns the internal representation of the bond length checker result, which contains all information required to fix bond length errors.
getWsdlURI() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Returns the WSDL URI
getX() - Method in class chemaxon.struc.MolAtom
Gets the X coordinate.
getX() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the X coordinate.
getX(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getX(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getXMLTokens() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Gets the XML tokens of the action
getXState() - Method in class chemaxon.struc.Sgroup
Gets the expanded/contracted state.
getY() - Method in class chemaxon.struc.MolAtom
Gets the Y coordinate.
getY() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets the Y coordinate.
getY(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getY(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getZ() - Method in class chemaxon.struc.MolAtom
Gets the Z coordinate.
getZ(int) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
getZ(int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
getZCoordinateTo2DPart() - Method in class chemaxon.marvin.space.GraphicComponent
Returns a third, z coordinate in order to display 2D parts in proper order.
getZCoordinateTo2DPart() - Method in class chemaxon.marvin.space.monitor.Label
Returns a third, z coordinate in order to display 2D parts in proper order.
gFuzzyIncrements - Variable in class chemaxon.descriptors.PFParameters
Fuzzy smoothing values for gaussian smoothing.
gl - Variable in class chemaxon.marvin.space.GraphicComponent
must be accessible in derived classes
glColor() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the default/constant color of the component for drawing.
GLInfo - Static variable in class chemaxon.marvin.space.GraphicScene
 
GLOBAL - Static variable in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
An options object with ValenceCheckOptions.isLocalAromatic() returning false and ValenceCheckOptions.isTraditionalNitrogensAllowed() returning true.
GlobalLocationControl - Class in chemaxon.marvin.space.monitor
This control is to change the location say translate a GraphicComponent in the global coordinate system.
GlobalLocationControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.GlobalLocationControl
Creates a new instance of GlobalLocationControl
GlobalOrientationControl - Class in chemaxon.marvin.space.monitor
This control is to change the orientation say rotate a GraphicComponent in the global coordinate system.
GlobalOrientationControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.GlobalOrientationControl
Creates a new instance of GlobalOrientationControl
gltext - Variable in class chemaxon.marvin.space.monitor.Label
This is to draw labels in the viewing plane.
glu - Variable in class chemaxon.marvin.space.GraphicComponent
 
GRAFT - Enum constant in enum class chemaxon.struc.SgroupType
 
GRAPH_INVARIANTS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "grinv".
GRAPH_INVARIANTS_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "grinvVisible".
graphicCell - Variable in class chemaxon.marvin.space.GraphicComponent
which cell of the scene is this component displayed in
GraphicCell - Class in chemaxon.marvin.space
GraphicCell is a rectangular part of the OpenGL2 canvas containing GraphicComponents.
GraphicCell() - Constructor for class chemaxon.marvin.space.GraphicCell
Creates a new instance of GraphicCell.
GraphicCell(GL2, GLU) - Constructor for class chemaxon.marvin.space.GraphicCell
Creates a new instance of GraphicCell.
GraphicComponent - Class in chemaxon.marvin.space
GraphicComponents are the basic objects what MarvinSpace can visualize and handle.
GraphicComponent() - Constructor for class chemaxon.marvin.space.GraphicComponent
Creates an empty object.
GraphicScene - Class in chemaxon.marvin.space
GraphicScene is the main "entry point" to MarvinSpace.
GraphicScene() - Constructor for class chemaxon.marvin.space.GraphicScene
Creates a hardware accelerated and double buffered GraphicScene.
GraphicScene(int, int) - Constructor for class chemaxon.marvin.space.GraphicScene
Creates a hardware accelerated and double buffered GraphicScene.
graphInvariant() - Method in class chemaxon.calculations.stereo.Stereochemistry
 
graphInvariant() - Method in class chemaxon.calculations.TopologyAnalyser
 
GRID_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by mapping values form a grid to the surface.
GRID_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: sketchGridVisible property.
GRINV_DONT_STORE - Static variable in class chemaxon.struc.MoleculeGraph
Graph invariant option to instruct that the graph invariant should not be stored in MoleculeGraph.
GRINV_NOHYDROGEN - Static variable in class chemaxon.struc.MoleculeGraph
Graph invariant option for ignoring explicit hydrogens.
GRINV_OLDSTEREO - Static variable in class chemaxon.struc.MoleculeGraph
Graph invariant option for calculating graph invariants using the old stereo method.
GRINV_STEREO - Static variable in class chemaxon.struc.MoleculeGraph
Graph invariant option for calculating graph invariants using stereo information.
GRINV_USEMAPS - Static variable in class chemaxon.struc.MoleculeGraph
Graph invariant option for calculating graph invariants considering atom maps also.
GRINV_VALUE_OPTIONS - Static variable in class chemaxon.struc.MoleculeGraph
Unified mask of graph invariant options affecting grinv value.
grinvCC - Variable in class chemaxon.struc.MoleculeGraph
Graph invariant change count.
GROUP_END_TOKEN - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
End of group list token of the action string
GROUP_LIST_KEY - Static variable in class chemaxon.standardizer.advancedactions.CreateGroupAction
Property key for group list modification
GROUP_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Group entry separator token of the action string
GROUP_START_TOKEN - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Start of group list token of the action string
GroupDefinition - Class in chemaxon.standardizer.advancedactions
Pattern of a group.
GroupDefinition() - Constructor for class chemaxon.standardizer.advancedactions.GroupDefinition
Creates an empty group pattern.
GroupDefinition(String, Molecule) - Constructor for class chemaxon.standardizer.advancedactions.GroupDefinition
Creates a new group pattern.
GROUPED_DOTDISCONNECTED_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "groupeddotdisconnectedformula".
GROUPTYPE_ALTERNATING_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_ANYPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_BLOCK_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_COMPONENT_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_CROSSLINK_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_GENERIC_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_GRAFT_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_MER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_MODIFICATION_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_MONOMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_MULTIPLE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_ORDERED_MIXTURE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_RANDOM_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_RANGE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_SRU_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_SUPERATOM_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
GROUPTYPE_UNORDERED_MIXTURE_GROUP - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
guessFormat(String) - Method in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated.
 
guessFormat(String) - Method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
 
guessFormat(String) - Method in class chemaxon.formats.recognizer.Recognizer
Tries to guess the format of the given line.
guessFormat(String) - Method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated.
MODIFIING THIS METHOD REQUIRES TO UPDATE THE SMILESRecognizer.tryToRecognize(String, int) METHOD AS WELL!!
guessPeptideFormat(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
GZIP - Static variable in class chemaxon.formats.MFileFormat
GZIP compressed file.

H

H - Static variable in class chemaxon.core.ChemConst
 
H - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
H_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator
Name of the 1H chemical shift atom property.
H1 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
1H NMR
HA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
Number of heavy atoms.
HAcc - Class in chemaxon.descriptors.scalars
Implements hydrogen bond acceptor atom count as a scalar descriptor.
HAcc() - Constructor for class chemaxon.descriptors.scalars.HAcc
Creates a new, empty HAcc descriptor.
HAcc(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.HAcc
Copy constructor.
HAcc(HBParameters) - Constructor for class chemaxon.descriptors.scalars.HAcc
Creates a new instance according to the parameters given.
HAcc(String) - Constructor for class chemaxon.descriptors.scalars.HAcc
Creates a new instance according to the parameters given.
HALT - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
Halts standardization process in case of standardization error
HaltOnErrorOption - Enum Class in chemaxon.sss.search.options
Option type describing the error handling behaviour.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ChargePlugin
 
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
This plugin handles multifrag molecules.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if the plugin handles multifragment molecules, false otherwise.
hararyIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
has2DPart() - Method in class chemaxon.marvin.space.GraphicComponent
Returns true, if the component resets the projection matrix in its draw method, so that the component is drawn in plane.
has2DPart() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns true if any of its visualizers have 2D part.
has2DPart() - Method in class chemaxon.marvin.space.monitor.Label
Returns true when the label is drawn in plane.
has2DPart() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns true, because the Control is always drawn in plane.
hasAlternativeName() - Method in class chemaxon.struc.sgroup.SgroupAtom
Checks whether there is an alternative name at all.
hasAromaticBond() - Method in class chemaxon.struc.MolAtom
Tests whether the atom has aromatic bonds.
hasAtom(MolAtom) - Method in class chemaxon.struc.Sgroup
Is the specified atom an element of this group?
hasAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Is the specified atom an element of this group?
hasAtomSet() - Method in class chemaxon.struc.Molecule
 
hasAtomSet() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the molecule graph has atom sets.
hasAtomSet() - Method in class chemaxon.struc.RgMolecule
Tests whether the molecule graph has atom sets.
hasAtomSet() - Method in class chemaxon.struc.RxnMolecule
Tests whether the molecule graph has atom sets.
HasAttachedDataFilter - Class in com.chemaxon.calculations.stereoanal.filters
Filter stereo centers which contains attached data.
HasAttachedDataFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter
 
hasBackground() - Method in class chemaxon.struc.graphics.MBracket
A bracket has no background.
hasBackground() - Method in class chemaxon.struc.graphics.MPolyline
A polyline has a background only if it is closed.
hasBackground() - Method in class chemaxon.struc.graphics.MTextBox
A text box has a background always.
hasBackground() - Method in class chemaxon.struc.MObject
Can the object have a background?
hasBondSet() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the molecule graph has atom sets.
hasBondSet() - Method in class chemaxon.struc.RgMolecule
Tests whether the molecule graph has atom sets.
hasBondSet() - Method in class chemaxon.struc.RxnMolecule
Tests whether the molecule graph has atom sets.
hasBrackets() - Method in class chemaxon.struc.sgroup.DataSgroup
Brackets are painted if mouse runs over sgroup atoms.
hasBrackets() - Method in class chemaxon.struc.Sgroup
Checks if brackets should be painted or not.
hasBrackets() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Does a bracket belong to this sgroup?
hasBrackets() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks if brackets should be painted or not.
hasChangesInUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Used in initializing searches.
hasCharge() - Method in class chemaxon.struc.MolAtom
 
hasColor() - Method in class chemaxon.struc.graphics.MPolyline
A polyline does not have a non-line, non-background color.
hasColor() - Method in class chemaxon.struc.graphics.MTextBox
A text box has a text color.
hasColor() - Method in class chemaxon.struc.MObject
Can the object have a color (non-line and non-background)?
hasContractedSgroup() - Method in class chemaxon.struc.Molecule
Tests if the molecule has contracted S-groups or not.
hasControl() - Method in class chemaxon.marvin.space.monitor.Monitor
Returns true if the monitor has a control.
hasElectronContainer(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
hasElectrons() - Method in class chemaxon.struc.MDocument
Returns whether MDocument contains any electrons.
hasError() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
hasExplicitLonePairs() - Method in class chemaxon.struc.MDocument
Returns true if the MDocument has any electrons drawn by the user.
hasExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
hasExtraLabelSet() - Method in class chemaxon.struc.MoleculeGraph
 
hasFace() - Method in class chemaxon.struc.graphics.MPolyline
Is it 2 dimensional?
hasFace() - Method in class chemaxon.struc.graphics.MTextBox
Is it 2 dimensional?
hashCode() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
 
hashCode() - Method in class chemaxon.checkers.AbstractStructureChecker
 
hashCode() - Method in class chemaxon.checkers.AromaticityErrorChecker
 
hashCode() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
hashCode() - Method in class chemaxon.checkers.AttachedDataChecker
 
hashCode() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
 
hashCode() - Method in class chemaxon.checkers.result.AromaticityCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.BondAngleCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.BondLengthCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
 
hashCode() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.ReactionCheckerResult
Deprecated.
 
hashCode() - Method in class chemaxon.checkers.result.RgroupCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.SgroupCheckerResult
 
hashCode() - Method in class chemaxon.checkers.result.SubstructureCheckerResult
 
hashCode() - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
hashCode() - Method in class chemaxon.checkers.ValencePropertyChecker
 
hashCode() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
 
hashCode() - Method in class chemaxon.fixers.StructureFixerDescriptor
 
hashCode() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
 
hashCode() - Method in class chemaxon.marvin.space.ComponentElement
 
hashCode() - Method in class chemaxon.sss.search.MarkushFeature
Deprecated.
 
hashCode() - Method in class chemaxon.sss.search.SearchHit
 
hashCode() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
hashCode() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
 
hashCode() - Method in class chemaxon.struc.AtropStereoDescriptor
 
hashCode() - Method in class chemaxon.struc.AxialStereoDescriptor
 
hashCode() - Method in class chemaxon.struc.CisTransStereoDescriptor
 
hashCode() - Method in class chemaxon.struc.CTransform3D
 
hashCode() - Method in class chemaxon.struc.DPoint3
 
hashCode() - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
hashCode() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
hashCode() - Method in class chemaxon.struc.graphics.MFont
 
hashCode() - Method in class chemaxon.struc.graphics.MMidPoint
 
hashCode() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
hashCode() - Method in class chemaxon.struc.graphics.MTextAttributes
 
hashCode() - Method in class chemaxon.struc.MPoint
 
hashCode() - Method in class chemaxon.struc.prop.MBooleanProp
 
hashCode() - Method in class chemaxon.struc.prop.MCollectionProp
 
hashCode() - Method in class chemaxon.struc.prop.MDoubleArrayProp
 
hashCode() - Method in class chemaxon.struc.prop.MDoubleProp
 
hashCode() - Method in class chemaxon.struc.prop.MHashProp
 
hashCode() - Method in class chemaxon.struc.prop.MHCoords3DProp
 
hashCode() - Method in class chemaxon.struc.prop.MIntegerArrayProp
 
hashCode() - Method in class chemaxon.struc.prop.MIntegerProp
 
hashCode() - Method in class chemaxon.struc.prop.MListProp
 
hashCode() - Method in class chemaxon.struc.prop.MMoleculeProp
 
hashCode() - Method in class chemaxon.struc.prop.MObjectProp
 
hashCode() - Method in class chemaxon.struc.prop.MStringProp
 
hashCode() - Method in class chemaxon.struc.StereoActivePart
 
hashCode() - Method in class chemaxon.struc.TetrahedralStereoDescriptor
 
HashCode - Class in chemaxon.sss.screen
Hash code generator for molecules.
HashCode() - Constructor for class chemaxon.sss.screen.HashCode
Creates a new instance of HashCode
HASHED - Static variable in class chemaxon.struc.MolBond
"Hashed" attribute of the bond.
hasId(String) - Method in class chemaxon.struc.Molecule
 
hasImplicitH() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the molecule has implicit hydrogen atoms.
hasInvisibleItem() - Method in class chemaxon.marvin.space.monitor.Label
Tells weather the label should or should not be drawn.
hasInvisibleItem() - Method in class chemaxon.marvin.space.monitor.Monitor
Retruns true if any of the selected elements is hidden.
hasLineColor() - Method in class chemaxon.struc.graphics.MPolyline
A polyline have a line color always.
hasLineColor() - Method in class chemaxon.struc.MObject
Can the object have a line color?
hasMoreStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns true if there are more structures.
hasNext() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
Returns true if there are more molecules, false if end has been reached.
hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator
Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator
Decides whether the iteration has more element.
hasNext() - Method in interface chemaxon.util.iterator.MoleculeIterator
Tests whether the iteration has more elements.
hasNext() - Method in class com.chemaxon.calculations.util.CloseableLineIterator
Deprecated.
 
hasNextResult() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Returns whether there are more results available.
hasNonCoordinateBond() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Decides whether the central atom of the sgroup has a non-coordinate bond.
hasOrder(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
hasOutline() - Method in class chemaxon.struc.graphics.MPolyline
Does it have an outline?
hasParameters(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Returns true if plugin has parameter panel, false otherwise.
hasQProps() - Method in class chemaxon.struc.MolAtom
Does it have query properties?
hasQueryBonds() - Method in class chemaxon.struc.MolAtom
Tests whether the atom has query bonds ("ANY" bonds).
hasRadicals() - Method in class chemaxon.struc.MDocument
Returns true if the MDocument has any Radical Electrons.
hasRgroupContainedBy(Set<?>) - Method in class chemaxon.struc.RgMolecule
Tests whether the molecule has an R-group that is a subset of the specified set of atoms.
hasRichText() - Method in class chemaxon.struc.graphics.MTextBox
Tests whether the document is rich text.
hasSameCharge(int) - Method in class chemaxon.struc.MolAtom
 
hasSelectedComponent() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if there is at least 1 selected component.
hasSelectedComponent() - Method in class chemaxon.marvin.space.GraphicScene
Returns true if there is at least 1 selected component in the active cell.
hasSelectedComponentElement() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if there is at least 1 component with a selected part.
hasSelectedComponentElement() - Method in class chemaxon.marvin.space.GraphicScene
Returns true if there is at least 1 selected ComponentElement in the active cell.
hasSelectedElements() - Method in class chemaxon.marvin.space.GraphicComponent
Tells whether the component has some selected parts.
hasSelectedElements() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns true if any of its visualizers have any selected part.
hasSelectedElements() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if the component has any selected part.
hasSelection() - Method in class chemaxon.struc.graphics.MChemicalStruct
Checks the existence of the selection.
hasSelection() - Method in class chemaxon.struc.graphics.MTextBox
Checks the existence of the selection.
hasSelection(MoleculeGraph) - Static method in class chemaxon.struc.graphics.MChemicalStruct
Checks the existence of the selection.
hasSelfReferringProperty() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the property list contains the molecule.
hasSMARTSProps() - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
hasSMARTSProps(MolAtom) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Tests whether it is a SMARTS query atom.
hasSMARTSPropsExcluding(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Tests whether it is a SMARTS query atom.
hasSMARTSPropsExcluding(String) - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
hasTautomers(Molecule) - Static method in class chemaxon.marvin.calculations.TautomerizationPlugin
Returns if a molecule has tautomers.
hasTransparentPart() - Method in class chemaxon.marvin.space.GraphicComponent
Returns true if a component has transparent part to draw.
hasTransparentPart() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns true if any of its visualizers have transparent part.
hasTransparentPart() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
hasTransparentPart() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns true if the drawing type of the molecular surface was MESH_TYPE or TRANSPARENT_TYPE.
hasTransparentPart() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if antialiased lines are drawn, that is in DRAW_TYPE_WIRE or DRAW_TYPE_BALL_AND_WIRE mode.
hasTransparentPart() - Method in class chemaxon.marvin.space.monitor.Label
The label is rendered as a transparent object in case of drawing in space.
hasTransparentPart() - Method in class chemaxon.marvin.space.monitor.Monitor
In wire mode (now only this is available) monitors are drawn with blending enabled.
hasTransparentPart() - Method in class chemaxon.marvin.space.PharmacophoreArrow
hasTransparentPart() - Method in class chemaxon.marvin.space.PharmacophorePoint
Checks is component has transparent part.
hasTransparentPart() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns true if the drawing type is MESH_TYPE or TRANSPARENT_TYPE.
hasUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Gets whether searcher has user defined comparators.
hasValenceError() - Method in class chemaxon.struc.MolAtom
Returns previously set valence error.
hasValenceError() - Method in class chemaxon.struc.MoleculeGraph
Determines if this molecule has a valence error on any of its atoms.
hasValenceError() - Method in class chemaxon.struc.sgroup.SgroupAtom
Checks if any atom of the Sgroup has a valence error.
hasValidConformer() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Returns true if the input molecule has a valid conformer (has a valid structure in 3D space).
hasWedgedBond() - Method in class chemaxon.struc.MolAtom
Tests whether the atom has a wedged bond.
hasWiggly(MolAtom) - Static method in class chemaxon.marvin.util.CleanUtil
Check if at least one wiggly bond starts from this atom.
haveEqualProperties(MolAtom) - Method in class chemaxon.struc.MolAtom
Tests if two atoms have the same properties.
haveEqualProperties(MolBond) - Method in class chemaxon.struc.MolBond
Tests whether two bonds have the same properties.
haveEqualProperties(MolBond) - Method in class chemaxon.struc.QueryBond
Checks if two bonds have the same properties.
haveSimilarBonds(MolAtom) - Method in class chemaxon.struc.MolAtom
Checks if two atoms have similar bonds.
HBD - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Number of hydrogen-bond donors.
HBDA - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
HBDA_MICROSPECIES - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
HBDA_PLUGIN - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: HBDA Plugin
HBDAPlugin - Class in chemaxon.marvin.calculations
Plugin class for H bond acceptor/donor calculation.
HBDAPlugin() - Constructor for class chemaxon.marvin.calculations.HBDAPlugin
Constructor.
HBONDED_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom wtih a MolBond.HYDROGEN bond on it.
HBParameters - Class in chemaxon.descriptors.scalars
Manages parameters for the HDon and HAcc scalar descriptor classes.
HBParameters() - Constructor for class chemaxon.descriptors.scalars.HBParameters
Creates an empty object.
HBParameters(File) - Constructor for class chemaxon.descriptors.scalars.HBParameters
Creates a new object based on a given configuration file.
HBParameters(String) - Constructor for class chemaxon.descriptors.scalars.HBParameters
Creates a new object based on a given configuration string.
hc - Variable in class chemaxon.marvin.space.MoleculeComponent
 
HCONNECTED_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom(s) connected to another hydrogen only.
HCOUNT_MATCHING_AUTO - Static variable in interface chemaxon.sss.SearchConstants
Default option for H count matching (setHCountMatching).
HCOUNT_MATCHING_EQUAL - Static variable in interface chemaxon.sss.SearchConstants
Option for H count matching.
HCOUNT_MATCHING_GREATER_OR_EQUAL - Static variable in interface chemaxon.sss.SearchConstants
Option for H count matching.
HDon - Class in chemaxon.descriptors.scalars
Implements hidrogen bond donor atom count as a scalar descriptor.
HDon() - Constructor for class chemaxon.descriptors.scalars.HDon
Creates a new, empty HDon descriptor.
HDon(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.HDon
Copy constructor.
HDon(HBParameters) - Constructor for class chemaxon.descriptors.scalars.HDon
Creates a new instance according to the parameters given.
HDon(String) - Constructor for class chemaxon.descriptors.scalars.HDon
Creates a new instance according to the parameters given.
He - Static variable in class chemaxon.core.ChemConst
 
HEAD - Static variable in class chemaxon.struc.graphics.MPolyline
Arrow head.
Heavy - Class in chemaxon.descriptors.scalars
Implements HeavyAtomCount (number of non-hydrogen atoms) as a scalar descriptor.
Heavy() - Constructor for class chemaxon.descriptors.scalars.Heavy
Creates a new, empty logD descriptor.
Heavy(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.Heavy
Copy constructor.
Heavy(SDParameters) - Constructor for class chemaxon.descriptors.scalars.Heavy
Creates a new instance according to the parameters given.
Heavy(String) - Constructor for class chemaxon.descriptors.scalars.Heavy
Creates a new instance according to the parameters given.
HEAVYATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Heavy atom count of the molecule
heavyAtomLimit(int) - Static method in interface chemaxon.calculator.CalculatorInputChecker
Creates a new input checker that only accepts molecules with at most the given number of heavy atoms.
help - Variable in class chemaxon.checkers.StructureCheckOptions
Help needs to be printed.
HELP_TEXT - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
help text for checker
HELP_TEXT - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
help text for action
helpCheckerAction - Variable in class chemaxon.checkers.StructureCheckOptions
Checker action help needs to be printed.
helpFixerAction - Variable in class chemaxon.checkers.StructureCheckOptions
Fixer action help needs to be printed.
helpText() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the help text of the checker
helpText() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the help text of the action
HergActivityPredictor - Class in com.chemaxon.calculations.admet
hERG activity predictor.
HergClass - Enum Class in com.chemaxon.calculations.admet
The possible values of hERG class prediction.
HergClassPredictor - Class in com.chemaxon.calculations.admet
hERG class predictor.
HETERO - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the hetero any atom Q.
heteroaliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
heteroaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaliphaticRingCount()
heteroaliphaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaliphaticRingCount(int)
heteroaliphaticRings() - Method in class chemaxon.calculations.Ring
Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
heteroaliphaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaliphaticRings()
heteroaliphaticRings(int) - Method in class chemaxon.calculations.Ring
Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaliphaticRings(int)
heteroaromaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing non-carbon atoms).
heteroaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaromaticRingCount()
heteroaromaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaromaticRingCount(int)
heteroaromaticRings() - Method in class chemaxon.calculations.Ring
Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).
heteroaromaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaromaticRings()
heteroaromaticRings(int) - Method in class chemaxon.calculations.Ring
Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroaromaticRings(int)
heteroRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
heteroRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroRingCount()
heteroRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
heteroRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroRingCount(int)
heteroRings() - Method in class chemaxon.calculations.Ring
Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
heteroRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroRings()
heteroRings(int) - Method in class chemaxon.calculations.Ring
Indentifies hetero rings in the molecule having a given size (number of atoms).
heteroRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.heteroRings(int)
Hf - Static variable in class chemaxon.core.ChemConst
 
Hg - Static variable in class chemaxon.core.ChemConst
 
HIDDEN - Static variable in class chemaxon.struc.sgroup.DataSgroup
Specifies that the data sgroup is hidden.
hideAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicCell
Sets all components of the given class to invisible.
hideAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
Sets all components of the given class in the active cell to be invisible.
hideAllMonitors() - Method in class chemaxon.marvin.space.GraphicCell
Sets all monitor type components (labels as well) to invisible.
hideAllMonitors() - Method in class chemaxon.marvin.space.GraphicScene
Sets all monitor component of the active cell to invisible.
hideSelected() - Method in class chemaxon.marvin.space.GraphicComponent
If the component is selected it will become hidden.
hideSelected() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The selected visualizers will be hidden.
hideSelected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
hideSelected() - Method in class chemaxon.marvin.space.MoleculeComponent
The selected atoms will be hidden.
hideSelectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all selected components to invisible.
hideSelectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Hides all selected components from the active cell with all related components (connected monitors, surface of a molecule).
hideUnselected() - Method in class chemaxon.marvin.space.GraphicComponent
If the component is unselected it will become hidden.
hideUnselected() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The unselected visualizers will be hidden.
hideUnselected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
hideUnselected() - Method in class chemaxon.marvin.space.MoleculeComponent
The unselected atoms will be hidden.
hideUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all selected components to invisible.
hideUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Hides all unselected components from the active cell with all related components (connected monitors, surface of a molecule).
hierarchize() - Method in class chemaxon.struc.MPropertyContainer
Converts hierarchically specified RDF properties to MListProp and MHashProp objects.
HIGH - Enum constant in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
High solubility.
HIGH_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
high priority value
HIGHEST_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
the highest priority value
highestEigenvalues - Variable in class chemaxon.descriptors.BCUT
 
highlight(MObject) - Method in class chemaxon.struc.MDocument
Highlight an object.
highPrecisions - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
HIT_EXCLUDEDQ - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting excluded query atom.
HIT_LP - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting isolated lone-pair match.
HIT_MULTICENTER - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting multicenter atoms in query.
HIT_NON_R - Static variable in interface chemaxon.sss.SearchConstants
Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.
HIT_ORDERING_NONE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
HIT_R - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting R-node matches in case of R-group search.
HIT_R_EMPTY_MATCH - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting R-node empty match.
HIT_UNMAPABLE - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting unmapable atoms in query (e.g.
HlbPlugin - Interface in chemaxon.marvin.calculations
Calculates hydrophilic-lipophilic balance (HLB) of a molecule.
HlbPlugin.Builder - Class in chemaxon.marvin.calculations
Builder class for HlbPlugin.
Ho - Static variable in class chemaxon.core.ChemConst
 
HomologyTranslationOption - Enum Class in chemaxon.sss.search.options
Option type describing the scope of homology matching.
Hs - Static variable in class chemaxon.core.ChemConst
 
HS_S - Static variable in interface chemaxon.struc.HybridizationStateConsts
S hybridization state.
HS_S - Static variable in class chemaxon.struc.MolAtom
S hybridization state.
HS_SP - Static variable in interface chemaxon.struc.HybridizationStateConsts
SP hybridization state.
HS_SP - Static variable in class chemaxon.struc.MolAtom
SP hybridization state.
HS_SP2 - Static variable in interface chemaxon.struc.HybridizationStateConsts
SP2 hybridization state.
HS_SP2 - Static variable in class chemaxon.struc.MolAtom
SP2 hybridization state.
HS_SP3 - Static variable in interface chemaxon.struc.HybridizationStateConsts
SP3 hybridization state.
HS_SP3 - Static variable in class chemaxon.struc.MolAtom
SP3 hybridization state.
HS_UNKNOWN - Static variable in interface chemaxon.struc.HybridizationStateConsts
Unknown hybridization state.
HS_UNKNOWN - Static variable in class chemaxon.struc.MolAtom
Unknown hybridization state.
HTML - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
 
HTML - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Property display type: display in html text.
HTTPServiceDescriptor - Class in chemaxon.marvin.services.httpservice
HTTP Request based ServiceDescriptor implementation for HTTP POST/GET based services
HTTPServiceDescriptor() - Constructor for class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
HUCKEL_ANALYSIS_PLUGIN - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Huckel Analysis Plugin
HuckelAnalysisPlugin - Class in chemaxon.marvin.calculations
Plugin class for Huckel Analysis calculation.
HuckelAnalysisPlugin() - Constructor for class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Constructor.
HybridizationStateConsts - Interface in chemaxon.struc
Hybridization state constants.
HYDR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
HYDROGEN - Static variable in class chemaxon.struc.MolBond
Hydrogen bond type.
HydrogenData(MolAtom, int, int, int) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
hydrogenize - Variable in class chemaxon.marvin.io.MolExportModule
Add Hydrogen atoms if 1, remove if -1, do nothing if 0.
hydrogenize(boolean) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
hydrogenize(int, String, boolean, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Hydrogenize molecule in the specified cell.
Hydrogenize - Class in chemaxon.calculations.hydrogenize
Addition and removal of explicit hydrogens or lone pairs.
Hydrogenize() - Constructor for class chemaxon.calculations.hydrogenize.Hydrogenize
 
hydrogenizeAll(boolean, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Hydrogenize molecules in all cells.
HYDROPHOBIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
hyperWienerIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the hyper Wiener index of the molecule.
Hz - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit
Hz unit

I

I - Static variable in class chemaxon.core.ChemConst
 
icell - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The viewer cell index (0 for sketcher).
ICON_PATH - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
icon path of checker
ICON_PATH - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
icon path of action
iconPath() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the path of the icon for the checker
iconPath() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the path of the icon for the action
id - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
 
id() - Method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Returns the ID of this result type.
ID - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
id property of action
ID_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction
The key of the ID parameter of the abstract action.
IDENTIFIER - Static variable in class chemaxon.naming.document.DocumentToStructure
 
IDENTITY - Static variable in enum class com.chemaxon.search.transformation.transformers.Aromatizer
Identity transformer.
ids - Variable in class chemaxon.descriptors.ECFP
Identifier list storage of the fingerprint
IGNORE - Enum constant in enum class com.chemaxon.search.mcs.RingHandlingMode
This option ignores the ring/chain topology of bonds, which is the default behavior.
ignoreConfigurationErrors - Variable in class chemaxon.checkers.StructureCheckOptions
Ignores configuration errors - errors found in input files does not cause the execution to stop on the input file, just skips the actual structure and tries the next - printing error message on the standard error
ignoreDrawProperties - Variable in class chemaxon.marvin.space.monitor.Label
 
ignoreDrawProperties(boolean) - Method in class chemaxon.marvin.space.monitor.Label
Sets the label whether it accepts draw properties or not.
ignoreErrors - Variable in class chemaxon.checkers.StructureCheckOptions
Ignores errors - errors found in input files does not cause the execution to stop on the input file, just skips the actual structure and tries the next - printing error message on the standard error
IMAGE_IMPORT_SERVICE_URL - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier for parameter: "imageImportServiceURL" See Parameters and Events documentation.
IMAGE_SAVE_FORMAT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "imageSaveFormat".
IMAGE_SAVE_URL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "imageSaveURL".
IMAGE_SHOW_URL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "imageShowURL".
ImageExportUtil - Class in chemaxon.util
Extends ImageExportBaseUtil with additional methods.
IMPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "implicitH".
IMPLICIT_H_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for default mode.
IMPLICIT_H_MATCHING_DISABLED - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen.
IMPLICIT_H_MATCHING_ENABLED - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for indicate matching between implicit and explicit hydrogens.
IMPLICIT_H_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching.
implicitizeHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int).
Usage:
             Hydrogenize.convertExplicitHToImplicit(molecule, f);
             
implicitizeHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int).
Usage:
             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
             
implicitizeHydrogens(int, MolAtom[], boolean) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:
             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             
implicitizeHydrogens0(int, MolAtom[], boolean) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:
             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             
implicitizeHydrogens0(int, MolAtom[], boolean) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:
             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             
IMPORT_CONVERSION - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "importConv".
IMPORT_ENABLED - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "importEnabled".
importDoc(byte[]) - Static method in class chemaxon.formats.MolImporter
Reads a document from a byte array.
importDoc(byte[], String, String) - Static method in class chemaxon.formats.MolImporter
Reads a document from a byte array.
importer - Variable in class chemaxon.marvin.io.formats.MoleculeImporter
The wrapped importer.
importMol(byte[]) - Static method in class chemaxon.formats.MolImporter
Read a molecule from a byte array.
importMol(byte[], Molecule) - Static method in class chemaxon.formats.MolImporter
Deprecated.
As of 23.15, use MolImporter.importMol(byte[]) instead
importMol(byte[], String, String) - Static method in class chemaxon.formats.MolImporter
Read a molecule from a byte array.
importMol(byte[], String, String, Molecule) - Static method in class chemaxon.formats.MolImporter
Deprecated.
importMol(String) - Static method in class chemaxon.formats.MolImporter
Read a molecule from a string.
importMol(String, ImportOptions) - Static method in class chemaxon.formats.MolImporter
Read a molecule from a string with the given options.
importMol(String, Molecule) - Static method in class chemaxon.formats.MolImporter
Deprecated.
As of 23.15, use MolImporter.importMol(String) instead
importMol(String, String) - Static method in class chemaxon.formats.MolImporter
Read a molecule from a string.
importMol(String, String, String) - Static method in class chemaxon.formats.MolImporter
Deprecated, for removal: This API element is subject to removal in a future version.
(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call MolImporter.importMol(String, String); if you have a byte array, call MolImporter.importMol(byte[], String, String).
importMol(String, String, String, Molecule) - Static method in class chemaxon.formats.MolImporter
Deprecated, for removal: This API element is subject to removal in a future version.
(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call MolImporter.importMol(String, String); if you have a byte array, call MolImporter.importMol(byte[], String, String, Molecule).
importNodes(Document, boolean) - Method in class chemaxon.descriptors.MDParameters
Imports nodes from the specified Document into the current (main) Document.
importNodes(Document, boolean) - Method in class chemaxon.descriptors.PFParameters
 
In - Static variable in class chemaxon.core.ChemConst
 
inAtomList(int, int) - Method in interface chemaxon.struc.Smolecule
Tests whether the specified element is in the atom list.
inc(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Increments the content of the specified hitogram bin by one.
inc(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Increments the histogram corresponding to two features ('fa'-'fb') and a distance, 'dist'.
inc(int, int, int, float[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
The fuzzy version of inc( int fa, int fb, int dist ).
inc(int, int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
The fuzzy version of inc( int fa, int fb, int dist ).
incGrinvCC() - Method in class chemaxon.struc.MoleculeGraph
Increases the graph invariant change count and sets grinv to null.
incGrinvCC(boolean) - Method in class chemaxon.struc.MoleculeGraph
 
incGrinvCCOnly() - Method in class chemaxon.struc.MoleculeGraph
Increases the graph invariant change count, but does not change grinv.
INCHI - Static variable in class chemaxon.formats.MFileFormat
IUPAC InChI files.
INCHIKEY - Static variable in class chemaxon.formats.MFileFormat
IUPAC InChIKey.
INCLUDE_ALL_ATOMS - Static variable in class chemaxon.util.iterator.IteratorFactory
Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.
INCLUDE_ALL_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
Include all bonds: covalent and coordinate bonds in bond iteration.
INCLUDE_CHEMICAL_ATOMS - Static variable in class chemaxon.util.iterator.IteratorFactory
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY instead.
INCLUDE_CHEMICAL_ATOMS_ONLY - Static variable in class chemaxon.util.iterator.IteratorFactory
Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.
Incomplecule - Interface in chemaxon.struc
Ancestor of molecule classes and interfaces.
INCORRECT_AROMATIC_NITROGEN_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Incorrect aromatic nitrogen remark.
INCORRECT_TETRAHEDRAL_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Represents incorrect/impossible arrangement of wedge bond around chiral centers.
IncorrectTetrahedralStereoChecker - Class in chemaxon.checkers
Incorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.
IncorrectTetrahedralStereoChecker() - Constructor for class chemaxon.checkers.IncorrectTetrahedralStereoChecker
Default constructor
incQProp(String) - Method in class chemaxon.struc.MolAtom
Increments the value of a query property.
incQueryAromaticity() - Method in class chemaxon.struc.MolAtom
Increments the value of the query aromaticity property.
incValenceProp() - Method in class chemaxon.struc.MolAtom
Increments the value of the valence property.
index(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Calculates the index of the bin specified by the arguments.
indexOf(MObject) - Method in class chemaxon.struc.MDocument
Searches for an object in the document or in the chemical structure that belongs to the document.
indexOf(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Gets the index of the specified atom.
indexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule
Gets the index of the specified node in the graph union.
indexOf(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Gets the index of the specified node in the graph union.
indexOf(MolAtom) - Method in class chemaxon.struc.Sgroup
Gets the atom index in the S-group graph.
indexOf(MolBond) - Method in class chemaxon.struc.MolAtom
Returns the index of the specified bond in this atom.
indexOf(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Gets the index of the specified bond.
indexOf(MolBond) - Method in class chemaxon.struc.RgMolecule
Gets the index of the specified edge in the graph union.
indexOf(MolBond) - Method in class chemaxon.struc.RxnMolecule
Gets the index of the specified edge in the graph union.
indexOf(MolBond) - Method in class chemaxon.struc.Sgroup
Gets the bond index in the S-group graph.
indexOf(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
Returns the index of the specified bond in this atom.
indexOf(Sgroup) - Method in class chemaxon.struc.Molecule
Gets the array index of an S-group.
indexOfButtonB(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane
Gets the index of the button on the visible area of the viewer.
indexOfButtonC(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane
Gets the index of the checkbox in the visible area of the viewer.
indexOfReferenced(MolBond) - Method in class chemaxon.struc.MolAtom
Returns the index of the referenced bond in this atom.
indicesOf(String) - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Gets the level and the index of the specified format.
INFO - Enum constant in enum class chemaxon.checkers.CheckerSeverity
This severity level should used for StructureChecker implementations which search for standard informations in a Molecule
init() - Method in class chemaxon.descriptors.CDParameters
This method is called by the constructors before processing the XML configuration.
init() - Method in class chemaxon.descriptors.CFParameters
This method is called by the constructors before processing the XML configuration.
init() - Method in class chemaxon.descriptors.ECFPParameters
This method is called by the constructors before processing the XML configuration.
init() - Method in class chemaxon.descriptors.PFParameters
Initializes the object.
init() - Method in class chemaxon.descriptors.RFParameters
This method is called by the constructors before processing the XML configuration.
init() - Method in class chemaxon.descriptors.SDParameters
This method is called by the constructors before processing the XML configuration.
init(MolPanel) - Method in class chemaxon.marvin.beans.MarvinPane
Initializes the content pane.
init(MolPanel, boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Initializes the content pane.
init(GLAutoDrawable) - Method in class chemaxon.marvin.space.GraphicScene
Called by the drawable immediately after the OpenGL2 context is initialized for the first time.
initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3.1, replaced by SwingUtil.initAction
initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.util.SwingUtil
Initializes an action from information in a resource.
initBrackets() - Method in class chemaxon.struc.Sgroup
Initializes the list of brackets in this S-group.
initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3.1, replaced by SwingUtil.initButton
initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
Utility method to initialize a button from information in a resource.
initButton(AbstractButton, ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
Utility method to initialize a button from information in a resource.
initCtrlShortcutForMac(JMenuItem) - Static method in class chemaxon.marvin.util.SwingUtil
Deprecated, for removal: This API element is subject to removal in a future version.
does nothing.
initDraw() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
initDraw() - Method in class chemaxon.marvin.space.MoleculeComponent
Initializes gl related drawing variables, for example display lists.
initDraw() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
initDraw() - Method in class chemaxon.marvin.space.PharmacophorePoint
Initializes all internal data structure needed for drawing the component.
initEmbeddedMD() - Method in class chemaxon.descriptors.ShapeParameters
This method is called by the constructors before processing the XML configuration.
initFields() - Method in class chemaxon.marvin.view.swing.TableOptions
Initialize field information before update.
initFunTab() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The function table will become unmodifiable. Configure the Evaluator instead before creating the ChemJEP.
initGenerator() - Method in class chemaxon.descriptors.CDParameters
This method is void in this class as custom descriptors are opaque, their internal structure is not known.
initGenerator() - Method in class chemaxon.descriptors.CFParameters
Initializes the fingerprint generator.
initGenerator() - Method in class chemaxon.descriptors.ECFPParameters
Initializes the fingerprint generator.
initGenerator() - Method in class chemaxon.descriptors.PFParameters
Creates and initializes a PFGenerator instance.
initGenerator() - Method in class chemaxon.descriptors.RFParameters
Initializes the reaction fingerprint generator.
initGenerator() - Method in class chemaxon.descriptors.ShapeParameters
 
INITIAL_CAPACITY - Static variable in class chemaxon.struc.MoleculeGraph
Initial capacity of the atoms and bonds vectors.
initialised - Variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
initialize() - Method in class chemaxon.checkers.ComponentChecker
Empty default implementation
initializeReader(String) - Static method in class chemaxon.standardizer.StandardizerUtil
Initializes a configuration reader based on a configuration string
initInApplet() - Static method in class chemaxon.marvin.util.SwingUtil
Deprecated, for removal: This API element is subject to removal in a future version.
does nothing.
initMolImport(MolInputStream) - Method in class chemaxon.marvin.io.formats.mdl.MolImport
Initializes the import module.
initMolImport(MolInputStream) - Method in class chemaxon.marvin.io.MolImportModule
Initializes the import module.
initMolImport(MRecord, String) - Method in class chemaxon.marvin.io.MolImportModule
Initializes the import module.
initOldDocuments(MDocument, boolean) - Static method in class chemaxon.marvin.modules.reaction.ReactionEditUtils
Adds plus signs to a document if it is potentially an old reaction.
initParameters() - Method in class chemaxon.descriptors.BCUTParameters
 
initParameters() - Method in class chemaxon.descriptors.CDParameters
Initializes data members that depend on the XML configuration but are not directly taken from it.
initParameters() - Method in class chemaxon.descriptors.CFParameters
Initializes those data members that depend on the XML configuration but are not directly taken from it.
initParameters() - Method in class chemaxon.descriptors.ECFPParameters
Initializes those data members that depend on the XML configuration but are not directly taken from it.
initParameters() - Method in class chemaxon.descriptors.MDParameters
Initializes object after configuration parameters are loaded.
initParameters() - Method in class chemaxon.descriptors.PFParameters
Initializes those data members that depend on the XML configuration but are not directly taken from it.
initParameters() - Method in class chemaxon.descriptors.RFParameters
Initializes those data members that depend on the XML configuration but are not directly taken from it.
initParameters() - Method in class chemaxon.descriptors.scalars.HBParameters
 
initParameters() - Method in class chemaxon.descriptors.scalars.LDParameters
 
initParameters() - Method in class chemaxon.descriptors.SDParameters
Initializes those data members that depend on the XML configuration but are not directly taken from it.
initProgressMonitor(String, int, int) - Method in interface chemaxon.common.util.MProgressMonitor
Create a progress monitor.
initSymTab() - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.
initVariables(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
inputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create InputStream from not nullable location.
inputStreamFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create InputStream from not nullable location.
inputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create in input stream from nullable location.
inputStreamFromNullableLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create in input stream from nullable location.
insert(int, MTextDocument) - Method in class chemaxon.struc.graphics.MTextDocument
 
insert(int, String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
Inserts a string.
insertAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolAtom).
insertBond(int, MolBond) - Method in class chemaxon.struc.MolAtom
Inserts a bond at a specified index.
insertBond(int, MolBond) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolBond).
insertBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
 
insertBondInOrder(MolBond, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
Insert a bond in the order specified as the second argument.
insertDocument(MTextDocument) - Method in class chemaxon.struc.graphics.MTextBox
Inserts document at the current cursor position.
insertNullAtoms(int, int) - Method in class chemaxon.struc.MoleculeGraph
Insert nulls into the atom array.
insertNullAtoms(int, int) - Method in class chemaxon.struc.RgMolecule
Insert nulls into the atom array.
insertNullBonds(int, int) - Method in class chemaxon.struc.MoleculeGraph
Insert nulls into the bond array.
insertNullBonds(int, int) - Method in class chemaxon.struc.RgMolecule
Insert nulls into the bond array.
insertText(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Inserts the given string to textPane at caret position.
insideLabel(double, double) - Method in class chemaxon.struc.MolAtom
Tests whether the specified point is inside the atom label.
INSTABLE_TAUTOMERIC_FORM_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Instable tautomeric form remark.
INSTANT_JCHEM - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Instant JChem
INSTANT_JCHEM_PIVOTING - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Instant JChem Pivoting
INSTANT_JCHEM_SERVER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Instant JChem Server
INSTANT_JCHEM_VIZ - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Instant JChem VIZ
intDescr - Variable in class chemaxon.descriptors.CustomDescriptor
storage for the integer or binary descriptors
INTEGER_ARRAY - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
 
INTEGER_ARRAY_BIT_REPR - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
 
INTEGER_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
 
internalSize - Variable in class chemaxon.descriptors.MDParameters
required memory size of one descriptor instance
internalsToString() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Print state to a String.
intValue() - Method in class chemaxon.struc.prop.MIntegerProp
Gets the integer value.
INVALID_CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that stereo center with no enhanced stereo property had found in the molecule
INVALID_COORD_SYSTEM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that invalid coordination system had found in the molecule
INVALID_LINKNODE_MESSAGE - Static variable in class chemaxon.struc.MoleculeGraph
 
INVALID_REACTION_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that invalid mapping had found in the molecule (represents a reaction)
INVALID_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule with invalid rgroup had found
INVALID_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Deprecated.
INVALID_WEDGE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Deprecated.
InvalidChecker - Class in chemaxon.checkers
An extremal checker implementation indicating error in the configuration imported from XML or action string
InvalidChecker(String) - Constructor for class chemaxon.checkers.InvalidChecker
Initializes an invalid structure checker instance
InvalidStandardizerAction - Class in chemaxon.standardizer.actions
Implementation of StandardizerAction representing an invalid instance of a standardizer action.
InvalidStandardizerAction(String) - Constructor for class chemaxon.standardizer.actions.InvalidStandardizerAction
Initializes an invalid standardizer instance
InvalidStandardizerAction(String, String, Map<String, String>) - Constructor for class chemaxon.standardizer.actions.InvalidStandardizerAction
Initializes an invalid standardizer instance
invert() - Method in class chemaxon.struc.CTransform3D
Inverts the matrix.
invertSelection() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
invertSelection() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
invertSelection() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the the given part of the component to be selected if it was not set and vice versa.
invertSelection(int) - Method in class chemaxon.marvin.space.GraphicCell
The previously picked part of the component will be selected if it was unselected and vice versa.
invertSelection(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the the given part of the component to be selected if it was not set and vice versa.
invertSelection(UOID) - Method in class chemaxon.marvin.space.GraphicScene
The previously picked part of the component will be selected if it was unselected and vice versa.
INVISIBLE_SETS - Static variable in class chemaxon.marvin.common.ParameterConstants
 
invokeAndWait(Runnable) - Method in interface chemaxon.marvin.view.TaskScheduler
Enqueues a task on the scheduler's thread and waits for its completion.
invokeAndWait(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil
Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object, blocks until it is finished and returns the result (calling FutureTask.get()).
invokeLater(Runnable, int) - Method in interface chemaxon.marvin.view.TaskScheduler
Enqueues a task on the scheduler's thread.
invokeLater(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil
Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object.
ionChargeOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the ion charge.
IonChargePlugin - Class in chemaxon.marvin.calculations
Plugin class for charge calculation on ionized microspecies.
IonChargePlugin() - Constructor for class chemaxon.marvin.calculations.IonChargePlugin
Constructor.
ionizer - Variable in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
 
Ir - Static variable in class chemaxon.core.ChemConst
 
irm - Variable in class chemaxon.marvin.space.GraphicComponent
Inverse of the Rotation matrix represented by a GeomCalc matrix.
is3d() - Method in class chemaxon.struc.CTransform3D
Tests whether the transformation is 3D.
isAbsoluteLabelsVisible() - Method in class chemaxon.marvin.MolPrinter
Is 'Absolute' label visible?.
isAbsolutePlacement() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets whether the placement of this attached data is absolute or relative to the objects it is attached.
isAbsoluteStereoRelevant(Molecule) - Static method in class chemaxon.checkers.StructureCheckerHelper
Determines if molecule contains a stereo center with no enhanced stereo property.
isAbsStereo() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Gets the absolute value of the action
isAbsStereo() - Method in class chemaxon.struc.MoleculeGraph
Gets the absolute stereoconfiguration flag.
isAbsStereo() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Gets the absolute stereoconfiguration flag.
isAcceptableGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.MultipleSgroup
Decides whether the given molecule graph can be the graph of a multiple s-group.
isAcceptablePolymerGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Checks if the given molecular graph can be the graph of a polymer SRU
isAcceptableRSRUGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Checks if the given molecular graph can be the graph of an RSRU
isAcceptableSru(String) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
 
isAcceptedSpecialLigand(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
isAcceptor() - Method in class chemaxon.marvin.space.PharmacophorePoint
Checks if actual pharmacophore type includes PharmacophorePoint.ACCEPTOR_TYPE.
isAcceptor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isActinideMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is an actinide metal Actinium is included.
isActive() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if this cell is the active cell of the entire scene.
isActive() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
isActive() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
isActive() - Method in interface chemaxon.standardizer.StandardizerAction
Returns true if the action is active, and can be used
isActiveCell(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the cell having cellIndex is the active cell of the scene.
isAddServices() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns true if services are displayed in the popup list
isAdvancedSave() - Method in class chemaxon.marvin.common.UserSettings
Gets wether the useres uses advanced save or not.
isAliphaticAtom(int) - Method in class chemaxon.calculations.Ring
Determines if an atom is not a member of an aromatic ring.
isAliphaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.isAliphaticAtom(int)
isAliphaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if aliphatic atom.
isAliphaticBond(int) - Method in class chemaxon.calculations.Ring
Determines if a bond is not a member of an aromatic ring.
isAliphaticRC(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isAlkaliMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is an alkali (group I.) metal.
isAlkalineEarthMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is an alkaline earth (group II.) metal.
isAllowTraditionalNitrogen() - Method in class chemaxon.checkers.ValenceErrorChecker
Gets whether the checker allows traditional N representation
isAllowValenceError() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Gets whether replace should be applied even in case of invalid valence in the result
isAmbiguousStereo() - Method in class chemaxon.struc.MolAtom
Check if the atom has ambiguous stereo wedge configuration.
isAminoAcid() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Gets whether the group represents an amino-acid
isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.common.UserSettings
Gets wether the user uses peptide bridge coloring or not.
isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.MolPrinter
Is peptide bridge coloring enabled?
isAnchor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isAnimated(int) - Method in class chemaxon.marvin.beans.MViewPane
Selected cell is animated or not.
isAnimSync() - Method in class chemaxon.marvin.beans.MViewPane
Gets the animation synchronization.
isAnionic() - Method in class chemaxon.marvin.space.PharmacophorePoint
Check if actual pharmacophore type includes PharmacophorePoint.ANIONIC_TYPE.
isAnnotationSupported() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Checks whether annotation is supported for the current document type.
isAntialiasEnabled() - Method in class chemaxon.marvin.space.GraphicScene
Returns true if full-screen antialias is enabled.
isApproximateCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns true if count is approximate due to multiple position bonds with multicenters of variable size, false otherwise.
isAromatic() - Method in class chemaxon.marvin.space.PharmacophorePoint
Checks if actual pharmacophore type includes PharmacophorePoint.AROMATIC_TYPE.
isAromatic(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isAromatic(int[], Molecule) - Static method in class chemaxon.checkers.StructureCheckerHelper
Determines if a ring in the molecule is aromatic or not
isAromaticAtom(int) - Method in class chemaxon.calculations.Ring
Determines if an atom is a member of an aromatic ring.
isAromaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.isAromaticAtom(int)
isAromaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if aromatic atom.
isAromaticBond(int) - Method in class chemaxon.calculations.Ring
Determines if a bond is a member of an aromatic ring.
isAromaticityChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects aromaticity atom query properties or not.
isAromaticRC(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isAromaticSMILESSubset(int) - Static method in class chemaxon.struc.MolAtom
Is the atom can be aromatic according to the daylight specification: Only atoms on the following list can be considered aromatic: C, N, O, P, S, As, Se, and * (wildcard).
isAromatize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
isArrow() - Method in class chemaxon.struc.graphics.MPolyline
Checks if it is an arrow.
isAssociatedWith(Molecule) - Method in class chemaxon.struc.NoStructure
Verifies the reference equality of molecule and the component associated with this instance.
isAsymmetric() - Method in class chemaxon.descriptors.MDParameters
Returns whether current parametrized metric is asymmetric or not.
isAsymmetricAtom(int) - Method in class chemaxon.calculations.stereo.Stereochemistry
Determines if an atom is asymmetric or not.
isAsymmetricAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.isAsymmetricAtom(int)
isAsymmetricAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if asymmetric atom.
isAtom() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isAtom() - Method in class chemaxon.struc.RgMolecule
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isAtom() - Method in class chemaxon.struc.RxnMolecule
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow
Gets whether the arrow's terminus is at an atom.
isAtomFaded(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
isAtomFaded(int) - Method in class chemaxon.marvin.space.MoleculeComponent
Tells whether the atom is faded or not.
isAtomicSymbol(String) - Static method in class chemaxon.struc.PeriodicSystem
Returns whether the given string corresponds to an atomic number of an element in the periodic system specified by its symbol.
isAtomInRing(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
isAtomMapMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether atom map numbers are considered in search.
isAtomMappingVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Determines the visibility of the atom mapping.
isAtomMappingVisible() - Method in class chemaxon.marvin.MolPrinter
Returns true if atom mapping is visible.
isAtomNumbersVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
in 6.2.0. Use getAtomNumberingType() instead.
isAtomNumbersVisible() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
in 6.2.0. Use getAtomNumberingType instead.
isAtomPropertiesVisible() - Method in class chemaxon.marvin.common.UserSettings
Tells wheter the atom properties are visible or not if exist.
isAtomPropertiesVisible() - Method in class chemaxon.marvin.MolPrinter
Get the atom properties visibility
isAtomSetColorModeSet() - Method in class chemaxon.struc.MDocument
Decides whether the atomset coloring mode is set.
isAtomSymbolsVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Tests the visibility of the atom symbols in 3D.
isAtomSymbolsVisible() - Method in class chemaxon.marvin.MolPrinter
Returns the atom symbol visibility of 3D mode.
isAtomTypeMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether atom types are considered in search.
isAtomVisible(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
isAtomVisible(int) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns if the atom is visible or hidden.
isAttachmentAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the given atom is an attachment atom or not.
isAutoCheckStructure() - Method in class chemaxon.marvin.common.UserSettings
Tells whether the automatic structure checking is enabled or not
isAutoHeight() - Method in class chemaxon.struc.graphics.MTextBox
Gets if it is autoHeight.
isAutomaticFogEnabled() - Method in class chemaxon.marvin.common.UserSettings
Gets the state of automatic fog calculation mode.
isAutomaticReactionEnabled() - Method in class chemaxon.marvin.common.UserSettings
Gets the state of automatic reaction calculation mode.
isAutoPopup() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns the auto popup behaviour
isAutoSize() - Method in class chemaxon.struc.graphics.MTextBox
 
isAvailable() - Method in class chemaxon.checkers.AbstractStructureChecker
 
isAvailable() - Method in class chemaxon.checkers.InvalidChecker
 
isAvailable() - Method in interface chemaxon.checkers.StructureChecker
Returns true if the checker is available, and can be used
isAvailable() - Method in class chemaxon.checkers.SubstructureChecker
 
isAvailable() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
isAvailable() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
isAvailable() - Method in interface chemaxon.standardizer.StandardizerAction
Returns true if the action is available, and can be used
isBarredAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines if an atom is is part of a certain functional group with high rotational barrier (amides, thioamides, sulphonamides).
isBold() - Method in class chemaxon.struc.graphics.MFont
Tests whether the font is bold.
isBold() - Method in class chemaxon.struc.MolBond
Decides whether this bond is bold or not.
isBond() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isBond() - Method in class chemaxon.struc.RgMolecule
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isBond() - Method in class chemaxon.struc.RxnMolecule
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow
Gets whether the arrow's terminus is at a bond.
isBondDraggedAlong() - Method in class chemaxon.marvin.beans.MSketchPane
Is the currently used bond shown at the mouse cursor?
isBondDraggedAlong() - Method in class chemaxon.marvin.common.UserSettings
Is the currently used bond shown at the mouse cursor?
isBondLengthVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the bond length display option.
isBondLengthVisible() - Method in class chemaxon.marvin.MolPrinter
Return whether the bond length is visible or not.
isBondParallelWith(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Checks if there is a bond parallel (having same endpoints) with the given bond in this MoleculeGraph.
isBondTypeMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether bond types are considered in search.
isBoundTo(MolAtom) - Method in class chemaxon.struc.MolAtom
Checks if this MolAtom is connected to another one or not.
isBracketCrossingBond(MolBond) - Method in class chemaxon.struc.Sgroup
 
isBracketVisible() - Method in class chemaxon.struc.Sgroup
Tests whether the bracket is visible.
isBracketVisible() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Tests whether the bracket is visible.
isBracketVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Tests whether the bracket is visible.
isBridgehead() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing bridgehead H
isBridgeHeadAtom(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.11.1, replaced by TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)
isBridgingRAllowed() - Method in class chemaxon.sss.search.SearchOptions
Returns true if different undefined R-atoms can match the same group of atoms.
isCanceled() - Method in interface chemaxon.common.util.MProgressMonitor
Tests whether the user canceled the dialog.
isCanceled() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Returns whether the process is cancelled
isCancelled() - Method in interface com.chemaxon.calculations.common.CancelObserver
Returns whether cancellation of current task has been requested.
isCanonical() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
isCationic() - Method in class chemaxon.marvin.space.PharmacophorePoint
Check if actual pharmacophore type includes PharmacophorePoint.CATIONIC_TYPE.
isCell() - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Returns true if this id identifies a cell.
isCellwiseWeights() - Method in class chemaxon.descriptors.MDParameters
Gets boolean telling whether cell weights are to be generated for current parametrized metric.
isChainAtom(int) - Method in class chemaxon.calculations.Ring
Determines if an atom a ring bond or a chain bond.
isChainAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.isChainAtom(int)
isChainAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if chain atom.
isChainBond(int) - Method in class chemaxon.calculations.Ring
Determines if a bond is a ring bond or a chain bond.
isChainBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.isChainBond(int)
isChainBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines if a bond is a ring bond or a chain bond.
isChargeAngleSet() - Method in class chemaxon.struc.MolAtom
 
isChargeCalc() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Returns true if pH-Charge calculation.
isCharged() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing charged H
isChargeMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether formal charges are considered in search.
isChargeWithCircle() - Method in class chemaxon.marvin.MolPrinter
Get the visibility of Charge with Circle
isChecking() - Method in interface chemaxon.checkers.runner.CheckerRunner
This function identifies the state of the checker thread
isChildOf(MObject) - Method in class chemaxon.struc.graphics.MMidPoint
Is this object a children of another one?
isChildOf(MObject) - Method in class chemaxon.struc.graphics.MRectanglePoint
Is this object a children of another one?
isChildOf(MObject) - Method in class chemaxon.struc.MObject
Is this object a children of another one?
isChildOf(MObject) - Method in class chemaxon.struc.MPoint
Is this object a children of another one?
isChiral() - Method in class chemaxon.calculations.stereo.Stereochemistry
Determines if the molecule contains an atom with R or S stereo configuration.
isChiral() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.isChiral()
isChiral(Molecule) - Static method in class chemaxon.checkers.StructureCheckerHelper
Determines if the molecule contains an atom with R or S stereo configuration.
isChiralCenter(int) - Method in class chemaxon.calculations.stereo.Stereochemistry
Determines if an atom can be a tetrahedral stereogenic center.
isChiralCenter(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.isChiralCenter(int)
isChiralCenter(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Determines if an atom can be a tetrahedral stereogenic center.
isChiralCenter(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines if an atom can be a tetrahedral stereogenic center.
isChirality() - Method in class chemaxon.standardizer.actions.ClearStereoAction
Gets the chirality value of absolute stereo action
isCleanable() - Method in class chemaxon.formats.MolExporter
Tests whether cleaning is meaningful for the chosen output format.
isCleanable() - Method in class chemaxon.marvin.io.MolExportModule
Tests whether 2D or 3D cleaning is meaningful for this output format.
isCleanHOptionEnabled() - Method in class chemaxon.marvin.common.UserSettings
Returns true if the H option for cleaning is enabled.
isCleanNeeded() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns true if clean is needed for GUI display.
isClearClipboardBeforeExport() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Returns whether the subsystem clears the clipboard before a copy operation.
isClipped() - Method in class chemaxon.marvin.space.SurfaceComponent
Returns true if there are clipping planes enabled that will clip part of the surface during drawing.
isCloseEnabled() - Method in class chemaxon.marvin.beans.MSketchPane
Determines if the File->Close menu item is enabled or not.
isCollinear(DPoint3, DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Checks whether three 3D points can be connected with a line.
isCollinear(MolAtom) - Method in class chemaxon.struc.MolBond
Returns whether atom is collinear with the bond or not.
isColorMapperEnabled() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
isComment(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
isCompatible(MTextAttributes, MTextAttributes, MFont) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether two attribute sets are compatible.
isComponent() - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Returns true if this id identifies a component.
isComponentPart() - Method in class chemaxon.marvin.space.ComponentElement
Returns true if the if the component is a structured component.
isConfirmExit() - Method in class chemaxon.marvin.beans.MSketchPane
Gets whether the confirmation dialog will be appear or not by exit.
isConjugated() - Method in class chemaxon.struc.MolBond
Gets the conjugation state of the bond set by the conjugation modul.
isConnected() - Method in class chemaxon.calculations.TopologyAnalyser
Determines if the molecule is a connected graph or not.
isConnected(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines if two atoms are members of a connected graph or not.
isConnected(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if two atoms are in the same connected component, false for atoms of disconnected structures.
isConnectedGraph() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines if the molecule is a connected graph or not.
isConnectedMode() - Method in class com.chemaxon.search.mcs.McsSearchOptions
Gets whether the common substructures should be connected or they can consist of multiple fragments.
isConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects connection count atom query properties or not.
isContracted() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Is this S-group contracted?
isContracted() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Decides whether this S-group is contracted or not.
isControllable(String) - Method in class chemaxon.marvin.space.GraphicComponent
A component must return true if it allows itself to be controlled by the given type controller.
isControllable(String) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns whether controling by the given type of controller is allowed to the component.
isControllable(String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Returns whether controling by the given type of controller is allowed to the component.
isControllable(String) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns whether controling by the given type of controller is allowed to the component.
isControllable(String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Returns whether controling by the given type of controller is allowed to the component.
isControllable(String) - Method in class chemaxon.marvin.space.PharmacophorePoint
Returns whether controling by the given type of controller is allowed to the component.
isCoordDependent() - Method in class chemaxon.struc.MProp
Tests whether the property depends on the molecular coordinates.
isCoordinate() - Method in class chemaxon.struc.MolBond
Tests whether the bond is coordinate.
isCopolymerMatching() - Method in class chemaxon.sss.search.SearchOptions
Specifies whether matching mode is copolymer.
isCopyAsTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Determines whether the MTransferable is appearing as an option in the Copy As dialog.
isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionChecker
This method determines if a component of the reaction correct or not.
isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionMapErrorChecker
 
isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Tells whether the spectrum is coupled.
isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator
Coupled/decoupled spectrum.
isCouplingNeeded() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns whether spin-spin couplings are taken into account.
isCreateRingCenters() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
isCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the bond is a crossing bond in a ladder-type polymer bracket.
isCubeLine(String, int) - Static method in class chemaxon.formats.recognizer.CubeRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
isCumulatedDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker
Returns the detectCummulatedDoubleBonds
isCurrentFontDefault() - Method in class chemaxon.struc.graphics.MTextBox
Tests whether the default font is used.
isCurrentFontRegular() - Method in class chemaxon.struc.graphics.MTextBox
Tests whether the current font is regular.
isCxSMILESLine(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
isDataDetached() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets whether the data should be displayed close to the objects or separately (detached).
isDataFlavorSupported(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Checks whether the MarvinTransferable.flavor equals with the given parameter.
isDaylightFormatWithoutOptions(String) - Static method in class chemaxon.checkers.StructureCheckerHelper
Returns true if daylight format with options supported, false otherwise
isDefault() - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether all attributes have default values.
isDefaultSelected() - Method in class chemaxon.marvin.util.OptionDescriptor
Tests whether the option is selected by default.
isDefaultTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Determines whether the MTransferable instance should be used by the default copy operation.
isDehidrogenize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
The explicit Hydrogens are not removed from the original input structure. No need to use.
isDescendantOf(Sgroup) - Method in class chemaxon.struc.Sgroup
Decides whether this is a descendant of another sgroup.
isDetachable() - Method in class chemaxon.marvin.beans.MViewPane
Gets the detachable property.
isDetectCumulatedDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker
Returns the detectCummulatedDoubleBonds
isDetectTransDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker
Returns the detectTransDoubleBonds
isDetectTripleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker
Returns the detectTripleBonds
isDialogVisible() - Method in interface chemaxon.common.util.MProgressMonitor
Tests whether the dialog is visible.
isDirty() - Method in class chemaxon.sss.search.SearchOptions
Returns the dirty flag.
isDisplayChargeWithCircle() - Method in class chemaxon.marvin.common.UserSettings
 
isDisplayLonePairsAsLine() - Method in class chemaxon.marvin.common.UserSettings
 
isDistancerangeSet() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties
 
isDistinctFirstAtomMatching() - Method in class chemaxon.sss.search.MolSearchOptions
Get option ensuring that upon the findNext() call the first atom must be stepped as well.
isDndTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
 
isDocumentExport() - Method in class chemaxon.marvin.io.MolExportModule
Tests if this export module is document export instead of a simple molecule export.
isDocumentImporter() - Method in class chemaxon.marvin.io.MolImportModule
Tests whether this module is a document importer or not.
isDonor() - Method in class chemaxon.marvin.space.PharmacophorePoint
Checks if actual pharmacophore type includes PharmacophorePoint.DONOR_TYPE.
isDonor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isDontRemoveLastComponent() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
isDoubleBond() - Method in class chemaxon.standardizer.actions.ClearStereoAction
Gets the double bond value of absolute stereo action
isDraggable() - Method in class chemaxon.marvin.beans.MViewPane
Determines whether mouse dragged evens are allowed or not.
isEditable() - Method in class chemaxon.standardizer.advancedactions.TransformAction
Returns if this action is editable.
isEditable() - Method in class chemaxon.struc.graphics.MTextBox
Determines if this text box's content can be edited by the user.
isEditable(int, Molecule, String) - Method in class chemaxon.marvin.io.MFieldAccessor
Tests whether a field is editable or not.
isEmpty() - Method in class chemaxon.jep.context.ReactionContext
Returns true if the context is empty.
isEmpty() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets whether the configuration contains actions
isEmpty() - Method in class chemaxon.struc.graphics.MChemicalStruct
A chemical structure object is empty if the molecule graph is empty.
isEmpty() - Method in class chemaxon.struc.graphics.MPolyline
A polyline becomes empty if it has less than 2 points.
isEmpty() - Method in class chemaxon.struc.graphics.MTextBox
A text box is empty if the string contains only whitespace.
isEmpty() - Method in class chemaxon.struc.MDocument
Tests whether the document is empty: the main molecule object in the document is empty no graphic object is included (neither simple nor extra)
isEmpty() - Method in class chemaxon.struc.MObject
An object may become empty if all the children are removed.
isEmpty() - Method in class chemaxon.struc.Molecule
Tests whether the molecule is empty.
isEmpty() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the molecule graph is empty.
isEmpty() - Method in class chemaxon.struc.RgMolecule
Ask if the molecule is empty or not.
isEmpty() - Method in class chemaxon.struc.RxnMolecule
Ask if the reaction is empty or not.
isEmpty() - Method in class chemaxon.struc.Sgroup
Is it an empty S-group?
isEmpty() - Method in class com.chemaxon.search.mcs.McsSearchResult
Checks whether the common substructure contains any bonds or is empty.
isEnabledT(int, int) - Method in class chemaxon.marvin.view.MDocStorage
Tests whether a text field is enabled.
isEnableTranslateAndRotate() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
isEndgroupMatching() - Method in class chemaxon.sss.search.SearchOptions
Get whether polymers end groups must match.
isEndReached() - Method in class chemaxon.formats.MolImporter
Tests whether the end of input is already reached.
isEndReached() - Method in class chemaxon.marvin.io.ArrayMDocSource
Tests whether the end of input is already reached.
isEndReached() - Method in class chemaxon.marvin.io.MDocSource
Tests whether the end of input is already reached.
isEndReached() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
Tests whether the end of storage is reached.
isEnforceAbsStereo() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
isErrorOccurred() - Method in class chemaxon.checkers.StructureCheck
Returns whether structure error found in the input files.
isExact() - Method in class chemaxon.standardizer.advancedactions.TransformAction
Gets the exact value of the action
isExactBondMatching() - Method in class chemaxon.sss.search.SearchOptions
Indicates whether bond types should match exactly - looking for query bonds target.
isExactQueryAtomMatching() - Method in class chemaxon.sss.search.SearchOptions
Returns whether exact matching of query atom information is set.
isExactQueryAtomMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether query atoms are matched only to query atoms of exactly the same type.
isExactQueryBondMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether query bonds are matched only to query bonds of exactly the same type.
isExceptionOccurred() - Method in class chemaxon.standardizer.concurrent.StandardizerResult
Gets whether an exception occurred during standardization
isExcluded() - Method in class chemaxon.marvin.space.PharmacophorePoint
Check if actual pharmacophore type is PharmacophorePoint.EXCLUDED_TYPE.
isExcludedAtom(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more atoms, than it would normally.
isExcludedBond(MolBond) - Method in class chemaxon.util.iterator.IteratorFactory
By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more bonds, than it would normally.
isExclusionRegexp() - Method in class chemaxon.checkers.AttachedDataChecker
Tells how to interpret the AtomLabels: A comma separated list or a regular expression.
isExitCanceled() - Method in class chemaxon.marvin.beans.MarvinPane
Check whether exiting is allowed or not.
isExpandable(int) - Method in class chemaxon.struc.Molecule
Tests if the molecule is expandable with the specified options.
isExpanded() - Method in interface chemaxon.struc.sgroup.Expandable
Is this S-group expanded?
isExpanded() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Is this S-group expanded?
isExpanded() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Is this S-group expanded?
isExperimentalEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Tests whether experimental features are enabled.
isExperimentalFeaturesAreAllowed() - Method in class chemaxon.marvin.common.UserSettings
 
isExpertMode() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Returns the expert mode
isExplicitConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects explicit connection count atom query properties or not.
isExplicitHVisible() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.5.1 this method always returns true. This method will be removed in a future release.
isExtraObject(MObject) - Method in class chemaxon.struc.MDocument
Decides whether a graphic object belongs to the main chemical structure of the document.
isEZLabelsVisible() - Method in class chemaxon.marvin.MolPrinter
Returns the visibility state of absolute double bond stereo configuration labels.
isEzVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the E/Z display option.
isEzVisible() - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.2, replaced by MolPrinter.isEZLabelsVisible()
isEZVisible() - Method in class chemaxon.marvin.common.UserSettings
Are E/Z labels visible?
isFallBackToBasic() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
Returns true if runner should fall back to basic runner when preferred fix failed.
isFileExists(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Check if a file exists.
isFiltered() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Return true if molecule filter is set.
isFixed(int) - Method in class chemaxon.marvin.view.MDocStorage
Tests whether a record is fixed.
isFlagSet(long) - Method in class chemaxon.formats.MFileFormat
Checks whether the format has a given (set of) flag(s) set.
isFlipped() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether this sgroup is flipped.
isFontDefault(MFont) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether the default font is used.
isFontDefaultInRange(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Tests whether the default font is used in the specified range.
isFontRegular() - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether the default font is used.
isFontRegularInRange(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Tests whether the default font is used in the specified range.
isFractionQuicklyAvailable(double) - Method in class chemaxon.marvin.view.MDocStorage
Tests whether the specified fraction of the total (estimated) number of records is quickly available.
isFreeAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the specified atom has free attachment point.
isFreeLegalAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by SuperatomSgroup.isFreeAttachAtom(MolAtom a).
isFull() - Method in class chemaxon.marvin.space.monitor.Monitor
Returns true if the monitor is full and can measure.
isFuzzyFingerprint() - Method in class chemaxon.descriptors.PFParameters
Gets whether the fuzzy fingerprints are used or not.
isGaussianSmoothing() - Method in class chemaxon.descriptors.PFParameters
Gets if fuzzy smmoothing is based on normal distribution.
isGenerateDistanceRanges() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
isGeneric() - Method in class chemaxon.struc.MolAtom
Tests whether the atom is a generic atom.
isGenNameShown() - Method in class chemaxon.marvin.view.swing.TableOptions
Are IUPAC names shown in the table?
isGLInitialized() - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the OpenGL2 canvas is already initialized.
isGrabbingEnabled() - Method in class chemaxon.formats.MolImporter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.2. It has no effect on the code.
isGraphicComponent() - Method in class chemaxon.marvin.space.GraphicComponent
 
isGraphicComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
 
isGraphInvariantVisible() - Method in class chemaxon.marvin.MolPrinter
Return whether the graph invariant is visible or not.
isGridVisible() - Method in class chemaxon.marvin.common.UserSettings
 
isGrinv() - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.5, use isGrinvVisible() instead
isGrinvCCValid() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the graph invariant change count is valid.
isGrinvCCValid() - Method in class chemaxon.struc.SelectionMolecule
Tests whether the graph invariant change count is valid.
isGrinvVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the visibility of the graph invariants.
isGUIContracted() - Method in class chemaxon.struc.Molecule
Deprecated.
as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()
isH(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isHalogen(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is a halogen (F, Cl, Br, I, At, Ts).
isHashed() - Method in class chemaxon.struc.MolBond
Decides whether this bond is hashed or not.
isHconnected() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing H connected H
isHierarchic() - Method in class chemaxon.struc.MPropertyContainer
Tests whether the property list contains subcollections like MListProp and MHashProp.
isHighlighted() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
isHighlighted() - Method in class chemaxon.marvin.space.MoleculeComponent
This functionality is currently unavailable.
isHighlighted() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Returns true if the component is highlighted.
isHighlighted() - Method in class chemaxon.marvin.space.PharmacophorePoint
Returns true if the component is highlighted.
isHighlighted(MObject) - Method in class chemaxon.struc.MDocument
Is the specified object currently highlighted?
isHinderedBiarylBridgeBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines if a bond bridges two aryl systems having more than two ortho substituents.
isHomologyEnumerated() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Indicates if homology groups are enumerated or not.
isHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects hydrogen count atom query properties or not.
isHydrophobic() - Method in class chemaxon.marvin.space.PharmacophorePoint
Checks if actual pharmacophore type includes PharmacophorePoint.HYDROPHOBIC_TYPE.
isHydrophobic(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isIdentity() - Method in class chemaxon.struc.CTransform3D
 
isIgnoreAxialStereo() - Method in class chemaxon.sss.search.SearchOptions
Retrieves if axial stereo is ignored during searching.
isIgnoreCumuleneOrRingCisTransStereo() - Method in class chemaxon.sss.search.SearchOptions
Retrieves if cumulene cis-trans stereo is ignored during searching.
isIgnoreDoubleBondStereo() - Method in class chemaxon.sss.search.SearchOptions
Retrieves if double bond stereo is ignored during searching.
isIgnoreSynAntiStereo() - Method in class chemaxon.sss.search.SearchOptions
Retrieves if syn-anti stereo is ignored during searching.
isIgnoreTetrahedralStereo() - Method in class chemaxon.sss.search.SearchOptions
Retrieves if tetrahedral stereo is ignored during searching.
isImplicitHcountImportant(MolAtom) - Static method in class chemaxon.marvin.io.MolExportModule
Checks whether the number of implicit hydrogens is important information for an atom or not.
isImplicitHcountImportant(MoleculeGraph) - Method in class chemaxon.marvin.io.MolExportModule
Checks whether the number of implicit hydrogens is important information for the atoms of mol or not.
isImplicitHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects implicit hydrogen count atom query properties or not.
isImplicitHydrogenMode() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Returns implicit hydrogen mode.
isImplicitizableH(int) - Method in class chemaxon.struc.MolAtom
Tests whether the hydrogen atom is implicitizable or not.
isIn3D() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Returns true if structures are returned in 3D.
isIncipBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow
Gets whether the arrow's sink is at an incipient bond.
isIncompleteReaction() - Method in class chemaxon.struc.RgMolecule
Check whether the reaction is incomplete or not.
isIncompleteReaction() - Method in class chemaxon.struc.RxnMolecule
Check whether the reaction is incomplete or not.
isInputAvailable() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Checks that the implementation supports input from clipboard.
isInputAvailable() - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
Checks that the implementation supports input from clipboard.
isInputMoleculeAromatized() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if the input molecule has aromatic bond.
isInternalSelectable() - Method in class chemaxon.struc.MObject
Is it a selection only internal object?
isInternalSelectable() - Method in class chemaxon.struc.MPoint
Is it a selection only internal object?
isIsotopeMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether isotopes are considered in search.
isIsotopic() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing isotopic H
isItalic() - Method in class chemaxon.struc.graphics.MFont
Tests whether the font is italic.
isKeepMapping() - Method in class chemaxon.standardizer.actions.MapAction
Returns if underlying mapper keeps existing maps should be kept when mapping.
isKeepMapping() - Method in class chemaxon.standardizer.actions.MapReactionAction
Returns if underlying mapper keeps existing maps should be kept when mapping.
isKeepMapping() - Method in class com.chemaxon.mapper.AutoMapper
Returns if the mapper will keep the initial mapping or not.
isKeepMapping() - Method in class com.chemaxon.mapper.AutoMapper.Options
 
isKeepQueryOrder() - Method in class chemaxon.sss.search.SearchOptions
Get options for rearranging query atoms for better search performance.
isLanthanideMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is a lanthanide metal Lanthanum is included.
isLargeMolecule() - Method in class chemaxon.struc.MoleculeGraph
Returns true if large molecule (number of atoms exceeds 1000).
isLastLine() - Method in class chemaxon.formats.recognizer.Recognizer
Tests whether it is the last line of file.
isLastTaskClean(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil
Deprecated, for removal: This API element is subject to removal in a future version.
isLegalAttachment(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by SuperatomSgroup.isAttachmentAtom(MolAtom).
isLicensed() - Method in class chemaxon.calculations.Ring
This method is for internal use only.
isLicensed() - Method in class chemaxon.calculations.TopologyAnalyser
 
isLicensed() - Method in class chemaxon.checkers.AbstractStructureChecker
 
isLicensed() - Method in class chemaxon.descriptors.BCUT
Returns information about the licensing of the product.
isLicensed() - Method in class chemaxon.descriptors.ECFP
Returns information about the licensing of the product.
isLicensed() - Method in class chemaxon.descriptors.ECFPGenerator
Returns information about the licensing of the product.
isLicensed() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Returns information about the licensing of the product.
isLicensed() - Method in class chemaxon.descriptors.ShapeDescriptor
 
isLicensed() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
isLicensed() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
 
isLicensed() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
 
isLicensed() - Method in class chemaxon.marvin.calculations.ChargePlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
 
isLicensed() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
 
isLicensed() - Method in class chemaxon.marvin.calculations.MSAPlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if the plugin is licensed.
isLicensed() - Method in class chemaxon.sss.search.MolSearch
 
isLicensed() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
isLicensed() - Method in class chemaxon.standardizer.Standardizer
Gets whether the standardizer is licensed
isLicensed() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Returns true if this action can be used in current license environment.
isLicensed() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Returns information about the licensing of the product.
isLicensed(String) - Static method in class chemaxon.license.LicenseManager
Returns true if the license manager recognizes the given product to be licensed.
isLigand() - Method in class chemaxon.marvin.space.MoleculeComponent
 
isLigandErrorVisible() - Method in class chemaxon.marvin.common.UserSettings
Tells wheter the bond's ligand error is visible or not.
isLigandErrorVisible() - Method in class chemaxon.marvin.MolPrinter
Gets the bond's ligand error visibility
isLinkNode() - Method in class chemaxon.struc.MolAtom
The atom is a link node if the maximum number of repetitions is nonzero.
isLoadedMolModified() - Method in class chemaxon.marvin.beans.MSketchPane
Determines whether the original molecule that is loaded in is modified or not.
isLocalAromatic() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
Do not calculate valence for ambiguous aromatic atoms behaving like aromatic Nitrogens (e.g.
isLonely() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing lonely H
isLonePairAsLine() - Method in class chemaxon.marvin.MolPrinter
Get the visibility of Lone Pairs: dots/line
isLonePairAutoCalc() - Method in class chemaxon.marvin.common.UserSettings
Returns the state of the automatic lone pair calculation.
isLonePairsAutoCalculated() - Method in class chemaxon.marvin.MolPrinter
Returns the state of the automatic calculation of lone pairs.
isLonePairsVisible() - Method in class chemaxon.marvin.MolPrinter
Returns the visibility state of lone pairs.
isLP(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isMacromoleculePart() - Method in class chemaxon.marvin.space.MoleculeComponent
Tells whether this MoleculeComponent is a visualizer of a ligand in a complex or an independent small molecule.
isMappable() - Method in class chemaxon.struc.MolAtom
Checks if this atom it a mappable.
isMapped() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing mapped H
isMarkBonds() - Method in class chemaxon.standardizer.actions.MapAction
Returns if bonds are marked while mapping.
isMarkBonds() - Method in class chemaxon.standardizer.actions.MapReactionAction
Returns if bonds are marked while mapping.
isMarkBonds() - Method in class com.chemaxon.mapper.AutoMapper
Returns if the mapper marks the reaction center bonds or not.
isMarkBonds() - Method in class com.chemaxon.mapper.AutoMapper.Options
 
isMarkushEnabled() - Method in class chemaxon.sss.search.MolSearchOptions
Specifies whether a target containing Markush features should be treated as a Markush library.
isMarvinCompMode() - Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Marvin compatibility mode.
isMatchCountBetween(int, boolean, int, boolean) - Method in class chemaxon.sss.search.Search
Decides questions like "does the query match the target between 2 and 5 times (inclusively)" Makes this efficiently, which means it only searches for the number of hits necessary to decide the question.
isMatchCountInRelation(String, int) - Method in class chemaxon.sss.search.Search
Decides questions like "does the query match the target at least 3 times", "[] up to 5 times", "[] exactly once".
isMatchCountInRelation(String, int, int) - Static method in class chemaxon.sss.search.Search
 
isMatching() - Method in class chemaxon.sss.search.MolSearch
 
isMatching() - Method in class chemaxon.sss.search.Search
Checks if the query structure matches the target structure with respect to the search options.
isMatching() - Method in interface com.chemaxon.search.SimpleSearcher
Determines if there is a matching between the specified query and target.
isMergedComponent(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Check whether given molecule is reaction component with a set of intentionally merged fragments or not.
isMetadataMol(Molecule) - Static method in class chemaxon.naming.document.DocumentToStructure
 
isMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Decides whether the element is a metal.
isMetalconnected() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing metal connected H
isMetalloid(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is a metalloid (B, Si, Ge, As, Sb, Te, Po).
isMinimumHeightSet() - Method in class chemaxon.struc.graphics.MTextBox
Gets if it is minimumHeightSet.
isMixSgroupMatching() - Method in class chemaxon.sss.search.SearchOptions
Get option whether search should consider consider COM, MIX and FOR sgroups during search.
isModified() - Method in class chemaxon.standardizer.Changes
Gets whether any modifications were applied on the molecule.
isMolecular() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns true if molecule output.
isMolecule() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 14.7.7, no replacement.
Usage:
 use myObject instanceof Molecule instead
             
isMolMovie() - Method in class chemaxon.formats.MolImporter
Are the imported molecules merged into one multi-set molecule?
isMolNameShown() - Method in class chemaxon.marvin.view.swing.TableOptions
Are molecule names shown in the table?
isMPLabelsVisible() - Method in class chemaxon.marvin.MolPrinter
Returns the visibility state of M/P labels.
isMPVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Gets the M/P display option.
isMPVisible() - Method in class chemaxon.marvin.common.UserSettings
 
isMsCalc() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns true if microspecies calculation.
isMsCalc() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns true if microspecies calculation.
isMsCalc() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if microspecies calculation.
isMSpaceDisplayLabelOnlyOnHeavyAtoms() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns if mspace should display label only on heavy atoms.
isMultiChiral() - Method in class chemaxon.struc.MoleculeGraph
Returns the multiple chirality flag.
isMultipleDisplay() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Returns true if results for more molecules can be displayed in a single component, false if each molecule should be displayed in a separate component.
isMultiSet() - Method in class chemaxon.formats.MolImporter
Are the imported molecules merged into one multi-set molecule?
isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.GeometryPlugin
For internal use only.
isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.MSAPlugin
For internal use only.
isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.ResonancePlugin
For internal use only.
isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
For internal use only.
isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
For internal use only.
isNegative(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isNegligible(double[]) - Method in class chemaxon.marvin.calculations.pKaPlugin
 
isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Returns whether the result can be ignored.
isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns whether the result can be ignored.
isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns whether the result can be ignored.
isNobleGas(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is a noble gas.
isNonAssociated() - Method in class chemaxon.struc.NoStructure
 
isNonPreferredStereoAtom(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Check if the atoms in the molecule is in SP2 hybridization state and has wedge whose getAtom1 is the specified atom, but wiggly bonds next to double bonds are allowed.
isNormal() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
isNormalized() - Method in class chemaxon.descriptors.MDParameters
Returns whether current parametrized metric is normalized or not.
ISOELECTRICPOINT - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
IsoelectricPointPlugin - Class in chemaxon.marvin.calculations
Plugin class for isoelectric point and pH - charge distribution calculation.
IsoelectricPointPlugin() - Constructor for class chemaxon.marvin.calculations.IsoelectricPointPlugin
Constructor.
isOK() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if no calculation error, false on error.
isOK() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns true if the calculation has run without error.
isOkActionEnabled() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
 
isOkActionEnabled() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Returns true if "OK" button is enabled.
isolate(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Isolates atom: a more efficient way of removing an atom than MoleculeGraph.removeAtom(chemaxon.struc.MolAtom), especially for large molecule graphs.
isolate(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Isolates bond: a more efficient way of removing a bond than MoleculeGraph.removeBond(chemaxon.struc.MolBond), especially for large molecule graphs.
ISOMERS_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Isomers Plugin Group
isOneLetterPeptideDisplay() - Method in class chemaxon.marvin.MolPrinter
Decides whether the Peptide display settings set to one letter.
isOnlyExpanded() - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
isOnlyFirstAtomInStereoCalculation() - Method in class chemaxon.struc.MoleculeGraph
Get how parity module interpret wedges.
isOptionsPaneLoaded(int) - Method in class com.chemaxon.calculations.gui.PluginFactory
Returns true is options pane is loaded for plugin, false otherwise.
isOrderedComponentSgroup() - Method in class chemaxon.struc.Sgroup
Returns if the Sgroup is ordered component Sgroup.
isOrderSensitiveSearch() - Method in class chemaxon.sss.search.SearchOptions
Indicates whether the search is order sensitive
isOrderSensitiveSearch() - Method in class com.chemaxon.search.MatchingOptions
Gets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple hits.
isOrigTargetMayBeMarkush - Variable in class chemaxon.sss.search.MolSearch
FS#9166 Should be set to 'false' to indicate that any bonds (Markush components) occurred only after generating generic tautomer of target.
isOtherMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is an "other metal", group IIIa-Va metal.
ISOTOPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that isotpoe atom had found in the molecule
ISOTOPE_2H3H - Enum constant in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
2H/3H isotope symbol
ISOTOPE_COMPOSITION - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "isotopecomposition".
ISOTOPE_DT - Enum constant in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
D/T isotope symbol
ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "isotopeformalchargeformula".
ISOTOPE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "isotopeformula".
ISOTOPE_H - Static variable in class chemaxon.struc.MolAtom
Include Hydrogen isotope(s).
ISOTOPE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).
ISOTOPE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).
ISOTOPE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignore isotope searching (isotope information is ignored during searching).
IsotopeChecker - Class in chemaxon.checkers
IsotopeChecker detects isotopes (non-elemental atoms).
IsotopeChecker() - Constructor for class chemaxon.checkers.IsotopeChecker
Default constructor
isotopeComposition(int) - Method in class chemaxon.calculations.ElementalAnalyser
Gets the molecular composition (w/w%).
isotopeComposition(int, boolean) - Method in class chemaxon.calculations.ElementalAnalyser
Gets the molecular composition (w/w%).
isotopeDistribution() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the isotopic distributions for the molecule.
IsotopeFixer - Class in chemaxon.fixers
Deprecated, for removal: This API element is subject to removal in a future version.
IsotopeFixer() - Constructor for class chemaxon.fixers.IsotopeFixer
Deprecated.
 
isotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the molecular formula (isotopes are separated).
isotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the molecular formula (isotopes are separated).
isotopeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
isotopeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether isotopes of atoms should be considered in search.
isotopeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
isotopeType(int, int) - Static method in class chemaxon.struc.MolAtom
Gets the type of an isotope.
isOuterAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether an atom is part of this repeating unit.
isOutputCleanable(String) - Static method in class chemaxon.formats.MFileFormatUtil
Tests whether the specified output format is cleanable.
isOverflowCalculation() - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns true if overflow calculation: maximum number of ionizable atoms exceeded and protein ionization invoked.
isPartSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup
Decides if part of the sgroup is selected or not.
isPassed() - Method in enum class com.chemaxon.common.annotations.RemovalDate
 
isPhaseShiftedMatching() - Method in class chemaxon.sss.search.SearchOptions
Get option whether phase shifted polymer matches on the original.
isPlainHydrogen() - Method in class chemaxon.struc.MolAtom
 
isPolymerendgroup() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing polymer end group H
isPolymerMatching() - Method in class chemaxon.sss.search.SearchOptions
Get option whether to search consider polymer sgroups during search.
isPositionVariation() - Method in class chemaxon.struc.MolBond
Decides whether this bond is a position variation bond.
isPositive(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
isPrefixModeSupported() - Method in interface chemaxon.naming.NameConverter
Returns true if prefix mode is supported.
isPrintEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Determines if the File->Print menu item is enabled or not.
isPropertyRecord() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
 
isPropertyRecord() - Method in interface chemaxon.marvin.io.MRecordReader
 
isPseudo() - Method in class chemaxon.struc.MolAtom
Tests whether if the atom is a pseudo atom.
isQProp() - Method in class chemaxon.struc.MolAtom
Tests whether this object represents a query property.
isQuery() - Method in class chemaxon.struc.MolAtom
Tests whether it is a query atom.
isQuery() - Method in class chemaxon.struc.MolBond
Tests whether it is query bond or has query property: any single or double single or aromatic double or aromatic smarts bond ring or chain topology For more information on smarts bond and query bonds, see The JChem Query Guide
isQuery() - Method in class chemaxon.struc.MoleculeGraph
Indicates if the molecule has query features: query atoms or query bonds.
isQuery() - Method in class chemaxon.struc.RgMolecule
Indicates if the molecule has query features.
isQuery() - Method in class chemaxon.struc.RxnMolecule
Indicates if the molecule has query features: query atoms or query bonds.
isQueryAbsoluteStereo() - Method in class chemaxon.sss.search.MolSearchOptions
Returns whether the chiral flag is ignored or not for the query molecule.
isRadical() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing radical H
isRadicalMatching() - Method in class com.chemaxon.search.MatchingOptions
Gets whether radicals are considered in search.
isRandomEnumeration() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns true if random enumeration is requested.
isReaction() - Method in class chemaxon.struc.Molecule
Checks if the structure represents a reaction or not.
isReaction() - Method in class chemaxon.struc.RgMolecule
Checks if the structure represents a reaction or not.
isReaction() - Method in class chemaxon.struc.RxnMolecule
Checks if the structure represents a reaction or not.
isReactionArrow(MoleculeGraph) - Method in class chemaxon.struc.MObject
 
isReactionErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.

Are reaction errors highlighted?

isReactionMappingIncomplete() - Method in class chemaxon.descriptors.ReactionFingerprint
Returns true if reaction molecule was not mapped completely during reaction fingerprint generation.
isReactionUnpairedMapMatching() - Method in class chemaxon.sss.search.SearchOptions
Get whether unpaired(orphan or widow) atom maps can match any atom.
isRealAtom(MolAtom) - Static method in class chemaxon.checkers.StructureCheckerUtility
Gets whether the provided atom represents an atom (and not something that should not be an atom)
isRealAtomParent() - Method in class chemaxon.struc.MoleculeGraph
Can it be a real atom parent?
isRealAtomParent() - Method in class chemaxon.struc.RgMolecule
R-group molecule objects cannot be real node parents.
isRealAtomParent() - Method in class chemaxon.struc.RxnMolecule
Reaction molecules cannot be real node parents.
isRealAtomParent() - Method in class chemaxon.struc.SelectionMolecule
Selection molecules are not real atom parents.
isRemovable() - Method in class chemaxon.struc.Sgroup
Decides whether an S-group should be ungrouped if its structure changes.
isRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Checks if the specified atom object is in the paradigmatic repeating unit or not.
isRestH(int) - Method in class chemaxon.struc.RgMolecule
Informs whether the restH condition is set to the referenced R-group definition.
isRewindable() - Method in class chemaxon.formats.MolImporter
Tests whether rewinding (seeking backwards) is possible in the underlying input stream.
isRewindable() - Method in class chemaxon.marvin.io.ArrayMDocSource
Tests whether rewinding (seeking backwards) is possible.
isRewindable() - Method in class chemaxon.marvin.io.MDocSource
Tests whether rewinding (seeking backwards) is possible.
isRewindable() - Method in class chemaxon.marvin.view.MDocStorage
Tests whether the document storage is rewindable.
isRgrouped(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if molecule with R-groups.
isRgroupsVisible() - Method in class chemaxon.marvin.beans.MarvinPane
Determines the visibility of R-group defintions.
isRgroupsVisible() - Method in class chemaxon.marvin.MolPrinter
Decides whether the R-group definitions are visible.
isRing() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isRingAtom(int) - Method in class chemaxon.calculations.Ring
Determines if an atom a ring bond or a chain bond.
isRingAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.isRingAtom(int)
isRingAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Returns true if ring atom.
isRingBond(int) - Method in class chemaxon.calculations.Ring
Determines if a bond is a ring bond or a chain bond.
isRingBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.isRingBond(int)
isRingBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines if a bond is a ring bond or a chain bond.
isRingBond(int) - Method in class chemaxon.struc.MoleculeGraph
Is this bond in ring?
isRingBondCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects ring bond count atom query properties or not.
isRingCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects ring count atom query properties or not.
isRLogicVisible() - Method in class chemaxon.marvin.MolPrinter
Is R-logic visible?.
isRotatableBond(int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines if a bond is a rotatable or not
isRotatableBond(int) - Method in class chemaxon.marvin.alignment.RotatableBondDetector
Not flexible if:
double, aromatic, triple bond single bond neighboring a triple like at cyanide chain end bonds amide thioamide: -C(=S)-NR2 sulphonamide R-S(=O)2-NR2 aniline N : C(aromatic)-N(sp3) aromatic amidine : C(aromatic)-C(=NH)-NH2 aromatic nitroso : C(aromatic)-N=O aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable) C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature: Ring bonds may be rotatable also.
isRotatableBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Determines if a bond is a rotatable or not
isRunning() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
isRunning() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
This function identifies the state of the standardizer thread
isSameParityClass(int, int, int, int, int, int, int, int) - Static method in class chemaxon.struc.MolAtom
Calculates if chirality centers in the structure and the query belong to the same parity class.
isSaveBOM() - Method in class chemaxon.marvin.common.UserSettings
 
isSaveIniEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Automatically saves user settings to an initialization file.
isScaled() - Method in class chemaxon.descriptors.MDParameters
Returns whether current parametrized metric is scaled or not.
isSearchAll() - Method in class chemaxon.checkers.RatomChecker
Gets the option determining if the checker detects all R-atoms or not.
isSearchBridgehead() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for bridgehead explicit hydrogens
isSearchCharged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for charged explicit hydrogens
isSearchContracted() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Returns if the checker is searching for contracted SGroups or not
isSearchDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker
Returns if the checker detects valence properties with the default valence of the current atom type.
isSearchDisconnected() - Method in class chemaxon.checkers.RatomChecker
Gets the option determining if the checker detects R-atoms not connected to any other atoms or not.
isSearchExpanded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Returns if the checker is searching for expanded SGroups or not
isSearchGeneric() - Method in class chemaxon.checkers.RatomChecker
Gets the option determining if the checker detects R-atoms without identifier numbers or not.
isSearchHConnected() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for H connected explicit hydrogens
isSearchIsotopic() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for isotopic explicit hydrogens
isSearchLinker() - Method in class chemaxon.checkers.RatomChecker
Gets the option determining if the checker detects R-atoms with more than one connection or not.
isSearchLonely() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for lonely explicit hydrogens
isSearchMapped() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for mapped explicit hydrogens
isSearchNested() - Method in class chemaxon.checkers.RatomChecker
Gets the option determining if the checker detects R-atoms within R-groups or not.
isSearchNonDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker
Returns if the checker detects valence properties with a non-default valence of the current atom type.
isSearchPolymerEndGroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for polymer end group explicit hydrogens
isSearchRadical() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for radical explicit hydrogens
isSearchSgroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for S-group explicit hydrogens
isSearchSgroupEnd() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for S-group end explicit hydrogens
isSearchValenceError() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for valence errored explicit hydrogens
isSearchWedged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Returns if the checker search for wedged explicit hydrogens
isSeekable() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Tests whether the record reader is seekable.
isSeekable() - Method in class chemaxon.marvin.io.MRecordImporter
Tests whether the record reader is seekable.
isSeekable() - Method in interface chemaxon.marvin.io.MRecordReader
Tests whether the record reader is seekable.
isSeekable() - Method in class chemaxon.marvin.io.PositionedInputStream
Tests whether the stream is seekable.
isSelectable() - Method in class chemaxon.marvin.beans.MViewPane
Are the cells selectable?
isSelectableNow() - Method in class chemaxon.struc.graphics.MMidPoint
 
isSelectableNow() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
isSelectableNow() - Method in class chemaxon.struc.MObject
Is the object selectable now?
isSelected() - Method in class chemaxon.marvin.space.GraphicComponent
Tells whether the component is being selected or not.
isSelected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
isSelected() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if the whole component is selected.
isSelected() - Method in class chemaxon.struc.MObject
Is the object selected?
isSelected() - Method in class chemaxon.struc.MolAtom
Tests whether this atom is selected.
isSelected() - Method in class chemaxon.struc.NoStructure
 
isSelected(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Tells whether a part of the component is selected.
isSelected(ComponentElement) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if the given item is selected.
isSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup
Is the sgroup or part of the sgroup selected?
isSelectedAtom(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
isSelectedAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if the atom with the given index is selected.
isSelectedComponent(int) - Method in class chemaxon.marvin.space.GraphicCell
Tells whether the given component is selected.
isSelfReference(MProp) - Method in class chemaxon.struc.MoleculeGraph
Tests whether the specified property is a self reference to the molecule.
isSelfReference(MProp) - Method in class chemaxon.struc.MPropertyContainer
Tests whether a property is a self reference to the containing molecule.
isSelfReference(MProp) - Method in class chemaxon.struc.RgMolecule
Tests whether the specified property is a self reference to the molecule.
isSetColoringEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Is the atom/bond set coloring enabled?
isSetColoringEnabled() - Method in class chemaxon.marvin.MolPrinter
Returns true if atoms and bonds are colored according to the color of the pre-defined set they belong to.
isSgroup() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing s-group H
isSgroup() - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 14.7.7, no replacement.
Not supported feature.
isSgroupDataFormatted() - Method in class chemaxon.marvin.beans.MarvinPane
Returns whether the Sgroup data is formatted.
isSgroupDataFormatted() - Method in class chemaxon.marvin.MolPrinter
Returns whether the Sgroup data is formatted.
isSgroupend() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing s-group end H
isShowMultiMoleculeOnEditSource() - Method in class chemaxon.marvin.common.UserSettings
 
isSimilarTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Tests if the molecule graph is similar to another graph.
isSimpleMolecule() - Method in class chemaxon.struc.MDocument
Tests whether the document is equivalent to a simple molecule.
isSingleCellLabelShown() - Method in class chemaxon.marvin.view.swing.TableOptions
Tests whether label should be shown for a single cell.
isSingleStepReaction() - Method in class chemaxon.struc.RxnMolecule
Deprecated, for removal: This API element is subject to removal in a future version.
isSingleUpOrDownBond() - Method in class chemaxon.standardizer.actions.ClearStereoAction
Gets the single wedge value of absolute stereo action
isSizeFinal() - Method in class chemaxon.marvin.view.MDocStorage
Tests whether the storage size is final.
isSketchWindowOpened(int) - Method in class chemaxon.marvin.beans.MViewPane
Checks whether the molecule from the specified cell is opened in a sketcher window or not.
isSmallestRingSizeChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects smallest ring size atom query properties or not.
isSmartsQueryChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects SMARTS query properties or not.
isSMILESShown() - Method in class chemaxon.marvin.view.swing.TableOptions
Are SMILES strings shown in the table?
isSmoothBackgroundEnabled() - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the background is enabled to be smooth, so that it does not have a homogenous color.
isSpecBeilsteinGeneric(String) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Tests whether the specified symbol is a Beilstein Generic except A, Q and X.
isSpecialAtom(MolAtom) - Static method in class chemaxon.checkers.StructureCheckerUtility
Gets whether the provided atom is special
isSpecIsotopeSymbolPreferred() - Method in class chemaxon.struc.MolAtom
Tests whether special symbol is used.
isSpecIsotopeSymbolUsed() - Method in class chemaxon.struc.MolAtom
Tests whether special symbol is used.
isStandardizationMandatory() - Method in class chemaxon.descriptors.MDParameters
Checks is Standardization of molecules is mandatory for the corresponding MolecularDescriptor before descriptor generation.
isStarAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether an atom is a star atom in this S-group.
isStartupSelectorShown() - Method in class chemaxon.marvin.common.UserSettings
 
isStereo(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility
Deprecated.
Gets whether the molecule is stereo
isStereoFix() - Method in class chemaxon.standardizer.Standardizer
Gets whether last stereo fix should be applied
isStreamOutput() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Returns true if stream output.
isSubFormatOf(String, String) - Static method in class chemaxon.formats.MFileFormatUtil
Tests whether a format is a sub-format of another format.
isSubsetChangable() - Method in class chemaxon.marvin.view.swing.TableOptions
Returns whether startAt and maxSize can be changed.
isSubsetOf(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.
isSubSetOf(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.
isSubSetOf(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.
isSubstitutionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects substitution count atom query properties or not.
isSupportedTransferFormat(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Checks whether the given format is available in the current environment or not.
isSwitchOffAllProtectsForTDF() - Method in class chemaxon.sss.search.MolSearchOptions
Deprecated, for removal: This API element is subject to removal in a future version.
Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.
isSymmetric() - Method in class chemaxon.struc.MoleculeGraph
Tests whether the molecule graph is symmetric.
isSymmetricalFuzzy() - Method in class chemaxon.descriptors.PFParameters
 
isTargetAbsoluteStereo() - Method in class chemaxon.sss.search.MolSearchOptions
Returns whether the chiral flag is ignored or not for the target molecule.
isTerminal(MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
This method returns true if the MolBond represented by molBond parameter is terminal in a Molecule structure, false otherwise
isTerminalAtom() - Method in class chemaxon.struc.MolAtom
Determines whether it is a terminal atom or not.
isThicknessSet() - Method in class chemaxon.struc.graphics.MPolyline
Checks if the line thickness is set.
isThreeLetterPeptideDisplay() - Method in class chemaxon.marvin.MolPrinter
Decides whether the Peptide display settings set to three letter.
isThrowExceptionOnTimeout() - Method in class chemaxon.sss.search.SearchOptions
Is search should throw exception upon timeout.
isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup
Decides if the whole sgroup is selected or not.
isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Decides if the whole superatom sgroup is selected or not.
isTraditionalNitrogensAllowed() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
Returns if the traditional way of the ylidene and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O, CN(=C)=O and c1ccccn1=O is accepted if false they are marked as valence error.
isTransDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker
Returns the detectTransDoubleBonds
isTransformable() - Method in class chemaxon.struc.graphics.MAtomSetPoint
Is it a transformable object?
isTransformable() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Is it a transformable object?
isTransformable() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
isTransformable() - Method in class chemaxon.struc.MObject
Is it a transformable object?
isTransformationEnabled() - Method in class chemaxon.marvin.common.UserSettings
Gets the transformation enabled/disabled.
isTransitionMetal(int) - Static method in class chemaxon.struc.PeriodicSystem
Checks if the given atom is a transition metal, IB-VIIIB.
isTransparent() - Method in class chemaxon.marvin.MolPrinter
Returns the transparency state of the painting.
isTransparentBackgroundEnabled() - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the background is transparent.
isTripleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker
Returns the detectTripleBonds
isUndecided(Object) - Static method in class chemaxon.jep.ChemJEP
Returns whether the result object is undecided.
isUndefinedRAtomMatchingGroup() - Method in class chemaxon.sss.search.SearchOptions
Gets whether undefined R atom matches group of atoms.
isUnitDisplayed() - Method in class chemaxon.struc.sgroup.DataSgroup
Gets whether the units string should be displayed.
isUnsaturationChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Gets the option determining if the checker detects unsaturation atom query properties or not.
isURL(String) - Static method in class chemaxon.marvin.space.MSpaceEasy
Tells whether the given path is an URL (Uniform Resource Locator) or not.
isURLOrFileName(String) - Static method in class chemaxon.formats.MFileFormatUtil
Tests whether the specified string is an URL (absolute or relative) or file name.
isUseDefaultSalts() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Gets whether default salt dictionary should be used
isUseDefaultSolvents() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Gets whether default solvent dictionary should be used
isUsefulForQuery() - Method in class chemaxon.sss.search.MolComparator
Decides based on the query and the search object if the comparator should be used or not.
isUsefulForTarget() - Method in class chemaxon.sss.search.MolComparator
Decides based on the query, target and the search object if the comparator should be used or not.
isValenceCheckEnabled() - Method in class chemaxon.struc.MoleculeGraph
Determines whether valence check is enabled on this molecule graph.
isValenceerror() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing valence error H
isValenceErrorvisible() - Method in class chemaxon.marvin.MolPrinter
Returns the visibility state of valence errors.
isValenceErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane
Are valence errors highlighted?
isValenceErrorVisible() - Method in class chemaxon.marvin.common.UserSettings
Are valence errors visible?
isValenceErrorVisibleInView() - Method in class chemaxon.marvin.beans.MViewPane
Are valence errors highlighted?
isValenceErrorVisibleInView() - Method in class chemaxon.marvin.common.UserSettings
Are valence errors visible in MarvinView?
isValenceMatching() - Method in class chemaxon.sss.search.SearchOptions
Get the valence matching option
isValencePropertyVisible() - Method in class chemaxon.marvin.common.UserSettings
Tells wheter the atom valence property is visible or not.
isValencePropertyVisible() - Method in class chemaxon.marvin.MolPrinter
Gets the atom valence property visibility
isValid() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Excluded object is initialized.
isValid() - Method in class chemaxon.checkers.AbstractStructureChecker
 
isValid() - Method in class chemaxon.checkers.AttachedDataChecker
 
isValid() - Method in class chemaxon.checkers.InvalidChecker
 
isValid() - Method in class chemaxon.checkers.PseudoAtomChecker
 
isValid() - Method in interface chemaxon.checkers.StructureChecker
Returns true if the checker's configuration is valid, false otherwise
isValid() - Method in class chemaxon.checkers.SubstructureChecker
 
isValid() - Method in class chemaxon.marvin.services.DynamicArgument
 
isValid() - Method in class chemaxon.marvin.services.ServiceArgument
Returns true if service argument is valid
isValid() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
Returns true if editor represents a valid descriptor in current state
isValid() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
isValid() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
isValid() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Gets whether the configuration contains only valid elements
isValid() - Method in interface chemaxon.standardizer.StandardizerAction
Returns true if the action's parameters are valid, false otherwise
isValid(MProp) - Method in class chemaxon.struc.MPropertyContainer
Tests whether a coordinate dependent property is still valid.
isValid(InputStream) - Static method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
Checks whether the contents of the provided input stream is a valid configuration XML
isvalidateSgroupsAtCreation() - Method in class chemaxon.marvin.common.UserSettings
Is the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.
isValidLinkNode(int, int, int) - Method in class chemaxon.struc.MoleculeGraph
Checks whether the specified link atom is valid or not.
isValidSourceAndSinkForMolecule(Object, Object, Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule) or one of the other implementations instead.
isValidSourceForMolecule(Object, Molecule) - Static method in class chemaxon.struc.graphics.MEFlow
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidSource(MolAtom, Molecule) or EFlowPlacementValidators.isValidSource(MolAtom[], Molecule) or EFlowPlacementValidators.isValidSource(MolBond, Molecule) .
isValidXMLConfiguration(InputStream) - Static method in class chemaxon.standardizer.configuration.reader.StandardizerXMLReader
Checks whether the contents of the provided input stream is a valid configuration XML
isVerbose() - Method in class chemaxon.marvin.space.GraphicCell
Gets the verbose level.
isVerbose() - Method in class chemaxon.marvin.space.GraphicScene
Gets the verbose level.
isVerbose() - Method in class chemaxon.sss.search.Search
For debugging purposes only.
isVerbose() - Method in class chemaxon.sss.search.SearchOptions
For debugging purposes only.
isViewAtomMarkEnabled() - Method in class chemaxon.marvin.common.UserSettings
Returns true if atom mark and highlight is enabled in View.
isViewWindowOpened(int) - Method in class chemaxon.marvin.beans.MViewPane
Checks whether the view canvas of the specified cell is detached into a separate window or not.
isVisible() - Method in class chemaxon.marvin.space.ComponentElement
Returns true if the ComponentElement is visible in the component.
isVisible() - Method in class chemaxon.marvin.space.GraphicComponent
Returns true if this component is allowed to be drawn.
isVisible() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns true if any of its visualizers is visible.
isVisible() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
isVisible() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if this component is allowed to be drawn.
isVisible() - Method in class chemaxon.marvin.space.monitor.Monitor
A monitor is visible if all of its selected components are visible, and it is not hidden explicitly.
isVisible() - Method in class chemaxon.struc.Sgroup
Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.
isVisible(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Returns true if the specified part of the component is allowed to be drawn.
isVisible(ComponentElement) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns true if the gien ComponentElement is visible.
isVisible(ComponentElement) - Method in class chemaxon.marvin.space.MoleculeComponent
Returns true if the given item is visible.
isVisible(ComponentElement) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns true, because a PositionMonitor cannot be hidden.
isVolumeVisible() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Tells whether the volumetric data is shown or not.
isWedged() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Gets the value of property for removing wedged H
isWeighted() - Method in class chemaxon.descriptors.MDParameters
Returns whether current parametrized metric is weighted or not.
isZoomToScaffoldOnLoad() - Method in class chemaxon.marvin.common.UserSettings
 
ITALIC - Static variable in class chemaxon.struc.graphics.MFont
Italic font style.
ITEM_COUNT - Static variable in class chemaxon.marvin.space.monitor.Label
 
items - Variable in class chemaxon.marvin.plugin.gui.ParameterPanel
 
iterator() - Method in class chemaxon.marvin.io.MDocSource
Gets a molecule iterator for this document source.
iterator(Iterator<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper
Returns an iterator that will return the mapped molecules from the specified iterator.
NOTE: the returned iterator provides the same molecule instances with maps added
iterator(Iterator<Molecule>, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Returns an iterator that will wrap the specified iterator and standardizes all molecules.
iterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
Returns an iterator that will return the mapped molecules from the specified iterator using the specified number of threads for mapping.
NOTE: the returned iterator provides the same molecule instances with maps added
iterator(Iterator<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
Returns an iterator that will return the mapped molecules from the specified iterator using the specified mappers for mapping.
IteratorFactory - Class in chemaxon.util.iterator
The IteratorFactory class provides implementations of Iterator to ease the handling of atoms and bonds used in Molecule objects and its descendants.
IteratorFactory(Molecule) - Constructor for class chemaxon.util.iterator.IteratorFactory
Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.
IteratorFactory(MoleculeGraph) - Constructor for class chemaxon.util.iterator.IteratorFactory
Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.
IteratorFactory(Molecule, int, int) - Constructor for class chemaxon.util.iterator.IteratorFactory
Constructs an iterator factory for the specified molecule with a specified atom and bond related behavior.
IteratorFactory.AtomIterator - Class in chemaxon.util.iterator
The AtomIterator class provides an iterator for the atoms of the specified molecule of the factory according to the atom related behavior set in the factory.
IteratorFactory.AtomNeighbourIterator - Class in chemaxon.util.iterator
The AtomNeighbourIterator class provides an iterator to process the atoms connecting to a specified atom according to the atom and bond related behavior of this factory.
IteratorFactory.BondIterator - Class in chemaxon.util.iterator
The BondIterator class provides an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.
IteratorFactory.BondNeighbourIterator - Class in chemaxon.util.iterator
The BondNeighbourIterator class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory.
IteratorFactory.NeighbourIterator<E> - Class in chemaxon.util.iterator
The NeighbourIterator class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory.
IteratorFactory.RgComponentIterator - Class in chemaxon.util.iterator
The RgComponentIterator class provides an iterator to process the rgroup definition components in the specified molecule of the factory.
IteratorFactory.RxnComponentIterator - Class in chemaxon.util.iterator
The RxnComponentIterator class provides an iterator to process the components (reactant, product and agent components) in the reaction molecule of the factory.
IteratorFactory.SgroupIterator - Class in chemaxon.util.iterator
The SgroupIterator class provides an iterator for the s-groups of the specified molecule of the factory.
IUPACNamingPlugin - Class in chemaxon.marvin.calculations
IUPAC name generator plugin.
IUPACNamingPlugin() - Constructor for class chemaxon.marvin.calculations.IUPACNamingPlugin
 

J

JAN_01_2025 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate
 
JAN_01_2026 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate
 
jar - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
 
JCHEM - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem Base
JCHEM_FOR_EXCEL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem for Excel
JCHEM_FOR_OFFICE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem for Office
JCHEM_FOR_SHAREPOINT - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem for SharePoint
JCHEM_FOR_SHAREPOINT_SEARCH - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem for SharePoint Search
JepException - Exception in chemaxon.jep
Exception thrown during the compilation or evaluation of Chemical Terms exceptions.
JepException() - Constructor for exception chemaxon.jep.JepException
 
JepException(String) - Constructor for exception chemaxon.jep.JepException
 
JepException(String, Throwable) - Constructor for exception chemaxon.jep.JepException
 
JepException(Throwable) - Constructor for exception chemaxon.jep.JepException
 
JKLUSTOR - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JKlustor
jointPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
JPEG - Static variable in class chemaxon.formats.MFileFormat
JPEG format.
JsonServiceDescriptor - Class in chemaxon.marvin.services.json
Service descriptor of JSON type requests.
JsonServiceDescriptor() - Constructor for class chemaxon.marvin.services.json.JsonServiceDescriptor
 
JsonServiceDescriptor.Method - Enum Class in chemaxon.marvin.services.json
request method
jSplitPane1 - Variable in class chemaxon.marvin.space.MSpaceEasy
 
JUL_01_2024 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate
 
JUL_01_2025 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate
 
JUL_01_2026 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate
 

K

K - Static variable in class chemaxon.core.ChemConst
 
keep - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
KEEP_BOTH_FLEXIBLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
Keep both structures flexible during the alignment.
KEEP_BOTH_RIGID - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
Keep both structures conformationally rigid during the alignment.
KEEP_FIRST_RIGID_SECOND_FLEXIBLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
Keep the first reference structure rigid, and the second as flexible during the alignment.
KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
As of AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).
KEEP_HYDROGENS - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
 
KEEP_MAPPING - Static variable in class chemaxon.standardizer.actions.MapAction
keep mapping property
KEEP_MAPPING - Static variable in class chemaxon.standardizer.actions.MapReactionAction
keep mapping property
KEEP_RINGS - Enum constant in enum class com.chemaxon.search.mcs.RingHandlingMode
This option specifies that rings should not be broken.
keepHydrogens - Variable in class chemaxon.marvin.plugin.CalculatorPlugin
 
KEEPLARGEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Keep largest fragment
keepLargestFragment(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
keeporiginalLineEnding - Variable in class chemaxon.marvin.io.PositionedInputStream
 
KEEPSMALLEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Keep largest fragment
KEKULE_MATCH_AMBIG - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
Ambiguous aromatic parts are not aromatized in the target Markush structures.
KEY_VALUE_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Parameter key and value separator token of the action string
KNOWN_TETRAHEDRAL_STEREO - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Known tetrahedral stereo centers (even, odd).
KnownAtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop
Filter for known atrop stereo centers.
KnownAtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter
 
knownAtropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the KNOWN atrop stereocenters.
KnownAxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial
Filter for known axial centers.
KnownAxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter
 
knownAxialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the KNOWN axial stereocenters.
KnownDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
Filter for known (CIS or TRANS) double bonds.
KnownDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter
 
knownResolvedStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the known, resolved tetrahedral stereogenic centers.
knownResolvedStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the known, resolved tetrahedral stereogenic centers (with attached data).
KnownResolvedTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral
Filter for known, resolved tetrahedral centers.
KnownResolvedTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter
 
Kr - Static variable in class chemaxon.core.ChemConst
 

L

La - Static variable in class chemaxon.core.ChemConst
 
label - Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
 
Label - Class in chemaxon.marvin.space.monitor
Label is a special monitor that watches 1 object and shows its description.
Label() - Constructor for class chemaxon.marvin.space.monitor.Label
Creates a new Label and sets the size of the font to medium.
LABEL - Static variable in class chemaxon.struc.NoStructure
Label for NoStructure.
LABEL - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Property display type: display in label.
LABEL_AUTO - Static variable in class chemaxon.struc.sgroup.SgroupAtom
 
LABEL_DEFAULT - Static variable in class chemaxon.struc.sgroup.SgroupAtom
 
labelAsAnchor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
labelScale - Variable in class chemaxon.marvin.space.monitor.Label
 
labelSize - Variable in class chemaxon.marvin.space.monitor.Label
Size of drawn labels.
LARGE_FONT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Label
 
largestring - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
largestRing() - Method in class chemaxon.calculations.Ring
Identifies the atoms of the largest ring (number of atoms) in the molecule.
largestRing() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.largestRing()
largestRingSize() - Method in class chemaxon.calculations.Ring
Calculates the size of the largest ring in the molecule (SSSR based).
largestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.largestRingSize()
largestRingSizeOfAtom(int) - Method in class chemaxon.calculations.Ring
Calculates the size of the largest ring an atom is a member of (SSSR based).
largestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.largestRingSizeOfAtom(int)
largestringsystem - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
largestRingSystem() - Method in class chemaxon.calculations.Ring
Identifies the atoms of the largest ring system (number of rings) in the molecule.
largestRingSystem() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.largestRingSystem()
largestRingSystemSize() - Method in class chemaxon.calculations.Ring
Calculates the size of the largest ring system (number of rings) in the molecule.
largestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.largestRingSystemSize()
LAST_LICENSE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
lastModified(String) - Static method in class chemaxon.util.DotfileUtil
Gets the last modification time for a dotfile.
lastPage - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
The last page of the document that should be annotated.
lastPage(Integer) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
LAYOUT - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "layout".
LAYOUT_HEADER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "layoutH".
LDIR_ABOVE - Static variable in class chemaxon.struc.MolAtom
Implicit Hydrogen(s) are above the element symbol.
LDIR_BELOW - Static variable in class chemaxon.struc.MolAtom
Implicit Hydrogen(s) are below the element symbol.
LDIR_LEFT - Static variable in class chemaxon.struc.MolAtom
Implicit Hydrogen(s) are left to element symbol.
LDIR_RIGHT - Static variable in class chemaxon.struc.MolAtom
Implicit Hydrogen(s) are right to element symbol.
LDParameters - Class in chemaxon.descriptors.scalars
Manages parameters for the LogD scalar descriptor class.
LDParameters() - Constructor for class chemaxon.descriptors.scalars.LDParameters
Creates an empty object.
LDParameters(File) - Constructor for class chemaxon.descriptors.scalars.LDParameters
Creates a new object based on a given configuration file.
LDParameters(String) - Constructor for class chemaxon.descriptors.scalars.LDParameters
Creates a new object based on a given configuration string.
LEAVE_COORDS_UNCHANGED - Static variable in interface chemaxon.struc.sgroup.Expandable
Coordinates are not calculated during expand or contract.
leftMul(CTransform3D) - Method in class chemaxon.struc.CTransform3D
Multiplies by another matrix from left.
length - Variable in class chemaxon.descriptors.MDParameters
the length of the descriptor: the number of cells
length() - Method in class chemaxon.marvin.io.MRecordImporter
Gets the length of the input file.
length() - Method in class chemaxon.marvin.io.PositionedInputStream
Gets the file length.
length() - Method in class chemaxon.struc.graphics.MTextDocument
Gets the length of the document.
length() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the number of characters.
length() - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets text length.
lengthSquare() - Method in class chemaxon.struc.DPoint3
Calculates the square of the length of the vector defining the point.
Li - Static variable in class chemaxon.core.ChemConst
 
license() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the license required for this action.
LICENSE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "license".
LICENSE_FILE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "licenseFile".
LicenseDialog - Class in chemaxon.marvin.uif.dialog
 
LicenseDialog(Window) - Constructor for class chemaxon.marvin.uif.dialog.LicenseDialog
 
licenseEnvironment - Variable in class chemaxon.marvin.plugin.CalculatorPlugin
Member storing license environment.
LicenseException - Exception in chemaxon.license
 
LicenseException(String) - Constructor for exception chemaxon.license.LicenseException
Constructs an instance of LicenseException with the specified detail message.
LicenseException(String, String) - Constructor for exception chemaxon.license.LicenseException
 
LicenseManager - Class in chemaxon.license
LicenseManager is a helper class to manage licenses of Chemaxon products.
LicenseManager() - Constructor for class chemaxon.license.LicenseManager
 
LIGAND_ERROR_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "ligandErrorVisible".
ligands() - Method in class chemaxon.struc.MolAtom
Provides a list view of the ligands of the atom.
lineByteBuffer - Variable in class chemaxon.marvin.io.PositionedInputStream
Lines are read into this buffer.
lineCurrentColumn - Variable in class chemaxon.marvin.io.PositionedInputStream
Column position of the next character to read.
lineIteratorFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create an Iterator that can be closed from a not nullable location.
lineIteratorFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create an Iterator that can be closed from a not nullable location.
lineWidth - Variable in class chemaxon.marvin.space.MoleculeComponent
 
LINKNODE - Static variable in class chemaxon.sss.search.MarkushFeature
Deprecated.
Expansion type: link node.
LIST - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the inclusive atom list.
LISTEN_MOUSE_EVENT - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "listenmouseevent".
LISTEN_PROPERTY_CHANGE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "listenpropertychange".
listener - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
A listener that will be notified of the progress of the annotation.
load() - Static method in class com.chemaxon.calculations.admet.HergActivityPredictor
Initializes the default hERG activity model.
load() - Static method in class com.chemaxon.calculations.admet.HergClassPredictor
Initializes the default hERG classification model.
load() - Method in class com.chemaxon.calculations.gui.PluginFactory
Loads default property file.
load(String, String) - Method in class com.chemaxon.calculations.gui.PluginFactory
Loads plugin data from property file.
load(Properties) - Method in class com.chemaxon.calculations.gui.PluginFactory
Loads plugin data from properties.
LOAD_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "loadMols".
loadClass(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Loads a class, first tries from original CALSSPATH, then from the class loader used to load this plugin class.
loadFrags() - Method in class chemaxon.marvin.util.MolFragLoader
Loads fragments, fuses them and returns the resulting molecule.
loadFrags(boolean) - Method in class chemaxon.marvin.util.MolFragLoader
Loads fragments, fuses them and returns the resulting molecule.
loadFrags(MoleculeGraph, boolean) - Method in class chemaxon.marvin.util.MolFragLoader
Loads fragments, fuses them to the specified molecule.
loadFrags(MoleculeGraph, int, boolean) - Method in class chemaxon.marvin.util.MolFragLoader
Loads fragments, fuses them to the specified molecule.
loadPluginClass(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Loads a plugin class, first tries to load it from CLASSPATH, then from JAR.
loadRgroupMembers(RgMolecule, int) - Method in class chemaxon.marvin.util.MolFragLoader
Loads fragments and adds them as R-group definition members in the specified molecule.
LOCAL_MENU_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
local menu name property of checker
LocalLocationControl - Class in chemaxon.marvin.space.monitor
This control is to change the location say translate a GraphicComponent in its local coordinate system.
LocalLocationControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.LocalLocationControl
Creates a new instance of LocalLocationControl
localMenuName() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the local menu name of the checker
LocalOrientationControl - Class in chemaxon.marvin.space.monitor
This control is to change the orientation say rotate a GraphicComponent in its local coordinate system.
LocalOrientationControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.LocalOrientationControl
Creates a new instance of LocalOrientationControl
LocalServiceDescriptor - Class in chemaxon.marvin.services.localservice
Service Descriptor for java based local services.
LocalServiceDescriptor() - Constructor for class chemaxon.marvin.services.localservice.LocalServiceDescriptor
 
locateCell(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Returns the internal index of the cell under x,y position.
locateCellId(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Returns the id of the cell under x, y position.
locateObject(int, int) - Method in class chemaxon.marvin.space.GraphicCell
Returns the internal id of the component under x, y location, or the id of the cell itself if there is no component in that location.
locateObject(int, int) - Method in class chemaxon.marvin.space.GraphicComponent
Picking action at x, y coordinates, returns the z coordinate of the nearest picked item, or -1.
locateObject(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Returns the identifire of the object under x,y position.
locateObject(int, int) - Method in class chemaxon.marvin.space.monitor.Label
Pickes the label in x, y position.
locateObject(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Pickes the control in x, y position.
locateObject(int, int, Class) - Method in class chemaxon.marvin.space.GraphicCell
Returns the internal id of the given class component under x, y location, or the id of the cell itself if there is no component in that location.
locateObject(int, int, Class) - Method in class chemaxon.marvin.space.GraphicScene
Returns the identifire of the given class object under x,y position.
locationNearEdge(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Tells whether the given location is near to any edges of any cell.
locationNearEdgeX(int, int) - Method in class chemaxon.marvin.space.GraphicCell
Tells whether the given location is near the vertical edges of the cell.
locationNearEdgeX(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Tells whether the given location is near the vertical edges of any cell.
locationNearEdgeY(int, int) - Method in class chemaxon.marvin.space.GraphicCell
Tells whether the given location is near the horizontal edges of the cell.
locationNearEdgeY(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Tells whether the given location is near the horizontal edges of any cell.
LOG - Static variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Logger object.
LogD - Class in chemaxon.descriptors.scalars
Implements logD value as a scalar descriptor.
LogD() - Constructor for class chemaxon.descriptors.scalars.LogD
Creates a new, empty logD descriptor.
LogD(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.LogD
Copy constructor.
LogD(LDParameters) - Constructor for class chemaxon.descriptors.scalars.LogD
Creates a new instance according to the parameters given.
LogD(String) - Constructor for class chemaxon.descriptors.scalars.LogD
Creates a new instance according to the parameters given.
LOGD - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Calculated distribution coefficient az pH 7.4.
LOGDCALCULATOR - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
logDPlugin - Class in chemaxon.marvin.calculations
Plugin class for logD calculation.
logDPlugin() - Constructor for class chemaxon.marvin.calculations.logDPlugin
Constructor.
logger - Variable in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
LogP - Class in chemaxon.descriptors.scalars
Implements LogP value as a scalar descriptor.
LogP() - Constructor for class chemaxon.descriptors.scalars.LogP
Creates a new, empty logP descriptor.
LogP(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.LogP
Copy constructor.
LogP(SDParameters) - Constructor for class chemaxon.descriptors.scalars.LogP
Creates a new instance according to the parameters given.
LogP(String) - Constructor for class chemaxon.descriptors.scalars.LogP
Creates a new instance according to the parameters given.
LOGP - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Lipophilicity, calculated partition coefficient.
logPath - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the program error log file.
logPPlugin - Class in chemaxon.marvin.calculations
Plugin class for logP calculation.
logPPlugin() - Constructor for class chemaxon.marvin.calculations.logPPlugin
Constructor.
LOGS - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
LOGS - Enum constant in enum class com.chemaxon.calculations.solubility.SolubilityUnit
Solubility is expressed in base-10 logarithm unit.
logToDebug(Log, String, boolean) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Append to log.
LONE_PAIR_TYPE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
LONE_PAIRS_AS_LINE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "lonePairsAsLine".
LONE_PAIRS_AUTO_CALCULATION - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "lonePairsAutoCalc".
LONE_PAIRS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "lonePairsVisible".
LONELY_H - Static variable in class chemaxon.struc.MolAtom
Include lonely Hydrogen atom(s).
lonePairCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
 
lonePairRealCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
 
lonePairState - Static variable in class chemaxon.struc.graphics.MEFlow
 
LOOSE - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Loose aromatization
LOOSE - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
LOW - Enum constant in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
Low solubility.
LOW_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
low priority value
LOWEST_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
the lowest priority value
lowestEigenvalues - Variable in class chemaxon.descriptors.BCUT
 
lowPrecisions - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
LP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
LP - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the lone pair.
Lr - Static variable in class chemaxon.core.ChemConst
 
Lu - Static variable in class chemaxon.core.ChemConst
 
Lv - Static variable in class chemaxon.core.ChemConst
 

M

m - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
 
m - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
 
M - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
 
M - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
 
m00 - Variable in class chemaxon.struc.CTransform3D
The m00 element of the matrix.
m01 - Variable in class chemaxon.struc.CTransform3D
The m01 element of the matrix.
m02 - Variable in class chemaxon.struc.CTransform3D
The m02 element of the matrix.
m03 - Variable in class chemaxon.struc.CTransform3D
The m03 element of the matrix.
m10 - Variable in class chemaxon.struc.CTransform3D
The m10 element of the matrix.
m11 - Variable in class chemaxon.struc.CTransform3D
The m11 element of the matrix.
m12 - Variable in class chemaxon.struc.CTransform3D
The m12 element of the matrix.
m13 - Variable in class chemaxon.struc.CTransform3D
The m13 element of the matrix.
m20 - Variable in class chemaxon.struc.CTransform3D
The m20 element of the matrix.
m21 - Variable in class chemaxon.struc.CTransform3D
The m21 element of the matrix.
m22 - Variable in class chemaxon.struc.CTransform3D
The m22 element of the matrix.
m23 - Variable in class chemaxon.struc.CTransform3D
The m23 element of the matrix.
m30 - Variable in class chemaxon.struc.CTransform3D
The m30 element of the matrix.
m31 - Variable in class chemaxon.struc.CTransform3D
The m31 element of the matrix.
m32 - Variable in class chemaxon.struc.CTransform3D
The m32 element of the matrix.
m33 - Variable in class chemaxon.struc.CTransform3D
The m33 element of the matrix.
MacroMoleculeComponent - Class in chemaxon.marvin.space
MacroMoleculeComponent is a visualizer of complex structures.
MacroMoleculeComponent() - Constructor for class chemaxon.marvin.space.MacroMoleculeComponent
Creates a new instance of MacroMoleculeComponent
MacroMoleculeComponent(MacroMolecule) - Constructor for class chemaxon.marvin.space.MacroMoleculeComponent
Creates a new instance of MacroMoleculeComponent
MacroMoleculeComponent.MoleculeVisualizer - Interface in chemaxon.marvin.space
 
main(String[]) - Static method in class chemaxon.checkers.StructureCheck
Standard JAVA Main function which delegates the run mechanism to the StructureCheck.run(String[]) method.
main(String[]) - Static method in class chemaxon.descriptors.MolecularDescriptor
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed, no replacement.
main(String[]) - Static method in class chemaxon.descriptors.ReactionFingerprint
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed, no replacement.
main(String[]) - Static method in class chemaxon.formats.MdlCompressor
Main program.
main(String[]) - Static method in class chemaxon.formats.MolConverter
Main method.
main(String[]) - Static method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
This main method will be removed, CLI interfaces should not be used directly from Java code.
main(String[]) - Static method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Command line entry point.
main(String[]) - Static method in class com.chemaxon.version.VersionInfo
Main method that prints out the version information into the standard output.
mainMChemicalStruct - Variable in class chemaxon.struc.MDocument
 
mainMMoleculeMovie - Variable in class chemaxon.struc.MDocument
 
mainWithoutExit(String[]) - Static method in class chemaxon.formats.MolConverter
Same as main(), but never calls System.exit().
MajorMicrospeciesAccessorPlugin - Class in chemaxon.marvin.calculations
Common base class for all plugins with possible major microspecies input.
MajorMicrospeciesAccessorPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Constructor.
MajorMicrospeciesPlugin - Class in chemaxon.marvin.calculations
Plugin class that calculates the major microspecies on a given pH.
MajorMicrospeciesPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Constructor.
makeColor(String) - Static method in class chemaxon.struc.MObject
 
makeEditMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
Adds menu items to the specified Edit menu.
makeHelpMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 3.4, MarvinPane.addHelpMenu(java.awt.Container) should be used.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.Molecule
Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Copies some properties of this molecule to the other one specified as argument.
makeRecentFileListMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
Read the recent file list from marvin.properties, and add it to the specified parent menu.
makeSaveAsMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
Creates the "Save As" menu and adds it to the specified parent menu.
makeStructureMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
 
makeTableMenu(Container) - Method in class chemaxon.marvin.view.swing.TableSupport
Creates Table menu items.
makeToolsMenu() - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 3.4, MarvinPane.addToolsMenu(java.awt.Container) should be used.
makeViewMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
Adds menu items to the specified View menu.
manuallySetNormals(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
If this is set by true, we do not want to explicitly set normal vectors, but SurfaceComponent will compute them automatically.
map(RxnMolecule) - Method in class com.chemaxon.mapper.AutoMapper
Maps the reaction.
map(T) - Method in interface com.chemaxon.mapper.Mapper
Marks the matching parts of item with the same identifier.
MapAction - Class in chemaxon.standardizer.actions
Map standardizer action
MapAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MapAction
Initializes the action
MapMoleculeFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which maps the atoms of the molecule incrementally
MapMoleculeFixer() - Constructor for class chemaxon.fixers.MapMoleculeFixer
 
MAPPED_H - Static variable in class chemaxon.struc.MolAtom
Mapped Hydrogen atom(s).
Mapper<T> - Interface in com.chemaxon.mapper
Provides support for mapping parts of <T> instances by finding the matching parts and mark them with the same identifier.
Mapper.MappingStyle - Enum Class in com.chemaxon.mapper
Available mapping styles by Mapper
MAPPING_STYLE - Static variable in class chemaxon.standardizer.actions.MapAction
mapping style property
MAPPING_STYLE - Static variable in class chemaxon.standardizer.actions.MapReactionAction
mapping style property
mapPropertyFile(String, float, float) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
mapPropertyToSurface(VolumetricData) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Coloring surface based on the given grid.
mapPropertyToSurface(Grid) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
mapReaction(MolImporter, MolExporter) - Static method in class com.chemaxon.mapper.AutoMapper
Reads the reactions from the importer, maps them, and writes to the exporter.
mapReaction(MolImporter, MolExporter, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
Reads the reactions from the importer, maps them, and writes to the exporter.
mapReaction(MolImporter, MolExporter, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
Reads the reactions from the importer, maps them, and writes to the exporter.
mapReaction(Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper
Maps the reactions in the specified collection using multiple threads if possible.
mapReaction(AutoMapper.Options, Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper
Maps the reactions in the specified collection using the specified options.
mapReaction(Mapper<RxnMolecule>[], Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper
Maps the reactions in the specified collection using the specified mappers in multiple threads.
mapReaction(Collection<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper
Maps the reactions in the specified collection using multiple threads if possible.
mapReaction(Collection<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
Maps the reactions in the specified collection using the specified options.
mapReaction(Collection<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
Maps the reactions in the specified collection using the specified mappers in multiple threads.
MapReactionAction - Class in chemaxon.standardizer.actions
Map reaction standardizer action
MapReactionAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MapReactionAction
Initializes the action
MapReactionFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which maps the reaction with AutoMapper.
MapReactionFixer() - Constructor for class chemaxon.fixers.MapReactionFixer
Default constructor
MARGIN_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "marginSize".
MARK_BONDS - Static variable in class chemaxon.standardizer.actions.MapAction
mark bonds property
MARK_BONDS - Static variable in class chemaxon.standardizer.actions.MapReactionAction
mark bonds property
MARKED - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption
Only marked atoms can have translation.
MARKUSH_EDITOR - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Markush Editor
MARKUSH_ENUM_PLUGIN - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Markush Enumeration Plugin
MARKUSH_HIT_INNER - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for returning hit indices of the inner, compiled representation of a Markush target.
MARKUSH_HIT_ORIGINAL - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for returning hit indices of the original Markush target.
MARKUSH_SEARCH - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Markush Search
MarkushAromaticityHandlingOption - Enum Class in chemaxon.sss.search.options
Option type describing the way aromaticity is handled in Markush structures.
MarkushEnumerationPlugin - Class in chemaxon.marvin.calculations
Plugin class for enumerating Markush molecules.
MarkushEnumerationPlugin() - Constructor for class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constructor.
MarkushFeature - Class in chemaxon.sss.search
Deprecated, for removal: This API element is subject to removal in a future version.
MarkushFeature(int...) - Constructor for class chemaxon.sss.search.MarkushFeature
Deprecated.
Constructor.
MarkushFeature(int, int[]) - Constructor for class chemaxon.sss.search.MarkushFeature
Deprecated.
Constructor.
MARVIN_APPLETS - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Marvin Applets
MARVIN_BEANS - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Marvin Beans
MARVIN_CONFIG_DEFAULT_PATH - Static variable in class chemaxon.marvin.common.UserSettings
The default configuration file path inside the chemaxon settings directory in user home.
MarvinPane - Class in chemaxon.marvin.beans
Ancestor of the Marvin Beans.
MarvinPane() - Constructor for class chemaxon.marvin.beans.MarvinPane
Constructor.
MarvinPaneBeanInfo - Class in chemaxon.marvin.beans
Ancestor of Marvin's BeanInfo classes that are needed by GUI builders.
MarvinPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MarvinPaneBeanInfo
 
MarvinTransferable - Class in chemaxon.marvin.modules.datatransfer
Abstract Adapter implementation of the MTransferable interface used by Marvin.
MarvinTransferable() - Constructor for class chemaxon.marvin.modules.datatransfer.MarvinTransferable
 
mass() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the molecular weight of the molecule.
mass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the molecular weight of the molecule.
Mass - Class in chemaxon.descriptors.scalars
Implements Mass (total mass of molecule) value as a scalar descriptor.
Mass() - Constructor for class chemaxon.descriptors.scalars.Mass
Creates a new, empty logD descriptor.
Mass(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.Mass
Copy constructor.
Mass(SDParameters) - Constructor for class chemaxon.descriptors.scalars.Mass
Creates a new instance according to the parameters given.
Mass(String) - Constructor for class chemaxon.descriptors.scalars.Mass
Creates a new instance according to the parameters given.
MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "mass".
MASS_SPECTRUM - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "massspectrum".
massPrecision() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the precision of the molecular weight (number of decimal digits).
match(MolAtom, MolAtom) - Method in interface com.chemaxon.search.CustomMatcher
Returns true if the given atoms are matchable according to some custom matching criteria.
match(MolBond, MolBond) - Method in interface com.chemaxon.search.CustomMatcher
Returns true if the given bonds are matchable according to some custom matching criteria.
MATCH_AMBIG_IF_POSSIBLE - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
Ambiguous aromatic parts can be matched by a query if it has the same aromaticity as the target Markush structure considering its reduction (enumeration) according to the hit candidate.
MATCH_COUNT_BETWEEN - Static variable in interface chemaxon.sss.SearchConstants
 
MATCH_COUNT_RELATION - Static variable in interface chemaxon.sss.SearchConstants
 
MATCH_RING_BONDS - Enum constant in enum class com.chemaxon.search.mcs.RingHandlingMode
This option allows the algorithm to match a query and a target bond only if both are in rings or both are in chains.
matches(MolAtom, MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Matches 2 atoms
matches(String, long, long) - Method in class chemaxon.formats.MFileFormat
Tests whether the format matches the specified pattern.
MATCHING - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
Only matching atoms will be mapped
MatchingOptions - Class in com.chemaxon.search
Abstract class containing search options used by multiple algorithms.
MatchingOptions(MatchingOptions.Builder) - Constructor for class com.chemaxon.search.MatchingOptions
Creates a MatchingOptions instance with the settings of the given builder object.
MatchingOptions.Builder - Class in com.chemaxon.search
Abstract builder class for creating the base part of immutable instances of any class inheriting the enclosing MatchingOptions class.
MAtomSetPoint - Class in chemaxon.struc.graphics
Point fixed to the location of one or more atoms.
MAtomSetPoint() - Constructor for class chemaxon.struc.graphics.MAtomSetPoint
Contructs an empty point object.
MAtomSetPoint(MAtomSetPoint) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint
Copy constructor.
MAtomSetPoint(MolAtom[]) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint
Contructs a point object.
Matrix - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView
 
MAX_LINE_LENGTH - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Maximum desired line length used to form multi-line text.
MAX_NUMBER_OF_COMPONENTS_PER_CELL - Static variable in class chemaxon.marvin.space.GraphicCell
 
MAX_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings
The maximum size of sketchRecentFileList
MAX_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "maxscale".
maxAbsOxStateOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the oxidation state that has the maximum absolute value
MaxCliqueMcs - Class in com.chemaxon.search.mcs.maxclique
Implements a heuristic MCS algorithm based on maximum clique detection.
MaxCliqueMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.maxclique.MaxCliqueMcs
Creates a MaxCliqueMcs object with the specified search options.
MaxCommonSubstructure - Class in com.chemaxon.search.mcs
Abstract base class of the algorithms for finding the maximum common substructure (MCS) of two molecules.
MaxCommonSubstructure(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.MaxCommonSubstructure
 
maxConsideredRingSize(int) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets the maximum size of rings considered for ring matching purposes.
MAXIMAL_DISTANCE_LIMIT - Static variable in class chemaxon.checkers.StructureCheckerHelper
This constant represents the the upper bound of bond length for Chemaxon built-in StructureChecker implementations
maximumItemCount() - Method in class chemaxon.marvin.space.monitor.AngleMonitor
Returns 3 as the angle is measured between 3 elements.
maximumItemCount() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Returns 4, as measuring dihedral is defined on 4 components.
maximumItemCount() - Method in class chemaxon.marvin.space.monitor.DistanceMonitor
Returns 2 as distance can be measured between 2 elements.
maximumItemCount() - Method in class chemaxon.marvin.space.monitor.Label
Returns 1, because this is the maximun number of selected elements.
maximumItemCount() - Method in class chemaxon.marvin.space.monitor.Monitor
Returns the number of items necessary for monitoring.
maximumItemCount() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Returns 1, because this is the maximun number of selected elements.
maxNonEmptyId - Variable in class chemaxon.descriptors.MDGenerator
 
maxNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator
 
maxParameterCount() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunction
The higher end of the allowed parameter count range (inclusive), or ChemContext.VARARG to signal that there is no maximum.
maxScale(Dimension) - Method in class chemaxon.marvin.MolPrinter
Calculates the maximum scaling factor for fitting the image in a rectangle of the specified size.
maxScale(Rectangle) - Method in class chemaxon.marvin.MolPrinter
Calculates the maximum scaling factor for fitting the image in the specified rectangle.
maxStereoisomerCount() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Returns the adjusted maximum number of generated stereoisomers or Optional#absent().
maxx() - Method in class chemaxon.marvin.space.BoundingBox
Returns the maximum x coordinate of the box.
maxy() - Method in class chemaxon.marvin.space.BoundingBox
Returns the maximum y coordinate of the box.
maxz() - Method in class chemaxon.marvin.space.BoundingBox
Returns the maximum z coordinate of the box.
MAYBE_USEFUL - Static variable in class chemaxon.sss.search.MolComparator
Describes that the MolComparator may be needed with the current search object and the current query, depending on the target.
MBooleanProp - Class in chemaxon.struc.prop
String property.
MBooleanProp(boolean) - Constructor for class chemaxon.struc.prop.MBooleanProp
Constructs a property.
MBooleanProp(String) - Constructor for class chemaxon.struc.prop.MBooleanProp
Constructs a property.
MBracket - Class in chemaxon.struc.graphics
Bracket object.
MBracket() - Constructor for class chemaxon.struc.graphics.MBracket
Constructs a bracket.
MBracket(MBracket) - Constructor for class chemaxon.struc.graphics.MBracket
Copy constructor.
MBracket(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MBracket
Constructs a bracket with the specified corner points.
MBracket(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MBracket
Constructs a bracket with the specified corner points and color.
Mc - Static variable in class chemaxon.core.ChemConst
 
MCES - Static variable in class chemaxon.license.LicenseManager
Identifier of product: MCES
MChemicalStruct - Class in chemaxon.struc.graphics
Molecule graph object.
MChemicalStruct(MChemicalStruct) - Constructor for class chemaxon.struc.graphics.MChemicalStruct
Copy constructor.
MChemicalStruct(MoleculeGraph) - Constructor for class chemaxon.struc.graphics.MChemicalStruct
Contructs a molecule graph object.
MCollectionProp - Class in chemaxon.struc.prop
Collection of properties.
MCollectionProp() - Constructor for class chemaxon.struc.prop.MCollectionProp
 
mcs - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
MCS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
Deprecated.
MCSAlignment - Interface in chemaxon.marvin.alignment
Align molecules using the the maximum common substructure (MCS) of the given molecules.
Usage examples:
MCSAlignment.Factory - Class in chemaxon.marvin.alignment
Factory class for ConformationAlignment.
MCSAlignmentResult - Interface in chemaxon.marvin.alignment
Result class for MCS alignment calculation.
McsSearchOptions - Class in com.chemaxon.search.mcs
Options class for MaxCommonSubstructure (MCS) search.
McsSearchOptions.Builder - Class in com.chemaxon.search.mcs
Builder class for creating immutable instances of the enclosing McsSearchOptions class.
McsSearchResult - Class in com.chemaxon.search.mcs
Class for representing the result of a MaxCommonSubstructure (MCS) search.
McsSearchResult(Molecule, int[], int[], int) - Constructor for class com.chemaxon.search.mcs.McsSearchResult
Creates a SearchResult object representing a common substructure of two molecules.
md - Variable in class chemaxon.descriptors.MDParameters
this object is needed to access default dissimilarity functions
Md - Static variable in class chemaxon.core.ChemConst
 
MDGenerator - Class in chemaxon.descriptors
Base class for all kinds of MolecularDescriptor generators.
MDGenerator() - Constructor for class chemaxon.descriptors.MDGenerator
Created an object.
MDGeneratorException - Exception in chemaxon.descriptors
Exception definition for the MolecularDescriptor.generate() interface.
MDGeneratorException() - Constructor for exception chemaxon.descriptors.MDGeneratorException
Creates new MDGeneratorException without detailed explanation.
MDGeneratorException(String) - Constructor for exception chemaxon.descriptors.MDGeneratorException
Constructs a MDGeneratorException with the specified detailed message.
MDGeneratorException(String, Throwable) - Constructor for exception chemaxon.descriptors.MDGeneratorException
Constructs a MDGeneratorException with the specified detail message and cause.
MDGeneratorException(Throwable) - Constructor for exception chemaxon.descriptors.MDGeneratorException
Constructs a MDGeneratorException with the specified cause.
MDL_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable
MDL like multiple group expansion flag.
MdlCompressor - Class in chemaxon.formats
Molfile compression.
MdlCompressor(InputStream, OutputStream, int) - Constructor for class chemaxon.formats.MdlCompressor
Create a(n un)compressor for the specified input and output streams.
MDLCT2MDL(byte[]) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Converts an MDLCT data to MDL.
MDocSource - Class in chemaxon.marvin.io
Marvin document source.
MDocSource() - Constructor for class chemaxon.marvin.io.MDocSource
 
MDocStorage - Class in chemaxon.marvin.view
Sparse dynamic document storage and reader.
MDocStorage() - Constructor for class chemaxon.marvin.view.MDocStorage
Constructs a document storage.
MDocStorage(int) - Constructor for class chemaxon.marvin.view.MDocStorage
Constructs a document storage.
MDocStorage.CancellationException - Exception in chemaxon.marvin.view
Exception indicating that records are not available because the user cancelled file reading.
MDocStorage.Listener - Interface in chemaxon.marvin.view
Document production listener.
MDocStorage.RecordUnavailableException - Exception in chemaxon.marvin.view
Requested record is not available in the source.
MDocument - Class in chemaxon.struc
Marvin document.
MDocument(MDocument) - Constructor for class chemaxon.struc.MDocument
Copy constructor.
MDocument(MDocument, boolean) - Constructor for class chemaxon.struc.MDocument
Copy constructor.
MDocument(Molecule[]) - Constructor for class chemaxon.struc.MDocument
Creates a document for the specified molecule animation.
MDocument(MoleculeGraph) - Constructor for class chemaxon.struc.MDocument
Creates a document for the specified molecule graph.
MDocument.CheckerMark - Class in chemaxon.struc
Provides informations for Structure Checker higlight
MDocument.Prop - Class in chemaxon.struc
Property that stores an MDocument.
MDoubleArrayProp - Class in chemaxon.struc.prop
Double array property.
MDoubleArrayProp(double[]) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp
Constructs a property object from a double array.
MDoubleArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp
Constructs a double array property from a string value.
MDoubleProp - Class in chemaxon.struc.prop
Double floating point property.
MDoubleProp(double) - Constructor for class chemaxon.struc.prop.MDoubleProp
Constructs a property object from a double floating point value.
MDoubleProp(String) - Constructor for class chemaxon.struc.prop.MDoubleProp
Constructs a double floating point property from a string value.
MDParameters - Class in chemaxon.descriptors
MolecularDescriptor parameter settings.
MDParameters() - Constructor for class chemaxon.descriptors.MDParameters
Creates and initializes an empty object.
MDParametersException - Exception in chemaxon.descriptors
MDParametersException reports all kinds of parametrization related failures.
MDParametersException() - Constructor for exception chemaxon.descriptors.MDParametersException
Creates an exception object with a default message.
MDParametersException(String) - Constructor for exception chemaxon.descriptors.MDParametersException
Creates an exception object with a given message.
MDParametersException(String, Throwable) - Constructor for exception chemaxon.descriptors.MDParametersException
Creates an exception object with a given message and cause.
MEAN_VALUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Will the mean of the affecting properties be mapped onto the surface.
measure - Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
 
measureFrameRate() - Method in class chemaxon.marvin.space.GraphicScene
Measures frame rate of drawing.
measurement - Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
 
measurement() - Method in class chemaxon.marvin.space.monitor.AngleMonitor
Does the angle measurement.
measurement() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Measures the dihedral.
measurement() - Method in class chemaxon.marvin.space.monitor.DistanceMonitor
Measures the distance.
measurement() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Returns the measurement measured by the monitor as a double.
MEASUREMENT_KEY - Static variable in class chemaxon.standardizer.actions.RemoveFragmentAction
Key of measurement for parsing and property change
MeasurementMonitor - Class in chemaxon.marvin.space.monitor
Monitor that measures something on its elements.
MeasurementMonitor() - Constructor for class chemaxon.marvin.space.monitor.MeasurementMonitor
Creates a new instance of MeasureMonitor
MEDIUM_FONT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Label
 
mediumPrecisions - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
MEFlow - Class in chemaxon.struc.graphics
Electron flow arrow.
Representing the movement of one or two electrons in a reaction as a curved arrow.
Electron flow can start from any atom or bond, but not from any atom pairs that has no connection bond.
The logic of the electron flows: If the source is an Atom, the sink can be: any Atom Bond connected to this Atom an atom pair from this atom and any other atom (incipient bond) If the source is a Bond, the sink can be: one of the Atoms on the end of this Bond a Bond connected to this Bond (has common ending Atom) an atom pair from one of the Atoms on the end of this Bond and any other atom (incipient bond) If only the sink/source is in an sgroup, the sink/source must be the attachment point.
MEFlow() - Constructor for class chemaxon.struc.graphics.MEFlow
Contructs an empty 2 electron flow arrow.
MEFlow(int) - Constructor for class chemaxon.struc.graphics.MEFlow
Contructs an empty electron flow arrow.
MEFlow(MEFlow) - Constructor for class chemaxon.struc.graphics.MEFlow
Copy constructor.
MEFlow(MPoint, MPoint, int) - Constructor for class chemaxon.struc.graphics.MEFlow
Contructs an electron flow arrow with the specified endpoints.
MEFlowBasePoint - Class in chemaxon.struc.graphics
Electron flow arrow base point.
MEFlowBasePoint() - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint
Contructs an empty point object.
MEFlowBasePoint(MEFlowBasePoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint
Copy constructor.
MEFlowBasePoint(MolAtom, MPoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint
Contructs a point object.
MEllipse - Class in chemaxon.struc.graphics
Ellipse object.
MEllipse() - Constructor for class chemaxon.struc.graphics.MEllipse
Constructs an ellipse.
MEllipse(MEllipse) - Constructor for class chemaxon.struc.graphics.MEllipse
Copy constructor.
MEllipse(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MEllipse
Constructs a ellipse with the specified corner points.
MEllipse(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MEllipse
Constructs a ellipse with the specified corner points and color.
MENU_CUSTOMIZATION_FILE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "menuconfig".
menubar - Variable in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "menubar".
MER - Enum constant in enum class chemaxon.struc.SgroupType
 
MERGE_DISTANCE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "mergedst".
mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.Molecule
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.RgMolecule
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.RxnMolecule
Deprecated.
As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
mergeBrackets(MolBond, MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the crossing bonds of this sgroup so that they will share a common bracket.
mergeComponentParts(MoleculeGraph, int, boolean) - Method in class chemaxon.struc.RxnMolecule
Finds those component parts that are contained in the molecule graph m and creates a new component containing all atoms of m, splitting them from the previous merges.
mergeFrags(int, int, int) - Method in class chemaxon.struc.MoleculeGraph
Merges two connected components of the given fragmentation type.
mergeProperties(UserSettings, MPropertyContainer, Rectangle) - Static method in class chemaxon.util.ImageExportUtil
Merge the properties of UserSettings with the GUI properties.
If both has a value for a given key, the value stored in GUI properties will be used.
MESH_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
MesomerizeAction - Class in chemaxon.standardizer.actions
Mesomerize standardizer action
MesomerizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MesomerizeAction
Initializes the action
message - Variable in class chemaxon.naming.document.annotate.DocumentAnnotator.ProgressInfo
A message about the current state of the annotation.
METABOLIZER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Metabolizer
METALCONNECTED_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom(s) connected to metal.
METALLOCENE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that incorrectly drawn metallocene had found in the molecule
METALLOCENE_AMBIGUOUS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that incorrectly drawn metallocenes had found in the molecule
MetalloceneCheckerResult - Class in chemaxon.checkers.result
 
MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult
MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>, int) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult
Constructor which initialize all the properties.
MetalloceneErrorChecker - Class in chemaxon.checkers
MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats, that are not coordinate multicenters.
MetalloceneErrorChecker() - Constructor for class chemaxon.checkers.MetalloceneErrorChecker
Default constructor
MetalloceneFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts a single incorrectly drawn metallocene into multicenter based coordinate bond representation.
MetalloceneFixer() - Constructor for class chemaxon.fixers.MetalloceneFixer
 
METHOD_KEY - Static variable in class chemaxon.standardizer.actions.RemoveFragmentAction
Key of method for parsing and property change
METHOD_KLOP - Static variable in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
This field will not be available from May 2016. Use LogPMethod instead.
METHOD_KLOP - Static variable in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
This field will not be available from May 2016. Use LogPMethod instead.
METHOD_PHYS - Static variable in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
This field will not be available from May 2016. Use LogPMethod instead.
METHOD_PHYS - Static variable in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
This field will not be available from May 2016. Use LogPMethod instead.
METHOD_USER_DEFINED - Static variable in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPMethod.USER_DEFINED instead.
METHOD_USER_DEFINED - Static variable in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPMethod.USER_DEFINED instead.
METHOD_VG - Static variable in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPMethod.CHEMAXON instead.
METHOD_VG - Static variable in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPMethod.CHEMAXON instead.
METHOD_WEIGHTED - Static variable in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPMethod.CONSENSUS instead.
METHOD_WEIGHTED - Static variable in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPMethod.CONSENSUS instead.
metricIndexes - Variable in class chemaxon.descriptors.MDParameters
convert parameterized indexes to MolecularDescriptor metric indexes
Metrics - Class in chemaxon.descriptors
The Metrics class implements dissimilarity metrics for MolecularDescriptors.
Metrics() - Constructor for class chemaxon.descriptors.Metrics
 
MetricsType - Enum Class in chemaxon.descriptors
 
MFieldAccessor - Class in chemaxon.marvin.io
Abstract class for extracting fields (properties) from input and storing them.
MFieldAccessor() - Constructor for class chemaxon.marvin.io.MFieldAccessor
 
MFileFormat - Class in chemaxon.formats
File format descriptor class.
MFileFormat(String, String, String, String, String, String, String, String, long) - Constructor for class chemaxon.formats.MFileFormat
MFileFormatUtil - Class in chemaxon.formats
File format related utility functions.
MFileFormatUtil() - Constructor for class chemaxon.formats.MFileFormatUtil
 
MFont - Class in chemaxon.struc.graphics
Font wrapper class that does not require an X server.
MFont(MFont) - Constructor for class chemaxon.struc.graphics.MFont
Copy constructor.
MFont(Font) - Constructor for class chemaxon.struc.graphics.MFont
Create a wrapper for the specified AWT font.
MFont(String) - Constructor for class chemaxon.struc.graphics.MFont
Parses a font from a string.
MFont(String, int, double) - Constructor for class chemaxon.struc.graphics.MFont
Contructs a font.
Mg - Static variable in class chemaxon.core.ChemConst
 
MGPERML - Enum constant in enum class com.chemaxon.calculations.solubility.SolubilityUnit
Solubility is expressed in mg/ml unit.
MHashProp - Class in chemaxon.struc.prop
Linked hash map of properties.
MHashProp() - Constructor for class chemaxon.struc.prop.MHashProp
Constructs a property object from an integer value.
MHashProp(MHashProp, Set) - Constructor for class chemaxon.struc.prop.MHashProp
Copy constructor.
MHCoords3DProp - Class in chemaxon.struc.prop
3D coordinates array property.
MHCoords3DProp(String) - Constructor for class chemaxon.struc.prop.MHCoords3DProp
Constructs a point array property from a string value.
MHCoords3DProp(Map<MolAtom, DPoint3[]>, MoleculeGraph) - Constructor for class chemaxon.struc.prop.MHCoords3DProp
Constructs a property object from a map.
MHCoords3DProp(Map<Integer, DPoint3[]>, long) - Constructor for class chemaxon.struc.prop.MHCoords3DProp
Constructs a property object from a map.
MICROSPECIES_MAJORMS2 - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
MICROSPECIES_MSDISTR2 - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
MIN_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings
The minimum size of sketchRecentFileList
MIN_RING_SIZE_FOR_TRANS_DB - Static variable in class chemaxon.struc.MoleculeGraph
The minimal size of the ring for the existence of TRANS double bond.
minFragmentSize(int) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets the minimum required size of the fragments of MCS.
MINIMAL_ATOM_DISTANCE_LIMIT - Static variable in class chemaxon.checkers.StructureCheckerHelper
This constant represents the minimal allowed atom distance (distance here means euclidean distance) between two atoms for Chemaxon built-in StructureChecker implementations
MINIMAL_DISTANCE_LIMIT - Static variable in class chemaxon.checkers.StructureCheckerHelper
This constant represents the minimal allowed bond distance (distance here means euclidean distance) between two bonds and the lower bound of bond length for Chemaxon built-in StructureChecker implementations
MinMaxDistance - Class in chemaxon.marvin.alignment
Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.
MinMaxDistance() - Constructor for class chemaxon.marvin.alignment.MinMaxDistance
 
minNonEmptyId - Variable in class chemaxon.descriptors.MDGenerator
 
minNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator
 
minParameterCount() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunction
The lower end of the allowed parameter count range (inclusive).
MIntegerArrayProp - Class in chemaxon.struc.prop
Integer array property.
MIntegerArrayProp(int[]) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp
Constructs a property object from an integer value.
MIntegerArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp
Constructs an integer array property from a string value.
MIntegerProp - Class in chemaxon.struc.prop
Integer property.
MIntegerProp(int) - Constructor for class chemaxon.struc.prop.MIntegerProp
Constructs a property object from an integer value.
MIntegerProp(String) - Constructor for class chemaxon.struc.prop.MIntegerProp
Constructs an integer property from a string value.
minx() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum x coordinate of the box.
miny() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum y coordinate of the box.
minz() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum z coordinate of the box.
MISSING_ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with no atom map had found in the molecule
MISSING_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule with missing R-group definition found
MissingAtomMapChecker - Class in chemaxon.checkers
MissingAtomMapChecker detects unmapped atoms.
MissingAtomMapChecker() - Constructor for class chemaxon.checkers.MissingAtomMapChecker
Default constructor
MissingRGroupChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting missing R-group definition errors.
MissingRGroupChecker() - Constructor for class chemaxon.checkers.MissingRGroupChecker
Initializes the checker
MIXTURE - Enum constant in enum class chemaxon.struc.SgroupType
 
MListProp - Class in chemaxon.struc.prop
Property list property.
MListProp() - Constructor for class chemaxon.struc.prop.MListProp
Constructs a property object from a list.
MListProp(MListProp, Set) - Constructor for class chemaxon.struc.prop.MListProp
Copy constructor.
mmc - Variable in class chemaxon.marvin.space.MoleculeComponent
 
MMF_FIELD - Static variable in class chemaxon.marvin.view.swing.TableOptions
Main molecule is a field in at least one record.
MMF_NOT_FIELD - Static variable in class chemaxon.marvin.view.swing.TableOptions
Main molecule is not a field in at least one record.
MMF_UNSET - Static variable in class chemaxon.marvin.view.swing.TableOptions
Not yet decided whether the main molecule is a field or not.
MMidPoint - Class in chemaxon.struc.graphics
Middle point in a line.
MMidPoint(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint
Copy constructor.
MMidPoint(MPolyline, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MMidPoint
Contructs a middle point object.
MMidPoint.Sticky - Class in chemaxon.struc.graphics
Fixed middle point that can be a point of a polyline.
MMoleculeProp - Class in chemaxon.struc.prop
Molecule property.
MMoleculeProp(Molecule) - Constructor for class chemaxon.struc.prop.MMoleculeProp
Constructs a property object from a molecule.
MMPAlignment - Class in chemaxon.marvin.alignment
3D Molecular alignment that uses the maximum common substructure to align a pair of structures.
MMPAlignment(Molecule, Molecule) - Constructor for class chemaxon.marvin.alignment.MMPAlignment
Constructs an MMPAlignment object for later alignment of two structures.
MMPAlignment(Molecule, Molecule, MMPAlignmentProperties) - Constructor for class chemaxon.marvin.alignment.MMPAlignment
Constructs an MMPAlignment object for later alignment of two structures.
MMPAlignmentProperties - Class in chemaxon.marvin.alignment
Input property settings for MMPAlignment.
MMPAlignmentProperties() - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
Deprecated.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean, int) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, int) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties
Constructs a MMPAlignmentProperties object.
MMPAlignmentResult - Class in chemaxon.marvin.alignment
Results of the MMPAlignment process.
Mn - Static variable in class chemaxon.core.ChemConst
 
Mo - Static variable in class chemaxon.core.ChemConst
 
MObject - Class in chemaxon.struc
Paintable object.
MObject(MObject) - Constructor for class chemaxon.struc.MObject
Copy constructor.
MObject(Color, Color, Color) - Constructor for class chemaxon.struc.MObject
Contructs a paintable object with the specified color.
MObjectProp - Class in chemaxon.struc.prop
Property that stores any object.
MObjectProp(Object) - Constructor for class chemaxon.struc.prop.MObjectProp
Constructs a property object.
MObjectProp(String) - Constructor for class chemaxon.struc.prop.MObjectProp
Constructs a property from a string value.
mode - Variable in class chemaxon.checkers.StructureCheckOptions
The mode of the structure check (only check or fixes too)
mode - Variable in class chemaxon.marvin.space.monitor.Monitor
 
MODE_MOVING - Static variable in class chemaxon.marvin.space.GraphicScene
 
MODE_NORMAL - Static variable in class chemaxon.marvin.space.GraphicCell
 
MODE_PICK - Static variable in class chemaxon.marvin.space.GraphicCell
 
MODE_STANDING - Static variable in class chemaxon.marvin.space.GraphicScene
 
ModeConverter() - Constructor for class chemaxon.checkers.StructureCheckOptions.ModeConverter
 
MODEL_LARGE - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Calculation model: large (always precise, can take more time).
MODEL_SMALL - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Calculation model: small (precise up to the specified number of ionizable atoms).
MODERATE - Enum constant in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
Moderate solubility.
MODIFICATION - Enum constant in enum class chemaxon.struc.SgroupType
 
modifiesOrigin - Variable in class chemaxon.marvin.space.GraphicComponent
Tells whether this component modifies the transformation center of the cell or not.
modifyAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "modified atom" list.
modifyAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "modified atom" list.
modifyAtom(MolAtom) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "modified atom" list.
modifyAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "modified atom" list.
mol - Variable in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
mol - Variable in class chemaxon.marvin.space.MoleculeComponent
 
MOL - Static variable in class chemaxon.formats.MFileFormat
MDL Molfiles and Rgfiles.
MOL - Static variable in class chemaxon.jep.context.MolContext
 
MOL_LOADER_FINISHED_EVENT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "molLoaderFinishedEvent".
MOL_UID_PROPERTY - Static variable in class chemaxon.naming.document.annotate.DocumentAnnotator
 
MOL_V2_OUT - Static variable in class chemaxon.formats.MFileFormat
 
MOL_V3_OUT - Static variable in class chemaxon.formats.MFileFormat
MDL Extended Molfiles and Rgfiles.
MOL2 - Static variable in class chemaxon.formats.MFileFormat
Tripos Mol2 files.
MolAligner - Class in chemaxon.marvin.alignment
Tool for aligning a target molecule to a pattern molecule.
MolAligner - Class in chemaxon.util
Deprecated, for removal: This API element is subject to removal in a future version.
Moved to a new package, use it from its new location: MolAligner.
MolAligner() - Constructor for class chemaxon.marvin.alignment.MolAligner
Creates a new MolAligner object.
MolAligner() - Constructor for class chemaxon.util.MolAligner
Deprecated.
 
MolAligner(Molecule, Molecule) - Constructor for class chemaxon.marvin.alignment.MolAligner
Creates a new MolAligner object while setting the pattern and target molecules
MolAtom - Class in chemaxon.struc
Atom object and the properties of the elements.
MolAtom(double, double) - Constructor for class chemaxon.struc.MolAtom
Construct a carbon atom at the specified location.
MolAtom(int) - Constructor for class chemaxon.struc.MolAtom
Construct an atom of the specified type at the origin.
MolAtom(int, double, double, double) - Constructor for class chemaxon.struc.MolAtom
Construct an atom.
MolBond - Class in chemaxon.struc
Chemical bond.
MolBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.MolBond
Construct a single bond between two atoms.
MolBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.MolBond
Construct a bond between two atoms.
MolBond(MolBond) - Constructor for class chemaxon.struc.MolBond
Copy constructor.
MolComparator - Class in chemaxon.sss.search
Interface for comparing atoms, bonds, etc.
MolComparator() - Constructor for class chemaxon.sss.search.MolComparator
 
MolCondition - Interface in chemaxon.jep
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed soon.
MolContext - Class in chemaxon.jep.context
Expression evaluation context containing a single molecule.
MolContext() - Constructor for class chemaxon.jep.context.MolContext
Constructor.
MolContext(Molecule) - Constructor for class chemaxon.jep.context.MolContext
Creates a MolContext with the given input molecule.
MolConverter - Class in chemaxon.formats
Converts between molecule file formats.
MolConverter(MolConverter.Builder) - Constructor for class chemaxon.formats.MolConverter
Creates a MolConverter object.
MolConverter(MolConverter.Options) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, use MolConverter.Builder.build() instead.
MolConverter(InputStream, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter
Creates a MolConverter object.
MolConverter(InputStream, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter
Use this constructor if you do not need output buffering but want to determine output file positions.
MolConverter(List<Object>, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object>, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object>, List<String>, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object>, List<String>, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter.Builder - Class in chemaxon.formats
MolConverter builder.
MolConverter.Options - Class in chemaxon.formats
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 5.2.3, use MolConverter.Builder instead.
molCount - Variable in class chemaxon.descriptors.MDGenerator
variables to collect statistical data in
MOLECULAR_DESCRIPTORS - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Molecular Descriptors
MolecularDescriptor - Class in chemaxon.descriptors
Generic definition of molecular descriptors.
MolecularDescriptor() - Constructor for class chemaxon.descriptors.MolecularDescriptor
Default constructor, creates an empty object.
MolecularDescriptor(MDParameters) - Constructor for class chemaxon.descriptors.MolecularDescriptor
Creates a new MolecularDescriptor with the given parameters.
MolecularDescriptor(MolecularDescriptor) - Constructor for class chemaxon.descriptors.MolecularDescriptor
Copy constructor, creates am identical copy of the MolecularDescriptor passed as a parameter.
MolecularDescriptorGenerator - Interface in chemaxon.descriptors
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
MolecularDynamicsPlugin - Class in chemaxon.marvin.calculations
Molecular Dynamics plugin.
MolecularDynamicsPlugin() - Constructor for class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Creates a new instance of MolecularDynamicsPlugin
MolecularFormulas - Class in com.chemaxon.calculations.elemanal.factory
Static utility methods related to molecular formula calculations.
MolecularFormulas - Class in com.chemaxon.calculations.elemanal
Deprecated, for removal: This API element is subject to removal in a future version.
MolecularSurfaceComponent - Class in chemaxon.marvin.space
Class that represents a surface of a molecule.
MolecularSurfaceComponent() - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
Creates a new instance of MolecularSurfaceComponent without setting anything.
MolecularSurfaceComponent(MoleculeIterators.MoleculeInterface, VolumetricData) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData, which usually comes from a Gaussian Cube file.
MolecularSurfaceComponent(MoleculeIterators.MoleculeInterface, VolumetricData, float) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
Creates a MolecularSurfaceComponent from the given MoleculeInterface and VolumetricData, which usually comes from a Gaussian Cube file.
MolecularSurfaceComponent(ArrayList) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces and MoleculeVisualizers.
MolecularSurfaceComponent(ArrayList, String) - Constructor for class chemaxon.marvin.space.MolecularSurfaceComponent
Creates a MolecularSurfaceComponent to the given list of MoleculeInterfaces and MoleculeVisualizers.
molecule - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
The Molecule which will be transferred to the clipboard.
molecule - Variable in class chemaxon.standardizer.runner.BasicStandardizerRunner
The Molecule instance to standardize
Molecule - Class in chemaxon.struc
Molecule class.
Molecule() - Constructor for class chemaxon.struc.Molecule
Construct a 2 dimensional molecule.
Molecule(Molecule, int, int) - Constructor for class chemaxon.struc.Molecule
Construct a molecule or fragment with the specified number of atoms and bonds.
Molecule(Molecule, MolAtom) - Constructor for class chemaxon.struc.Molecule
Construct a molecule consisting of a single atom (node).
Molecule(Molecule, MolBond) - Constructor for class chemaxon.struc.Molecule
Construct a molecule consisting of a single bond (edge).
MOLECULE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "mol".
MOLECULE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Calculation domain type: calculation refers to the molecule.
MOLECULE_BACKGROUND - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "molbg".
MOLECULE_CHANGED - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "molChanged".
MOLECULE_CHARGE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that the sum charge of the molecule wasn't zero
MOLECULE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "molFormat".
MoleculeAtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
MoleculeChargeChecker - Class in chemaxon.checkers
MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.
MoleculeChargeChecker() - Constructor for class chemaxon.checkers.MoleculeChargeChecker
Default constructor
MoleculeComponent - Class in chemaxon.marvin.space
MoleculeComponent is the basic visualizer of simple molecules in MarvinSpace.
MoleculeComponent() - Constructor for class chemaxon.marvin.space.MoleculeComponent
Creates a new instance of MoleculeComponent.
MoleculeComponent(MacroMolecule.HeteroComponent, MacroMoleculeComponent) - Constructor for class chemaxon.marvin.space.MoleculeComponent
Creates a new instance of MoleculeComponent from the given HeteroComponent and MacroMoleculeComponent; this class can be used as a visualizer of a ligand.
MoleculeComponent(Molecule) - Constructor for class chemaxon.marvin.space.MoleculeComponent
Creates a new instance of MoleculeComponent from the given molecule.
MoleculeGraph - Class in chemaxon.struc
A graph consisting of MolAtom nodes and MolBond edges.
MoleculeGraph() - Constructor for class chemaxon.struc.MoleculeGraph
Construct a 2 dimensional molecule.
MoleculeGraph(MoleculeGraph, int, int) - Constructor for class chemaxon.struc.MoleculeGraph
Construct a molecule or fragment with the specified number of atoms and bonds.
MoleculeGraph.ValenceCheckState - Enum Class in chemaxon.struc
Deprecated, for removal: This API element is subject to removal in a future version.
MoleculeImporter - Class in chemaxon.marvin.io.formats
Molecule importer.
MoleculeImporter(File) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the file.
MoleculeImporter(File, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the file.
MoleculeImporter(InputStream) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the input stream.
MoleculeImporter(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the stream.
MoleculeImporter(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the stream.
MoleculeImporter(String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the file.
MoleculeImporter(String, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter
Constructs a new importer for the file.
MoleculeIterator - Interface in chemaxon.util.iterator
Molecule iterator.
MoleculeIteratorFactory - Class in chemaxon.util.iterator
Molecule iterator factory.
MoleculeIteratorFactory() - Constructor for class chemaxon.util.iterator.MoleculeIteratorFactory
 
MOLECULES - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Calculation domain type: calculation refers to multiple molecule output.
MolExport - Class in chemaxon.marvin.io.formats.mdl
Exports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
MolExport() - Constructor for class chemaxon.marvin.io.formats.mdl.MolExport
Constructor.
MolExporter - Class in chemaxon.formats
Molecule exporter class.
MolExporter(OutputStream, String) - Constructor for class chemaxon.formats.MolExporter
Creates a molecule exporter.
MolExporter(OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolExporter
Creates a molecule exporter.
MolExporter(OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolExporter
Creates a molecule exporter.
MolExporter(OutputStream, String, String) - Constructor for class chemaxon.formats.MolExporter
Creates a molecule exporter.
MolExporter(String, String) - Constructor for class chemaxon.formats.MolExporter
Creates a molecule exporter.
MolExporter(String, String, int, String[], String) - Constructor for class chemaxon.formats.MolExporter
Creates a molecule exporter.
MolExportException - Exception in chemaxon.marvin.io
Molecule export exception.
MolExportException(String) - Constructor for exception chemaxon.marvin.io.MolExportException
Creates a molecule export exception with the specified message.
MolExportException(String, Throwable) - Constructor for exception chemaxon.marvin.io.MolExportException
Creates a molecule export exception with the specified message and cause.
MolExportException(Throwable) - Constructor for exception chemaxon.marvin.io.MolExportException
Creates a molecule export exception with the specified cause.
MolExportModule - Class in chemaxon.marvin.io
Abstract base class of molecule export modules.
MolExportModule() - Constructor for class chemaxon.marvin.io.MolExportModule
 
MolExportModuleFactory - Interface in chemaxon.formats.factory
Factory interface for MolExportModules.
MolfileUtil - Class in chemaxon.marvin.io.formats.mdl
MDL molfile related utility methods.
MolfileUtil() - Constructor for class chemaxon.marvin.io.formats.mdl.MolfileUtil
 
MolFilter - Interface in chemaxon.util
Molecule filter.
MolFormatException - Exception in chemaxon.formats
Something's wrong with a molecule file format.
MolFormatException() - Constructor for exception chemaxon.formats.MolFormatException
Creates a molecule format exception.
MolFormatException(String) - Constructor for exception chemaxon.formats.MolFormatException
Creates a molecule format exception with the specified message.
MolFormatException(String, Throwable) - Constructor for exception chemaxon.formats.MolFormatException
Creates a molecule format exception with the specified message and cause.
MolFormatException(Throwable) - Constructor for exception chemaxon.formats.MolFormatException
Creates a molecule format exception with the specified cause.
MolFragLoader - Class in chemaxon.marvin.util
Molecule fragment loader.
MolFragLoader() - Constructor for class chemaxon.marvin.util.MolFragLoader
Constructor.
MolFragLoader(MolImporter) - Constructor for class chemaxon.marvin.util.MolFragLoader
Constructor: sets the molecule fragment iterator from the specified importer.
MolFragLoader(MoleculeIterator) - Constructor for class chemaxon.marvin.util.MolFragLoader
Constructor: sets the molecule fragment iterator.
MolFragLoader.RgroupAttachmentCountFilter - Class in chemaxon.marvin.util
Molecule filter which accepts molecules with a specified number of R-group attachments.
molID - Variable in class chemaxon.marvin.alignment.AlignmentMolecule
 
MolImport - Class in chemaxon.marvin.io.formats.mdl
Imports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
MolImport() - Constructor for class chemaxon.marvin.io.formats.mdl.MolImport
 
MolImporter - Class in chemaxon.formats
Molecule file importer.
MolImporter(File) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for a file.
MolImporter(File, String) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for a file.
MolImporter(InputStream) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for an input stream.
MolImporter(InputStream, String) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for an input stream.
MolImporter(InputStream, String, String) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for an input stream.
MolImporter(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for an input stream.
MolImporter(String) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer for a file.
MolImporter(String, Component, String) - Constructor for class chemaxon.formats.MolImporter
Create a molecule importer with a progress monitor.
MolImporter(String, Object, String) - Constructor for class chemaxon.formats.MolImporter
Deprecated, for removal: This API element is subject to removal in a future version.
MolImportModule - Class in chemaxon.marvin.io
Base class of Molecule import modules.
MolImportModule() - Constructor for class chemaxon.marvin.io.MolImportModule
 
MolImportModule.PreferredView - Enum Class in chemaxon.marvin.io
 
MolImportModuleFactory - Interface in chemaxon.formats.factory
Factory interface for MolImportModules.
MolInputProducer - Class in chemaxon.util.concurrent.marvin
Input producer wrapping a MolImporter object.
MolInputProducer() - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer
Constructor.
MolInputProducer(MolImporter) - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer
Constructor.
MolInputProducer(MolImporter[]) - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer
Constructor.
MolInputStream - Class in chemaxon.formats
Molecule input stream that has the ability to determine the input file format.
MolInputStream(InputStream) - Constructor for class chemaxon.formats.MolInputStream
Create a molecule input stream from an ordinary one, and determine the format.
MolInputStream(InputStream, String) - Constructor for class chemaxon.formats.MolInputStream
Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(InputStream, String, String) - Constructor for class chemaxon.formats.MolInputStream
Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolInputStream
Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MOLMASS - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Mass of the molecule
MOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil
Read multi-molecule files as movies.
molPanel - Variable in class chemaxon.marvin.beans.MarvinPane
Underlying panel.
MOLPERL - Enum constant in enum class com.chemaxon.calculations.solubility.SolubilityUnit
Solubility is expressed in mol/l unit.
MolPrinter - Class in chemaxon.marvin
Molecule renderer that can draw a molecule to a graphics context using various display settings.
MolPrinter() - Constructor for class chemaxon.marvin.MolPrinter
Constructs a molecule renderer for an empty molecule.
MolPrinter(MDocument) - Constructor for class chemaxon.marvin.MolPrinter
Constructs a molecule renderer for the specified document.
MolPrinter(MoleculeGraph) - Constructor for class chemaxon.marvin.MolPrinter
Constructs a molecule renderer for the specified molecule.
MolRenderer - Class in chemaxon.marvin.beans
MolRenderer is a simple TableCellRenderer component based on MolPrinter that can be used to render Molecule objects in JTables.
MolRenderer() - Constructor for class chemaxon.marvin.beans.MolRenderer
 
MolSearch - Class in chemaxon.sss.search
Atom-by-atom structure search.
MolSearch() - Constructor for class chemaxon.sss.search.MolSearch
Constructs a MolSearch object.
MolSearchOptions - Class in chemaxon.sss.search
Class to encapsulate search parameters used by Search implementations(ex: MolSearch).
MolSearchOptions(int) - Constructor for class chemaxon.sss.search.MolSearchOptions
Creates a MolSearchOptions object while setting different search options according to a predefined search type.
molToScreenCoords(DPoint3, Point2D) - Method in class chemaxon.marvin.MolPrinter
Converts molecular coordinates to 2D screen coordinates.
monitor - Variable in class chemaxon.marvin.space.monitor.Control
 
Monitor - Class in chemaxon.marvin.space.monitor
The Monitor is for "watching" something in the scene.
Monitor() - Constructor for class chemaxon.marvin.space.monitor.Monitor
Creates a new instance of Monitor.
MONOMER - Enum constant in enum class chemaxon.struc.SgroupType
 
MONOVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Monovalent radical center.
MORE_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "moreEnabled".
MORE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
multiple error message for checker
moreErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the more than one error message for the checker
motionMode - Variable in class chemaxon.marvin.space.GraphicComponent
Indicates if the component is in standing or in moving mode.
mousex - Variable in class chemaxon.marvin.space.GraphicComponent
Mouse position in picking mode.
mousey - Variable in class chemaxon.marvin.space.GraphicComponent
Mouse position in picking mode.
moveCorners(double, double) - Method in class chemaxon.struc.MolAtom
Translates the coordinates of the atom label.
moveMainMoleculeGraphToFront() - Method in class chemaxon.struc.MDocument
Move the main molecule graph to the top of stack.
moveMoleculeMovieToFront() - Method in class chemaxon.struc.MDocument
Move the molecule movie (if exists) to the top of stack.
moveObject(MObject, int) - Method in class chemaxon.struc.MDocument
Move an object to another place in the stack.
moveTo(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Move the molecule.
MP_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "mpVisible".
MP_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "mpVisible" property.
MPoint - Class in chemaxon.struc
Point object.
MPoint(double, double) - Constructor for class chemaxon.struc.MPoint
Contructs a point object.
MPoint(double, double, double) - Constructor for class chemaxon.struc.MPoint
Contructs a point object.
MPoint(DPoint3) - Constructor for class chemaxon.struc.MPoint
Constructs a point object.
MPoint(MPoint) - Constructor for class chemaxon.struc.MPoint
Copy constructor.
MPolyline - Class in chemaxon.struc.graphics
Polyline object.
MPolyline() - Constructor for class chemaxon.struc.graphics.MPolyline
Contructs an empty line.
MPolyline(boolean, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline
Creates a closed polyline.
MPolyline(MPolyline) - Constructor for class chemaxon.struc.graphics.MPolyline
Copy constructor.
MPolyline(MPolyline, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline
Contructs a polyline from the specified starting polyline and endpoint.
MPolyline(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline
Contructs a line with the specified endpoints.
MPolyline(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline
Contructs a line with the specified endpoints.
MProgressMonitor - Interface in chemaxon.common.util
Progress monitor interface.
MProp - Class in chemaxon.struc
Property base class.
MProp() - Constructor for class chemaxon.struc.MProp
 
MPropertyContainer - Class in chemaxon.struc
Property container.
MPropertyContainer() - Constructor for class chemaxon.struc.MPropertyContainer
Creates an empty property container.
MPropHandler - Class in chemaxon.marvin.io
Property factory.
MPropHandler() - Constructor for class chemaxon.marvin.io.MPropHandler
 
MRecord - Class in chemaxon.marvin.io
Record in a multi-molecule file.
MRecord() - Constructor for class chemaxon.marvin.io.MRecord
Default constructor.
MRecord(long, long, int, String, MPropertyContainer, int[]) - Constructor for class chemaxon.marvin.io.MRecord
Creates a record.
MRecord(long, long, int, String, MPropertyContainer, int[], int) - Constructor for class chemaxon.marvin.io.MRecord
Creates a record.
MRecord(long, long, int, String, MPropertyContainer, int[], int, String) - Constructor for class chemaxon.marvin.io.MRecord
Creates a record.
MRecordImporter - Class in chemaxon.marvin.io
Marvin molecule file reader.
MRecordImporter(MolInputStream, String) - Constructor for class chemaxon.marvin.io.MRecordImporter
Creates a reader for the specified molecule input stream in concurrent mode.
MRecordParseException - Exception in chemaxon.marvin.io
Record reading exception.
MRecordParseException(MRecordReader.Position, String) - Constructor for exception chemaxon.marvin.io.MRecordParseException
Creates an exception with the specified message.
MRecordParseException(MRecordReader.Position, String, Throwable) - Constructor for exception chemaxon.marvin.io.MRecordParseException
Creates an exception with the specified message and cause.
MRecordParseException(MRecordReader.Position, Throwable) - Constructor for exception chemaxon.marvin.io.MRecordParseException
Creates an exception with the specified cause.
MRecordReader - Interface in chemaxon.marvin.io
Marvin record reader.
MRecordReader.Position - Class in chemaxon.marvin.io
Position in the input file.
MRecordReaderFactory - Interface in chemaxon.formats.factory
Factory interface for MRecordReaders.
MRectangle - Class in chemaxon.struc.graphics
Rectangle object.
MRectangle() - Constructor for class chemaxon.struc.graphics.MRectangle
Constructs a rectangle.
MRectangle(MRectangle) - Constructor for class chemaxon.struc.graphics.MRectangle
Copy constructor.
MRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRectangle
Constructs a rectangle with the specified corner points.
MRectangle(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MRectangle
Constructs a rectangle with the specified corner points.
MRectanglePoint - Class in chemaxon.struc.graphics
Rectangle point object.
MRectanglePoint(MRectangle, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MRectanglePoint
Contructs a rectangle corner point object.
MRectanglePoint(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint
Copy constructor.
MRectanglePoint.Sticky - Class in chemaxon.struc.graphics
Fixed rectangle point that can be a point of a polyline.
MRoundedRectangle - Class in chemaxon.struc.graphics
Rounded rectangle object.
MRoundedRectangle() - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
Constructs a rounded rectangle
MRoundedRectangle(MRoundedRectangle) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
Copy constructor.
MRoundedRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
Constructs a rounded rectangle with the specified corner points.
MRoundedRectangle(MPoint, MPoint, double, double) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
Constructs a rounded rectangle with the specified corner points.
MRoundedRectangle(MPoint, MPoint, double, double, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
Constructs a rounded rectangle with the specified corner points and color.
MRoundedRectangle(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle
Constructs a rounded rectangle with the specified corner points and color.
MRV - Static variable in class chemaxon.formats.MFileFormat
Chemaxon Marvin Document.
MRV_OUTPUT_LEVEL - Static variable in class chemaxon.sss.search.Search
MRV format of the query and target is logged at this level.
MSA - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
MSAPlugin - Class in chemaxon.marvin.calculations
Plugin class for molecular surface area calculation.
MSAPlugin() - Constructor for class chemaxon.marvin.calculations.MSAPlugin
Constructor.
MSBMP - Static variable in class chemaxon.formats.MFileFormat
Windows Bitmap format.
MSelectionDocument - Class in chemaxon.struc
Selection document.
MSelectionDocument(MSelectionDocument) - Constructor for class chemaxon.struc.MSelectionDocument
Copy constructor.
MSelectionDocument(SelectionMolecule) - Constructor for class chemaxon.struc.MSelectionDocument
Creates a document for the specified molecule graph.
MSketch - Class in chemaxon.marvin.beans
Java independent serialization of the sketcher bean.
MSketch() - Constructor for class chemaxon.marvin.beans.MSketch
Constructor used for deserialization.
MSketch(MSketchPane) - Constructor for class chemaxon.marvin.beans.MSketch
Constructor used for serialization.
MSketchPane - Class in chemaxon.marvin.beans
The MarvinSketch Bean.
MSketchPane() - Constructor for class chemaxon.marvin.beans.MSketchPane
Constructs the sketcher.
MSketchPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MSketchPane
Constructs the sketcher with the specified user settings object.
MSketchPane(UserSettings, boolean) - Constructor for class chemaxon.marvin.beans.MSketchPane
Constructs the sketcher with the specified user settings object.
MSketchPane(UserSettings, boolean, JComponent) - Constructor for class chemaxon.marvin.beans.MSketchPane
Constructs the sketcher with the specified user settings object.
MSketchPaneBeanInfo - Class in chemaxon.marvin.beans
MarvinSketch bean information.
MSketchPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MSketchPaneBeanInfo
 
MSPACE_CONFIG_DEFAULT_PATH - Static variable in class chemaxon.marvin.space.GraphicScene
 
MSpaceEasy - Class in chemaxon.marvin.space
Easy-to-use functions of MarvinSpace, customizable gui for applets and applications.
MSpaceEasy() - Constructor for class chemaxon.marvin.space.MSpaceEasy
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.
MSpaceEasy(boolean) - Constructor for class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
Use MSpaceEasy() instead. The "install" argument is ignored.
MSpaceEasy(boolean, boolean, URL) - Constructor for class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
Use MSpaceEasy() and MSpaceEasy.setVerbose(boolean) instead. The "install" and "codebase" arguments are ignored.
MSpaceEasy(int, int) - Constructor for class chemaxon.marvin.space.MSpaceEasy
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.
MSpaceEasy(int, int, boolean) - Constructor for class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
Use MSpaceEasy(int, int) instead. The "install" argument is ignored.
MSpaceEasy(int, int, boolean, boolean, URL) - Constructor for class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
Use MSpaceEasy(int, int) and MSpaceEasy.setVerbose(boolean) instead. The "install" and "codebase" arguments are ignored.
MStringProp - Class in chemaxon.struc.prop
String property.
MStringProp(String) - Constructor for class chemaxon.struc.prop.MStringProp
Constructs a property.
Mt - Static variable in class chemaxon.core.ChemConst
 
MTextAttributes - Class in chemaxon.struc.graphics
Text attributes.
MTextAttributes(int, int, Color, MFont, double, double, double) - Constructor for class chemaxon.struc.graphics.MTextAttributes
Constructs a attributes object.
MTextBox - Class in chemaxon.struc.graphics
Text box object.
MTextBox() - Constructor for class chemaxon.struc.graphics.MTextBox
Contructs an empty text box.
MTextBox(MTextBox) - Constructor for class chemaxon.struc.graphics.MTextBox
Copy constructor.
MTextDocument - Class in chemaxon.struc.graphics
Text document consisting of sections with different attributes.
MTextDocument() - Constructor for class chemaxon.struc.graphics.MTextDocument
Constructs an empty document.
MTextDocument(MTextDocument) - Constructor for class chemaxon.struc.graphics.MTextDocument
Copy constructor.
MTextDocument(String) - Constructor for class chemaxon.struc.graphics.MTextDocument
Constructs a document from the specified string.
MTextDocument.Portion - Class in chemaxon.struc.graphics
Selected text.
MTextDocument.Section - Class in chemaxon.struc.graphics
Plain text section with uniform attributes.
MTransferable - Interface in chemaxon.marvin.modules.datatransfer
The interface of Marvin transferable implementations.
MTransformable - Interface in chemaxon.struc
Interface for 3D transformable classes.
mul(CTransform3D) - Method in class chemaxon.struc.CTransform3D
Multiplies by another matrix from right.
MULTI_CENTER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that invalid R-group definition is in the molecule
MULTI_COMPONENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule had contained multiple components
MULTIBOND - Static variable in class chemaxon.sss.search.MarkushFeature
Deprecated.
Expansion type: multiple position bond.
MULTICENTER - Enum constant in enum class chemaxon.struc.SgroupType
 
MULTICENTER - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of a central atom of a MulticenterSgroup.
MultiCenterChecker - Class in chemaxon.checkers
MultiCenterChecker detects structures containing multicenter atoms.
MultiCenterChecker() - Constructor for class chemaxon.checkers.MultiCenterChecker
 
MulticenterSgroup - Class in chemaxon.struc.sgroup
Multicenter S-group to represent complexes like markush ring structures, ferrocenes, metallocenes...
MulticenterSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup
Constructs a Multicenter S-group.
MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup
Copy constructor.
MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup
Copy constructor.
MultiComponentChecker - Class in chemaxon.checkers
MultiComponentChecker detects structures containing disconnected components/fragments.
MultiComponentChecker() - Constructor for class chemaxon.checkers.MultiComponentChecker
Default constructor
MULTIPLE - Enum constant in enum class chemaxon.struc.SgroupType
 
MULTIPLE - Static variable in class chemaxon.formats.MolExporter
Use this flag to produce multiple output files.
MULTIPLE_STEREO_CENTER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule contains multiple stereo centers
MultipleSgroup - Class in chemaxon.struc.sgroup
Multiple S-group.
MultipleSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup
Constructs a multiple S-group.
MultipleSgroup(MultipleSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup
Copy constructor.
MultipleStereocenterChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting molecules containing multiple stereocenters.
MultipleStereocenterChecker() - Constructor for class chemaxon.checkers.MultipleStereocenterChecker
Initializes a multiple stereo checker
multipliedScore() - Method in class chemaxon.calculations.bbb.BBB.Property
 
MULTISET - Static variable in class chemaxon.formats.MFileFormatUtil
The multi-molecule file really contains multiple atom sets of one molecule.
MView - Class in chemaxon.marvin.beans
Java independent serialization of the viewer bean.
MView() - Constructor for class chemaxon.marvin.beans.MView
Constructor used for deserialization.
MView(MViewPane) - Constructor for class chemaxon.marvin.beans.MView
Constructor used for serialization.
MViewEditor - Class in chemaxon.marvin.beans
MViewEditor is an implementation of AbstractCellEditor and TableCellEditor that can be used to assign a cell editor to Molecule objects in JTables.
MViewEditor() - Constructor for class chemaxon.marvin.beans.MViewEditor
Creates the cell editor.
MViewPane - Class in chemaxon.marvin.beans
The MarvinView Bean.
MViewPane() - Constructor for class chemaxon.marvin.beans.MViewPane
Constructs the viewer.
MViewPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MViewPane
Constructs the viewer with the specified user settings.
MViewPaneBeanInfo - Class in chemaxon.marvin.beans
MarvinView bean information.
MViewPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MViewPaneBeanInfo
 
MViewParams - Class in chemaxon.marvin.beans
MViewParams is a helper tool to generate parameter string to MViewPane.
MViewParams() - Constructor for class chemaxon.marvin.beans.MViewParams
For each new parameter generation a new MViewParams instance is necessary to be created.
MViewRenderer - Class in chemaxon.marvin.beans
MViewRenderer is a TableCellRenderer component that can be used to render Molecule objects in JTables.
MViewRenderer() - Constructor for class chemaxon.marvin.beans.MViewRenderer
Creates the cell renderer.
MW - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Molecular weight.
MWHBN - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
MW^(-0.5) * (HBN), where HBN = HBA + HBD.

N

N - Static variable in class chemaxon.core.ChemConst
 
Na - Static variable in class chemaxon.core.ChemConst
 
name - Variable in class chemaxon.marvin.services.ServiceArgument
the name of the argument
name - Variable in class chemaxon.marvin.space.GraphicComponent
 
name() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the name of the checker
name() - Element in annotation interface chemaxon.fixers.FixerInfo
Returns the name of the fixer.
name() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the name of the action
NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
name property of checker
NAME - Static variable in class chemaxon.fixers.StructureFixerDescriptor
name property of fixer
NAME - Static variable in class chemaxon.formats.MFileFormat
IUPAC Name files.
NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
name property of action
NAME_IO_WEB_SERVICE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier for parameter: "namingWebServiceURL" See Parameters and Events documentation.
NAME_TO_STRUCTURE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Name to Structure
NameConverter - Interface in chemaxon.naming
The interface of a converter from names to structures.
NameConverters - Class in chemaxon.naming
Maintains the list of custom and built-in name-to-structures converters.
NameFormatException - Exception in chemaxon.naming
A failure to convert a name to a structure.
NameFormatException(String) - Constructor for exception chemaxon.naming.NameFormatException
 
NameFormatException(String, String) - Constructor for exception chemaxon.naming.NameFormatException
 
NameFormatException(String, Throwable) - Constructor for exception chemaxon.naming.NameFormatException
 
NameFormatException(Throwable) - Constructor for exception chemaxon.naming.NameFormatException
 
NameFormatException.FilteredCase - Exception in chemaxon.naming
Exception signaling that the given input name should not be converted.
nameOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the name of the specified element.
NamePrefixException - Exception in chemaxon.naming
This exception should be thrown by a NameConverter to indicate that even though a name cannot be converted to a structure, it is the prefix of a valid name.
NamePrefixException() - Constructor for exception chemaxon.naming.NamePrefixException
 
NamePrefixException(String) - Constructor for exception chemaxon.naming.NamePrefixException
 
NamePrefixException(String, String) - Constructor for exception chemaxon.naming.NamePrefixException
 
names() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunction
The names of the functions which are registered by this annotation.
NAMESPACE - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Property key for namespace as String
nameStructureFormat - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
The structure format used to represent hits converted from names.
nameStructureFormat(String) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
NAN - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Double constant for Double.NaN.
naturalWeightOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the natural weight of the element.
NAVIGATION_MODE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "navmode".
Nb - Static variable in class chemaxon.core.ChemConst
 
Nd - Static variable in class chemaxon.core.ChemConst
 
Ne - Static variable in class chemaxon.core.ChemConst
 
NEAREST_VALUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Will only the property of the nearest atom be mapped onto the surface.
needError() - Method in class chemaxon.marvin.calculations.logPPlugin
 
needRecreateBall - Variable in class chemaxon.marvin.space.PharmacophorePoint
 
needRecreateDisplayList - Variable in class chemaxon.marvin.space.PharmacophorePoint
 
needsAnalysisBoxWarning() - Method in class chemaxon.marvin.common.UserSettings
 
needsConfig() - Method in class chemaxon.descriptors.MolecularDescriptor
Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.Heavy
Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.LogP
Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.Mass
Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.TPSA
Indicates if class takes parameters from configuration file.
needsMore - Variable in class chemaxon.formats.recognizer.Recognizer
 
needsMore() - Method in class chemaxon.formats.recognizer.Recognizer
Should we read more lines?
NEG - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
negOxOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the negative oxidation number.
NeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Constructs an iterator to process the bonds connecting to the specified atom.
NeutralizeAction - Class in chemaxon.standardizer.actions
Neutralization standardizer action
NeutralizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.NeutralizeAction
Initializes the action
NeutralizeChargeFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which neutralize the charge of the atoms of the molecule
NeutralizeChargeFixer() - Constructor for class chemaxon.fixers.NeutralizeChargeFixer
 
never() - Static method in interface com.chemaxon.calculations.common.CancelObserver
Returns a cancel observer which won't cancel execution.
newBond(BondInfo) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when start to visit a new bond.
newCalculation(Molecule, Molecule) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when a new structure is processed.
newInstance() - Method in interface chemaxon.common.util.MProgressMonitor
Creates new monitor with same parent, message, levels.
newInstance() - Method in class chemaxon.struc.Molecule
Creates a new Molecule object.
newInstance() - Method in class chemaxon.struc.MoleculeGraph
Creates a new MoleculeGraph object.
newInstance() - Method in class chemaxon.struc.RgMolecule
Creates a new RgMolecule object.
newInstance() - Method in class chemaxon.struc.RxnMolecule
Creates a new RxnMolecule object.
newInstance() - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets a new MultipleSgroup instance.
newInstance() - Static method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Creates a new instance of MCS search algorithm using the default search options.
newInstance(int, int, int) - Method in interface chemaxon.struc.WSmolecule
Creates a new WSmolecule instance with the specified capacity.
newInstance(McsSearchOptions) - Static method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Creates a new instance of MCS search algorithm using the given search options.
newInstance(String) - Static method in class chemaxon.descriptors.MolecularDescriptor
Creates a MolecularDescriptor specified by its name.
newInstance(String, String) - Static method in class chemaxon.descriptors.MolecularDescriptor
Creates a MolecularDescriptor specified by its name and xml parameter.
newInstanceFromXML(String) - Static method in class chemaxon.descriptors.MolecularDescriptor
Creates a new MolecularDescriptor instance according to the given parameter string.
newInstanceSupplier(String) - Static method in class chemaxon.descriptors.MolecularDescriptor
Deprecated, for removal: This API element is subject to removal in a future version.
This method will be removed. Call MolecularDescriptor.newInstance(String) instead in a lambda.
newSelectionMolecule() - Method in class chemaxon.struc.Molecule
Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
newSelectionMolecule() - Method in class chemaxon.struc.RgMolecule
Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
newToOld() - Method in class chemaxon.standardizer.Changes
Returns the new -> old atom index mapping.
newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
newToOld(List<Changes>, Molecule) - Static method in class chemaxon.standardizer.Changes
Calculates the new -> old atom index mapping based on a list of changes.
newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
next() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator
Returns the next atom in the iteration.
next() - Method in class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
Returns the next atom in the iteration.
next() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
Returns the next bond in the iteration.
next() - Method in class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
Returns the next bond in the iteration.
next() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
Returns the next component in the iteration.
next() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
Returns the next component in the iterator.
next() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator
Returns the next s-group in the iteration.
next() - Method in interface chemaxon.util.iterator.MoleculeIterator
Gets the next molecule.
next() - Method in class com.chemaxon.calculations.util.CloseableLineIterator
Deprecated.
 
nextAtom() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.AtomIterator.next() instead.
nextAtom() - Method in class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.AtomNeighbourIterator.next() instead.
nextBond() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.BondIterator.next() instead.
nextBond() - Method in class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.BondNeighbourIterator.next() instead.
nextBondIndex(int) - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Returns the next bond index in the iteration according to the atom and bond related behavior specified in the factory.
nextComponent() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.RgComponentIterator.next() instead.
nextComponent() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.2, Use IteratorFactory.RxnComponentIterator.next() instead.
nextDoc() - Method in class chemaxon.formats.MolImporter
Reads the next document.
nextDoc() - Method in class chemaxon.marvin.io.ArrayMDocSource
Produces the next document.
nextDoc() - Method in class chemaxon.marvin.io.MDocSource
Produces the next document.
nextOpt(String, int, String) - Static method in class chemaxon.marvin.io.MolExportModule
Tests whether the option string contains the specified substring at the specified position.
nextRecord() - Method in interface chemaxon.marvin.io.MRecordReader
Reads the next record.
nextResult() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Finds the next MCS search result according to the specified options.
Nh - Static variable in class chemaxon.core.ChemConst
 
Ni - Static variable in class chemaxon.core.ChemConst
 
NMR - Static variable in class chemaxon.license.LicenseManager
Identifier of product: NMR plugin
NMR_CNMR - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
NMR_HNMR - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
NMRCalculator - Class in chemaxon.calculations.nmr
Class for NMR spectrum calculation.
NMRCalculator.Builder - Class in chemaxon.calculations.nmr
Builder class for NMRCalculator.
NMRExporter - Class in chemaxon.calculations.nmr.io
Class for NMR spectrum export.
NMRExporter() - Constructor for class chemaxon.calculations.nmr.io.NMRExporter
 
NMRSpectrum - Class in chemaxon.calculations.nmr
Class for the representation of NMR spectra.
NMRSpectrum(Molecule) - Constructor for class chemaxon.calculations.nmr.NMRSpectrum
Constructor.
NMRSpectrum(Molecule, NMRSpectrum.Nucleus) - Constructor for class chemaxon.calculations.nmr.NMRSpectrum
Constructor.
NMRSpectrum.Nucleus - Enum Class in chemaxon.calculations.nmr
Nucleus enumeration type.
NMRSpectrum.Unit - Enum Class in chemaxon.calculations.nmr
Unit enumeration type.
No - Static variable in class chemaxon.core.ChemConst
 
NO - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption
Recover from record level errors if possible.
NO - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
NO - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
NO_ABAS - Static variable in interface chemaxon.sss.SearchConstants
Substructure search that applies only screening.
NO_DECREASE - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will not decrease when getting farther from the atom center.
NO_ERROR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type for results sign no error.
NO_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
no error message for checker
NO_LICENSE_REQUIRED - Static variable in annotation interface chemaxon.standardizer.StandardizerActionInfo
no license required
NO_RADICAL - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Not radical center.
NO_SCREEN - Static variable in interface chemaxon.sss.SearchConstants
Substructure search that applies only atom-by-atom search.
noCanceller() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
nodes - Variable in class chemaxon.marvin.alignment.AlignmentMolecule
 
noErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the no error message for the checker
NOMINAL_MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Result type with the string id "nominalmass".
nominalMass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
NOMOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil
Do not read multi-molecule XYZ files as movies.
NON_STANDARD_WEDGE_SCHEME - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Wedge configuration around a chiral center doesn't follow IUPAC recommendations.
NON_STEREO_WEDGE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
The wedge is connected to a non-stereo atom.
NONE - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption
No atom can have translation.
NONE - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
NONE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Property display type: no property display.
NONNEGATIVE_REAL - Static variable in class chemaxon.marvin.util.OptionDescriptor
Positive real number.
nonPositiveToInfinite(int) - Static method in class chemaxon.sss.search.SearchOptions
 
NONRECURSIVE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable
Non recursive expansion of child groups.
NonStandardWedgeSchemeChecker - Class in chemaxon.checkers
Non-standard Wedge Scheme Checker detects wedge configurations not following the IUPAC recommendations.
NonStandardWedgeSchemeChecker() - Constructor for class chemaxon.checkers.NonStandardWedgeSchemeChecker
Default constructor
NonStereoWedgeBondChecker - Class in chemaxon.checkers
Non-stereo Wedge Bond Checker detects wedge bonds connected to non-stereo atoms.
NonStereoWedgeBondChecker() - Constructor for class chemaxon.checkers.NonStereoWedgeBondChecker
Default constructor
NOPARAMS - Static variable in class com.chemaxon.calculations.gui.PluginFactory
No parameter panel sign in property file: if present then no parameter panel belongs to the plugin.
noReport - Variable in class chemaxon.checkers.StructureCheckOptions
The execution does not generate report to file or property (the execution does only effect structures with fixable structure errors in fix mode.)
NORMAL - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
Atomic contribution only, no correction terms.
NORMAL - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
 
NORMAL - Enum constant in enum class com.chemaxon.search.mcs.SearchMode
Normal search mode.
NORMAL_CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
normalized - Variable in class chemaxon.descriptors.MDParameters
flags indicating if the metric is normalized or not
NORMALIZED_EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType
 
normalizedEuclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the normalized Euclidean distance.
normalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the normalized Euclidean distance.
NoStructure - Class in chemaxon.struc
This class represents NoStructure labels.
NoStructureFormat - Static variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
Use this format constant to avoid exporting any structural format in the HTML output.
NOT_USEFUL - Static variable in class chemaxon.sss.search.MolComparator
Describes that the MolComparator is not needed with the current search object, the current query (and target).
notifyCoordinateChange() - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the associated components of changing coodinates.
notifyInvisibility() - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the associated components of being invisible.
notifySelection() - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the associated components of being selected.
notifyUnSelection() - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the associated components of being unselected.
notifyVisibility() - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the associated components of being visible.
notifyZCoordinateChange() - Method in class chemaxon.marvin.space.GraphicCell
Components with 2D parts should notify the container cell when their 'pseudo z' coordinate changes in order to display them in a correct order.
NOTLIST - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the exclusive atom list.
Np - Static variable in class chemaxon.core.ChemConst
 
nullObserver() - Static method in interface com.chemaxon.calculations.common.ProgressObserver
Returns an observer that ignores progress report and cannot be cancelled.
nullProgressObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
nullProgressObserver(CancelObserver) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed without replacement.
numberOfAtoms() - Method in class chemaxon.util.iterator.IteratorFactory
Returns the number of atoms iterated by AtomIterator.
numberOfBonds() - Method in class chemaxon.util.iterator.IteratorFactory
Returns the number of bonds iterated by BondIterator.
numberOfNeighbours(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Returns the number of atoms/bonds iterated by (Atom/Bond)NeighbourIterator (the two values are the same).
numOf(String) - Static method in class chemaxon.struc.MolAtom
Deprecated.
As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String).
The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
numoxstatesOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the number of oxidation states for the specified element.

O

O - Static variable in class chemaxon.core.ChemConst
 
objectContainingSelection - Variable in class chemaxon.struc.MDocument
 
objectInputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create ObjectInputStream from a not nullable location.
objectInputStreamFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create ObjectInputStream from a not nullable location.
objectInputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Create in object input stream from nullable location.
objectOutputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
ObjectOutputStream from a location.
objectOutputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
ObjectOutputStream from a nullable location.
objects - Variable in class chemaxon.struc.MDocument
 
ocr - Variable in class chemaxon.checkers.StructureCheckOptions
OCR check involved
OCRErrorChecker - Class in chemaxon.checkers
OCRErrorChecker detects structures which do not look like chemical structures.
OCRErrorChecker() - Constructor for class chemaxon.checkers.OCRErrorChecker
Default constructor
ODD - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
 
ODD - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
 
ODD - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
 
ODD - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
Deprecated, for removal: This API element is subject to removal in a future version.
ODD - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
Deprecated, for removal: This API element is subject to removal in a future version.
ODD - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
Deprecated, for removal: This API element is subject to removal in a future version.
ODD - Static variable in class chemaxon.calculations.stereo.Stereochemistry
 
of(CalculatorTag...) - Static method in interface chemaxon.calculator.TaggedCalculator
Creates a TaggedCalculator that always returns the given tags.
of(String, Predicate<Molecule>) - Static method in interface chemaxon.calculator.CalculatorInputChecker
Creates a new input checker that accepts those molecules which satisfy the given lambda.
of(Collection<CalculatorTag>) - Static method in interface chemaxon.calculator.TaggedCalculator
Creates a TaggedCalculator that always returns the given tags.
OFF - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckEnabled(boolean). Usage:
             molecule.setValenceCheckEnabled(false);
             
OFFICE - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
 
Og - Static variable in class chemaxon.core.ChemConst
 
oldToNew() - Method in class chemaxon.standardizer.Changes
Returns the old -> new atom index mapping.
oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
oldToNew(List<Changes>, Molecule) - Static method in class chemaxon.standardizer.Changes
Calculates the old -> new atom index mapping based on a list of changes.
oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
OMIT_POSTCLEAN - Static variable in class chemaxon.struc.MolAtom
Omit arranging process after the hydrogen addition.
OMIT_POSTCLEAN - Static variable in class chemaxon.struc.MoleculeGraph
Omit arranging process after the hydrogen addition.
onAnyCancelled(CancelObserver...) - Static method in interface com.chemaxon.calculations.common.CancelObserver
Returns a cancel observer which cancels when any of the specified observers is cancelled.
ONE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
single error message for checker
oneErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the one error message for the checker
onFailure(ServiceException) - Method in interface chemaxon.marvin.services.AsyncCallback
Called when asynchronous call is failed
onRemove() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
onRemove() - Method in class chemaxon.marvin.space.MoleculeComponent
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.GraphicComponent
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.MoleculeComponent
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.monitor.Monitor
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
onRemoveGraphicComponent() - Method in class chemaxon.marvin.space.SurfaceComponent
 
onSuccess(T) - Method in interface chemaxon.marvin.services.AsyncCallback
Called when asynchronous call is completed successfully
onTimeout(long) - Static method in interface com.chemaxon.calculations.common.CancelObserver
Returns a cancel observer which cancels after a specified timeout.
open(String) - Method in class chemaxon.marvin.io.MolExportModule
Opens the exporter stream.
open(String) - Static method in class chemaxon.util.DotfileUtil
Opens a dotfile for reading.
open(String, MPropertyContainer) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Open the exporter stream.
open(String, MPropertyContainer) - Method in class chemaxon.marvin.io.MolExportModule
Opens the exporter stream.
openMolecule(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Closes all components from the viewer, and reads the molecule(s).
openSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane
Opens the sketcher window with the molecule from the specified cell if the viewer is editable.
openUrlStream(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Open an URL connection.
openWindow(int) - Method in class chemaxon.marvin.beans.MViewPane
Detaches the view canvas of the specified cell into a separate window if the viewer is detachable.
OPTIMIZATION_NORMAL - Static variable in class chemaxon.marvin.calculations.ConformerPlugin
 
OPTIMIZATION_STRICT - Static variable in class chemaxon.marvin.calculations.ConformerPlugin
 
OPTIMIZATION_VERY_LOOSE - Static variable in class chemaxon.marvin.calculations.ConformerPlugin
 
OPTIMIZATION_VERY_STRICT - Static variable in class chemaxon.marvin.calculations.ConformerPlugin
 
OPTION_NAME_STRING - Static variable in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
 
OPTION_NAME_STRING - Static variable in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
OptionDescriptor - Class in chemaxon.marvin.util
General option descriptor class.
OptionDescriptor(String, String, int, String, String[], String[], String[]) - Constructor for class chemaxon.marvin.util.OptionDescriptor
Creates an option.
Options() - Constructor for class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
Options() - Constructor for class com.chemaxon.mapper.AutoMapper.Options
 
optionsDialog - Variable in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
OptionsPane - Class in chemaxon.marvin.plugin.gui
Displays plugin parameter tabbed panes.
OptionsPane(Dialog, String, String, ParameterPanelHandler, ActionListener) - Constructor for class chemaxon.marvin.plugin.gui.OptionsPane
Creates an options pane: plugin parameter panel with "Display", "OK", "Cancel" buttons.
OptionsPane(Frame, String, String, ParameterPanelHandler, ActionListener) - Constructor for class chemaxon.marvin.plugin.gui.OptionsPane
Creates an options pane: plugin parameter panel with "Display", "OK", "Cancel" buttons.
OptionsPane(String, String, ParameterPanelHandler, ActionListener) - Constructor for class chemaxon.marvin.plugin.gui.OptionsPane
Creates an options pane: plugin parameter panel with "Display", "OK", "Cancel" buttons.
OR - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
Stereogenic centers belonging to an ORn group (e.g.
OR - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
OrbitalElectronegativityPlugin - Class in chemaxon.marvin.calculations
Plugin class for orbital electronegativity calculation.
OrbitalElectronegativityPlugin() - Constructor for class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Constructor.
orderSensitive - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
orderSensitive(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.
orderSensitive(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
ORIGINAL_MOLECULE - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
In case of standardization error the original molecule is provided on the output
orix - Variable in class chemaxon.struc.MoleculeGraph
Origin x.
oriy - Variable in class chemaxon.struc.MoleculeGraph
Origin y.
oriz - Variable in class chemaxon.struc.MoleculeGraph
Origin z.
orTimeout(CancelObserver, long) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
Os - Static variable in class chemaxon.core.ChemConst
 
OSRA - Static variable in class chemaxon.formats.MFileFormat
 
otell() - Method in class chemaxon.formats.MolConverter
Get the current file position.
outputIn3d() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Returns true if 3D structures will be generated.
outputPath - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the valid/fixed output structures
outputPrecision - Variable in class chemaxon.descriptors.MDParameters
number of fraction digits in floating point output format
outputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
OutputStream from a location.
OVERLAPPING_ATOMS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that overlapping atoms had found in the molecule
OVERLAPPING_BONDS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that overlapping bonds had found in the molecule
OverlappingAtomsChecker - Class in chemaxon.checkers
OverlappingAtomsChecker detects atoms that are too close to each other.

This checker checks 2D structures only.

Two atoms considered as overlapping when their euclidean distance is less than the half of the Chemaxon standard bond length ( MolBond.CCLENGTH ).
OverlappingAtomsChecker() - Constructor for class chemaxon.checkers.OverlappingAtomsChecker
 
OverlappingBondsChecker - Class in chemaxon.checkers
OverlappingBondsChecker detects bonds that are too close to each other.

This checker checks two dimensional structures only.

Two bonds considered as overlapping when they crossing each other, or their distance is smaller then the 80% of the standard Chemaxon bond length ( MolBond.CCLENGTH ).
OverlappingBondsChecker() - Constructor for class chemaxon.checkers.OverlappingBondsChecker
Default constructor
overridesAtMerge(MolBond) - Method in class chemaxon.struc.MolBond
Checks if this bond should override another one when two structures are merged.
ownOverlap(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
oxstateOf(int, int) - Static method in class chemaxon.struc.MolAtom
Gets the oxidation states.

P

p - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
 
p - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
 
P - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
 
P - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
 
P - Static variable in class chemaxon.core.ChemConst
 
P_CENTER - Static variable in class chemaxon.struc.graphics.MRectangle
Central point ID.
P_E - Static variable in class chemaxon.struc.graphics.MRectangle
Middle point on right edge.
P_N - Static variable in class chemaxon.struc.graphics.MRectangle
Middle point on top edge.
P_NE - Static variable in class chemaxon.struc.graphics.MRectangle
Top-right corner index.
P_NW - Static variable in class chemaxon.struc.graphics.MRectangle
Top-left corner index.
P_S - Static variable in class chemaxon.struc.graphics.MRectangle
Middle point on bottom edge.
P_SE - Static variable in class chemaxon.struc.graphics.MRectangle
Botton-right corner index.
P_SW - Static variable in class chemaxon.struc.graphics.MRectangle
Bottom-left corner index.
P_W - Static variable in class chemaxon.struc.graphics.MRectangle
Middle point on left edge.
Pa - Static variable in class chemaxon.core.ChemConst
 
pack() - Method in class chemaxon.struc.MolAtom
Reduce memory usage.
pack() - Method in class chemaxon.struc.MoleculeGraph
Reduce memory usage.
PAGE - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the page number, if applicable (e.g.
paint(Graphics) - Method in class chemaxon.marvin.space.GraphicScene
 
paint(Graphics2D, Dimension) - Method in class chemaxon.marvin.MolPrinter
Paints the molecule on the specified graphics context in the given size.
paint(Graphics2D, Rectangle) - Method in class chemaxon.marvin.MolPrinter
Paints the molecule into the center of the specified rectangle.
paint(Graphics, Rectangle) - Method in class chemaxon.marvin.MolPrinter
Paints the molecule into the center of the specified rectangle.
paintComponent(Graphics) - Method in class chemaxon.marvin.beans.MolRenderer
 
PAIRED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties
 
PairwiseAlignment - Class in chemaxon.marvin.alignment
Align pairs of molecules (query and the target) using the shape Alignment
PairwiseAlignment() - Constructor for class chemaxon.marvin.alignment.PairwiseAlignment
 
PairwiseAlignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.PairwiseAlignment
 
PairwiseComparison - Interface in chemaxon.marvin.alignment
This interface designed for comparing two molecules in 3D by various overlay methodologies.
PairwiseSimilarity3D - Class in chemaxon.marvin.alignment
Align pairs of molecules (query and the target) using the atom/atom matcher Similarity3D
PairwiseSimilarity3D() - Constructor for class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
PairwiseSimilarity3D(boolean) - Constructor for class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
paletteId - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
PARAM_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Parameter separator token of the action string
ParameterConstants - Class in chemaxon.marvin.common
Parameters of Marvin Applets and Beans.
ParameterConstants() - Constructor for class chemaxon.marvin.common.ParameterConstants
 
ParameterPanel - Class in chemaxon.marvin.plugin.gui
A configurable implementation of the plugin specific parameter setting panel.
ParameterPanel(ParameterTab, ParameterTab[]) - Constructor for class chemaxon.marvin.plugin.gui.ParameterPanel
Constructor.
ParameterPanel(ParameterTab, ParameterTab[], ParameterItem[]) - Constructor for class chemaxon.marvin.plugin.gui.ParameterPanel
Constructor.
ParameterPanelHandler - Interface in com.chemaxon.calculations.gui
Plugin parameter panel handler interface.
parameters - Variable in class chemaxon.descriptors.CDParameters
node in the DOM tree built from the XML configuration
PARAMETERS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "param".
PARAMETERS_HEADER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "paramH".
ParameterTab - Class in chemaxon.marvin.plugin.gui
Represents a parameter tab.
ParameterTab(String, String) - Constructor for class chemaxon.marvin.plugin.gui.ParameterTab
 
parametrizedMetricNodes - Variable in class chemaxon.descriptors.MDParameters
 
parametrizedMetrics - Variable in class chemaxon.descriptors.MDParameters
symbolic names (mnemonics) of parametrized metrics
parametrizedMetricsNode - Variable in class chemaxon.descriptors.MDParameters
 
params - Variable in class chemaxon.descriptors.MolecularDescriptor
Parameter settings related to the descriptor.
params - Variable in class chemaxon.marvin.beans.MarvinPane
Parameter string.
params - Variable in class com.chemaxon.calculations.cli.CalculatorPluginOutput
The plugin parameter table.
parent - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The parent component.
parentGraph - Variable in class chemaxon.struc.MoleculeGraph
The structure that contains this molecule graph as a substructure.
parentLine - Variable in class chemaxon.struc.graphics.MMidPoint
 
parentRect - Variable in class chemaxon.struc.graphics.MRectanglePoint
 
parentSgroup - Variable in class chemaxon.struc.Sgroup
 
PARITY_ALLENE - Static variable in interface chemaxon.struc.StereoConstants
Atom with allene like parity.
PARITY_EITHER - Static variable in interface chemaxon.struc.StereoConstants
Odd or even parity.
PARITY_EVEN - Static variable in interface chemaxon.struc.StereoConstants
Chiral atom of even parity (counterclockwise arrangement).
PARITY_MASK - Static variable in interface chemaxon.struc.StereoConstants
Parity mask in flags.
PARITY_NONE - Static variable in interface chemaxon.struc.StereoConstants
Atom with no parity.
PARITY_ODD - Static variable in interface chemaxon.struc.StereoConstants
Chiral atom of odd parity (clockwise arrangement).
PARITY_TETRAHEDRAL - Static variable in interface chemaxon.struc.StereoConstants
Atom with tetrahedral parity.
PARITY_UNSPEC - Static variable in interface chemaxon.struc.StereoConstants
Unspecified parity flag.
paritySign(int, int, int, int) - Static method in class chemaxon.struc.MolAtom
Calculates the sign of the parity for the specified indexes.
parse(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
 
parse(String) - Static method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
Parses the type of the absolute stereo action
parse(String) - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Parses the type of the aromatize action
parse(String) - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
Parses the type of the convert double bonds action
parse(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Parses the measurement of the remove fragment action
parse(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Parses the method of the remove fragment action
parse(String) - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
Parses the hydrogen isotope representation type
parse(String) - Static method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Parses the type of the clean action
parseCharIfOptionSign(String, int) - Method in class chemaxon.marvin.io.MolExportModule
Parse the current character if it is an option sign.
parseExpression(String) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
parseMolecule(String) - Static method in class chemaxon.marvin.io.MPropHandler
 
parseMRV(String) - Static method in class chemaxon.formats.MolImporter
Parses a document from a string in Marvin Document (MRV) format.
parseMRV(String) - Static method in class chemaxon.struc.MDocument
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.7, replaced by MolImporter.parseMRV(String)
parseOption(String, int) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Parses the bond length (b###) option.
parseOption(String, int) - Method in class chemaxon.marvin.io.MolExportModule
Parses the following option in the option string.
parseType(String) - Static method in class chemaxon.marvin.util.OptionDescriptor
Parses an option type from a string.
PARTIAL - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Partial clean
PARTIAL_CLEAN_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction
Key for partial clean necessary property change
partialClean(int, int[], String) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
partialClean(Molecule[], String) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
partialClean(MoleculeGraph, int[], String) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
partialClean(MoleculeGraph, int, int[], String) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates by using fixed atoms.
partialClean(MoleculeGraph, MoleculeGraph, int[], String) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates by using the given template molecule.
partialClean(MoleculeGraph, MoleculeGraph, int[], String, AtomChangeEventListener) - Static method in class chemaxon.calculations.clean.Cleaner
 
partialClean(Molecule, Molecule[], String) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates by using the given template molecule array.
partialClean(Molecule, Molecule[], String, AtomChangeEventListener) - Static method in class chemaxon.calculations.clean.Cleaner
A specific overloading for partial clean.
PartialCleanFixer - Class in chemaxon.fixers
Partial clean
PartialCleanFixer() - Constructor for class chemaxon.fixers.PartialCleanFixer
 
partialCleanWithStereo(MoleculeGraph, int, int[], String) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates by using fixed atoms.
PARTITIONING_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Partitioning Plugin Group
PATOM - Static variable in class chemaxon.jep.context.ReactionContext
 
Pb - Static variable in class chemaxon.core.ChemConst
 
Pd - Static variable in class chemaxon.core.ChemConst
 
PDB - Static variable in class chemaxon.formats.MFileFormat
Protein Data Bank format.
PDBRecognizer - Class in chemaxon.formats.recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
PDBRecognizer() - Constructor for class chemaxon.formats.recognizer.PDBRecognizer
Deprecated.
 
PDF - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
 
PDF - Static variable in class chemaxon.formats.MFileFormat
Portable Document Format.
PEPTIDE_DISPLAY_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier for parameter: "peptideDisplayType" See Parameters and Events documentation.
PEPTIDE_IN - Static variable in class chemaxon.formats.MFileFormat
Peptide Sequence.
PEPTIDE1_OUT - Static variable in class chemaxon.formats.MFileFormat
Peptide Sequence (1-letter).
PEPTIDE3_OUT - Static variable in class chemaxon.formats.MFileFormat
Peptide Sequence (3-letter).
PeptideRecognizer - Class in chemaxon.formats.recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
PeptideRecognizer() - Constructor for class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
 
PeriodicSystem - Class in chemaxon.struc
Periodic System of the Elements.
PeriodicSystem() - Constructor for class chemaxon.struc.PeriodicSystem
 
Persistent - Annotation Interface in chemaxon.checkers
This annotation signs if a property of a StructureChecker should be persisted
PFGenerator - Class in chemaxon.descriptors
The PFGenerator class generates 2-dimensional pharmacophore fingerprints for molecular graphs.
PFGenerator(PMapper) - Constructor for class chemaxon.descriptors.PFGenerator
Creates a new instance of PFGenerator which can be used to generate fingerprints for an arbitrary number of molecules.
PFParameters - Class in chemaxon.descriptors
Manages 2D pharmacophore fingerprint parameters.
PFParameters() - Constructor for class chemaxon.descriptors.PFParameters
Creates an empty object.
PFParameters(File) - Constructor for class chemaxon.descriptors.PFParameters
Creates a new object based on a given configuration file.
PFParameters(String) - Constructor for class chemaxon.descriptors.PFParameters
Creates a new object based on a given configuration string.
PHARMACOPHORE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
 
Pharmacophore3D - Class in chemaxon.marvin.alignment
3D Pharmacophore representation for 3D alignments.
Pharmacophore3D() - Constructor for class chemaxon.marvin.alignment.Pharmacophore3D
 
Pharmacophore3D(Molecule) - Constructor for class chemaxon.marvin.alignment.Pharmacophore3D
Deprecated.
Use Pharmacophore3DGenerator instead.
Pharmacophore3D(Molecule, int[]) - Constructor for class chemaxon.marvin.alignment.Pharmacophore3D
 
PharmacophoreArrow - Class in chemaxon.marvin.space
PharmacophoreArrow provides an extension of PharmacophorePoint to represent pharmacophores by introducing directionality.
PharmacophoreArrow() - Constructor for class chemaxon.marvin.space.PharmacophoreArrow
Creates a new instance of PharmacophoreArrow.
PharmacophoreArrow(double, double, double) - Constructor for class chemaxon.marvin.space.PharmacophoreArrow
Creates a PharmacophoreArrow at the given position.
PharmacophoreArrow(ComponentElement) - Constructor for class chemaxon.marvin.space.PharmacophoreArrow
Creates a PharmacophoreArrow at the position of the given ComponentElement getting the coordinates by getCoordinates().
PharmacophoreFingerprint - Class in chemaxon.descriptors
The PharmacophoreFingerprint class implements 2D pharmacophoric fingerprints.
PharmacophoreFingerprint() - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint
Creates a new, empty instance of PharmacophoreFingerprint without allocating internal storage.
PharmacophoreFingerprint(PFParameters) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint
Creates a new instance of PharmacophoreFingerprint according to the parameters given.
PharmacophoreFingerprint(PharmacophoreFingerprint) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint
Copy constructor.
PharmacophoreFingerprint(String) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint
Creates a new instance of PharmacophoreFingerprint according to the parameters given.
PharmacophorePoint - Class in chemaxon.marvin.space
Simple spherical representation of a pharmacophoric point/area.
PharmacophorePoint() - Constructor for class chemaxon.marvin.space.PharmacophorePoint
Creates a new instance of PharmacophorePoint.
PharmacophorePoint(double, double, double) - Constructor for class chemaxon.marvin.space.PharmacophorePoint
Creates a PharmacophorePoint at the given position.
PharmacophorePoint(ComponentElement) - Constructor for class chemaxon.marvin.space.PharmacophorePoint
Creates a PharmacophorePoint at the position of the given ComponentElement getting the coordinates by getCoordinates().
pickedIndicator() - Method in class chemaxon.marvin.space.monitor.Monitor
Monitors do not really have z coordinate, they are the nearer to us.
pickedItem - Variable in class chemaxon.marvin.space.GraphicComponent
Identifies the most recently selected element
pickObject(int, double[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Sets GraphicComponent.pickedItem to be the picked part of the component.
pickObject(int, double[], float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
 
pickObject(int, double[], float[]) - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
pickObject(int, double[], float[]) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets GraphicComponent.pickedItem to the pharmacophore point.
PKA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
PKa calculation for bbb score.
PKA - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Most basic center (pKa).
PKACALCULATOR - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
pKaPlugin - Class in chemaxon.marvin.calculations
Plugin class for macro/micro pKa calculation.
pKaPlugin() - Constructor for class chemaxon.marvin.calculations.pKaPlugin
Constructor.
PKAT - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
PLAIN - Static variable in class chemaxon.struc.graphics.MFont
Plain font style.
plattIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
PLEXUS - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Plexus
PLEXUS_CONNECT - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Plexus Connect
plugin - Variable in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
The plugin object.
plugin - Variable in class com.chemaxon.calculations.cli.CalculatorPluginOutput
The CalculatorPlugin object.
PLUGIN_CLASS_KEY - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Plugin class key in manifest.
PLUGIN_DIR - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
The plugin directory (relative to CLASSPATH).
PluginException - Exception in chemaxon.marvin.plugin
Exception thrown in case of plugin processing or calculation errors.
PluginException() - Constructor for exception chemaxon.marvin.plugin.PluginException
Default constructor.
PluginException(String) - Constructor for exception chemaxon.marvin.plugin.PluginException
Constructor with message.
PluginException(String, Throwable) - Constructor for exception chemaxon.marvin.plugin.PluginException
Constructor with wrapped exception.
PluginException(Throwable) - Constructor for exception chemaxon.marvin.plugin.PluginException
Constructor with wrapped exception.
PluginExecutionException - Exception in chemaxon.marvin.plugin.concurrent
Exception wrapping a cause Throwable and the plugin object which has thrown the Throwable.
PluginExecutionException(CalculatorPlugin, String, Throwable) - Constructor for exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
Constructor.
PluginExecutionException(CalculatorPlugin, Throwable) - Constructor for exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
Constructor.
PluginFactory - Class in com.chemaxon.calculations.gui
Plugin factroy: responsible for plugin parameter panel and plugin creation and central management.
PluginFactory() - Constructor for class com.chemaxon.calculations.gui.PluginFactory
Constructor.
PluginFactory.PluginRecord - Class in com.chemaxon.calculations.gui
Stores plugin data.
PluginInputCheckerException - Exception in chemaxon.marvin.plugin
Exception thrown when a CalculatorInputChecker rejects an input molecule of a CalculatorPlugin.
PluginInputCheckerException(CalculatorError) - Constructor for exception chemaxon.marvin.plugin.PluginInputCheckerException
 
PluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent
Work unit performing plugin calculation.
PluginWorkUnit() - Constructor for class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Constructor.
PluginWorkUnit(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Constructor.
Pm - Static variable in class chemaxon.core.ChemConst
 
PNG - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat
 
PNG - Static variable in class chemaxon.formats.MFileFormat
Portable Network Graphics.
Po - Static variable in class chemaxon.core.ChemConst
 
points - Variable in class chemaxon.struc.graphics.MPolyline
 
POLARIZABILITY - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
POLARIZABILITY_GEOM3D - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
PolarizabilityPlugin - Class in chemaxon.marvin.calculations
Plugin class for atom polarizability calculation.
PolarizabilityPlugin() - Constructor for class chemaxon.marvin.calculations.PolarizabilityPlugin
Constructor.
polylinePointIndex - Variable in class chemaxon.struc.graphics.MMidPoint
 
POLYMERENDGROUP_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup) and the H is not in the same sgroup should be kept.
pop() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Clears the last stored item from the display.
popup - Variable in class chemaxon.marvin.space.MSpaceEasy
 
popupImageFormat - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
The image format which should be used for popups in the annotated document.
popupImageFormat(DocumentAnnotatorOptions.ImageFormat) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
PORT - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Property key for port name as String
portionWidth(Graphics, MFont, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the width of this portion.
portionXAdvance(Graphics, MFont, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the x coordinate change from the beginning to the end of this portion.
portionXAdvance(Graphics, MFont, FontMetrics, boolean) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the width of this portion.
POS - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
position - Variable in class chemaxon.marvin.space.monitor.Label
 
position - Variable in class chemaxon.marvin.space.monitor.PositionMonitor
 
Position(int, int) - Constructor for class chemaxon.marvin.io.MRecordReader.Position
Creates a locator.
POSITION_ON_0TH_HEAVY_ATOM - Static variable in interface chemaxon.sss.SearchConstants
Hit constant denoting hit position of a non-heavy atom (e.g.
PositionedInputStream - Class in chemaxon.marvin.io
Positioned input stream that has the ability to set / get the stream position as well as put back some parts already read.
PositionedInputStream(InputStream) - Constructor for class chemaxon.marvin.io.PositionedInputStream
Constructor.
PositionedInputStream(InputStream, int) - Constructor for class chemaxon.marvin.io.PositionedInputStream
Constructor.
PositionedInputStream(InputStream, int, String) - Constructor for class chemaxon.marvin.io.PositionedInputStream
Constructor.
PositionedInputStream(InputStream, int, String, int) - Constructor for class chemaxon.marvin.io.PositionedInputStream
Constructor.
PositionedInputStream(InputStream, String) - Constructor for class chemaxon.marvin.io.PositionedInputStream
Constructor.
positionInPlane - Variable in class chemaxon.marvin.space.monitor.Label
 
positionInRect - Variable in class chemaxon.struc.graphics.MRectanglePoint
 
PositionMonitor - Class in chemaxon.marvin.space.monitor
Monitors a specific location in the space and has a control that can change the coordinates of the monitored elements with a transformation.
PositionMonitor() - Constructor for class chemaxon.marvin.space.monitor.PositionMonitor
Creates a new instance of PositionMonitor
posOxOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the smallest positive oxidation number.
POST - Enum constant in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method
method POST
POSTGRES_CARTRIDGE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Postgres Cartridge
POVRAY - Static variable in class chemaxon.formats.MFileFormat
POVRay file.
ppm - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit
ppm unit
pptNames - Variable in class chemaxon.descriptors.PFParameters
Pharmacophore point type names.
Pr - Static variable in class chemaxon.core.ChemConst
 
PR_ATSYMS - Static variable in class chemaxon.struc.Sgroup
Print atom symbols.
PRE_CONFIGURED_TRANSFORMATIONS - Static variable in class chemaxon.standardizer.StandardizerActionFactory
Pre-configured transformation configuration path
precisionThresholds - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
preconvert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule
Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(MoleculeGraph, boolean, int, boolean) - Method in class chemaxon.marvin.io.MolExportModule
Deprecated, for removal: This API element is subject to removal in a future version.
preconvert(Molecule, boolean) - Method in class chemaxon.marvin.io.MolExportModule
Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(Molecule, boolean, int, boolean) - Method in class chemaxon.marvin.io.MolExportModule
Optionally performs aromatization or addition of explicit Hydrogens atoms.
predict(Molecule) - Method in class com.chemaxon.calculations.admet.HergActivityPredictor
Runs the prediction of the given molecule.
predict(Molecule) - Method in class com.chemaxon.calculations.admet.HergClassPredictor
Runs the prediction of the given molecule.
PREDICTOR_PLUGIN - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Predictor Plugin
PRELOAD - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "preload".
PRELOAD - Static variable in class com.chemaxon.calculations.gui.PluginFactory
Deprecated, for removal: This API element is subject to removal in a future version.
Not used.
preMatchMap - Variable in class chemaxon.sss.search.Search
Map for storing pre-match data.
preprocess(Molecule, boolean) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
preprocessFormatAndOptions(String[]) - Static method in class chemaxon.formats.MFileFormatUtil
Parses options like "MULTISET", "MOLMOVIE" or "NOMOLMOVIE".
presetTextDraw() - Method in class chemaxon.marvin.space.monitor.Label
 
primaryAtomIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated, for removal: This API element is subject to removal in a future version.
print() - Method in class chemaxon.marvin.beans.MViewPane
Prints the molecule table.
printProperties() - Static method in class chemaxon.marvin.space.GraphicScene
 
printStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
PrintStream from a location.
printStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
PrintStream from a nullable location.
priority() - Element in annotation interface chemaxon.fixers.FixerInfo
Returns the priority of the fixer.
PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
priority of fixer
process() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Process the complete input at once, generating the annotated document.
process(String) - Static method in class chemaxon.naming.document.DocumentToStructure
Creates a MolImporter instance to import structures from a given text using the default format options.
process(String, String) - Static method in class chemaxon.naming.document.DocumentToStructure
Creates a MolImporter instance to import structures from a given text.
processArguments(int, ArrayList, ArrayList, boolean, boolean, boolean, Properties, String) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
processAwtEvent(AWTEvent, String, String) - Method in class chemaxon.marvin.space.GraphicScene
The given awt event will go to the queue of events, and will be performed during the next draw.
processCellEvent(String, String) - Method in class chemaxon.marvin.space.GraphicScene
The given event will go to the queue of events, and will be performed during the next draw.
processComponentEvent(Object, String, String) - Method in class chemaxon.marvin.space.GraphicScene
The given event will go to the queue of events, and will be performed during the next draw.
processDocument(boolean) - Method in class chemaxon.descriptors.CDParameters
Processes parts of the XML configuration that are specific to CustomDescriptor.
processDocument(boolean) - Method in class chemaxon.descriptors.CFParameters
Processes pars of the XML configuration specific to ChemicalFingerprint.
processDocument(boolean) - Method in class chemaxon.descriptors.ECFPParameters
Processes pars of the XML configuration specific to ECFP.
processDocument(boolean) - Method in class chemaxon.descriptors.MDParameters
Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.
processDocument(boolean) - Method in class chemaxon.descriptors.PFParameters
 
processDocument(boolean) - Method in class chemaxon.descriptors.RFParameters
Processes pars of the XML configuration specific to ReactionFingerprint.
processDocument(boolean) - Method in class chemaxon.descriptors.SDParameters
Processes parts of the XML configuration specific to ScalarDescriptor.
processDocument(boolean) - Method in class chemaxon.descriptors.ShapeParameters
Processes pars of the XML configuration specific to Shape.
processError(Throwable) - Method in interface chemaxon.util.ErrorProcessor
Error processing method.
processEvent(String, String) - Method in class chemaxon.marvin.space.GraphicScene
The given event will go to the queue of events, and will be performed during the next draw.
processMolecule(Molecule) - Method in class chemaxon.descriptors.ECFPFeatureLookup
Performs the necessary preprocessing for the given molecule.
PRODUCT - Static variable in class chemaxon.jep.context.ReactionContext
 
PRODUCTS - Static variable in class chemaxon.struc.RxnMolecule
"Product" structure type.
progress - Variable in class chemaxon.naming.document.annotate.DocumentAnnotator.ProgressInfo
The estimated ratio of work that has already been done, between 0 and 1.
progress(DocumentAnnotator.ProgressInfo) - Method in interface chemaxon.naming.document.annotate.DocumentAnnotator.Listener
 
progressBar - Variable in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
ProgressObserver - Interface in com.chemaxon.calculations.common
Observer for reporting the progress of long running tasks.
ProgressObservers - Class in com.chemaxon.calculations.common
Deprecated, for removal: This API element is subject to removal in a future version.
Use the static factory methods on ProgressObserver and CancelObserver instead.
projectVector(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Projects a vector from the scene to the viewport.
projectVector(float[]) - Method in class chemaxon.marvin.space.monitor.Control
 
Prop() - Constructor for class chemaxon.struc.MDocument.Prop
 
properties - Variable in class chemaxon.marvin.io.MRecord
 
properties - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Display properties of the Molecule.
properties() - Method in class chemaxon.calculations.bbb.BBB
Returns the calculated phys-chem properties and scores.
properties() - Method in class chemaxon.calculations.cnsmpo.CnsMpo
Returns the calculated phys-chem properties and scores.
properties() - Method in interface chemaxon.struc.Incomplecule
Gets the property container.
properties() - Method in class chemaxon.struc.MDocument
Gets the property container.
properties() - Method in class chemaxon.struc.MoleculeGraph
Gets the property container.
properties() - Method in class chemaxon.struc.RgMolecule
Gets the property container.
PROPERTY_KEY_ABSOLUTE - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Key of type for property change of mode
PROPERTY_KEY_ABSSTEREO - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Key of type for property change of mode
PROPERTY_KEY_ALLOW_VALENCE_ERROR - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction
Property key for serialization/deserialization an event changes for valence check (boolean value type)
PROPERTY_KEY_AROM_TYPE - Static variable in class chemaxon.checkers.AromaticityErrorChecker
This public constant String represents the name of the property which represents the arom type String property
PROPERTY_KEY_AROMATCITY - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Aromaticity atom query property.
PROPERTY_KEY_AROMATICITY_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Aromaticity checking property
PROPERTY_KEY_BRIDGEHEAD - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching Bridgehead property
PROPERTY_KEY_BRIDGEHEAD - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Bridgehead property
PROPERTY_KEY_CHARGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching charged explicit hydrogens in the molecule
PROPERTY_KEY_CHARGED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Charged property
PROPERTY_KEY_CHIRALITY - Static variable in class chemaxon.standardizer.actions.ClearStereoAction
Key of type for property change of mode
PROPERTY_KEY_CONNECTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Connection count atom query property.
PROPERTY_KEY_CONNECTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Connection count checking property
PROPERTY_KEY_CONTRACTED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker
This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups
PROPERTY_KEY_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker
Search for valence properties that are equal to the default valence.
PROPERTY_KEY_DETECT_CUMULATED_DOUBLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker
Property key detect cumulated double bonds
PROPERTY_KEY_DETECT_TRANS_DOUBLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker
Property key detect trans double bonds
PROPERTY_KEY_DETECT_TRIPLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker
Property key detect triple bonds
PROPERTY_KEY_DOUBLE_BOND - Static variable in class chemaxon.standardizer.actions.ClearStereoAction
Key of type for property change of mode
PROPERTY_KEY_ENFORCE_ABS - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Key of type for property change of mode
PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker
This public constant String represents the name of the property which is responsible for the list of excluded groups
PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.AttachedDataChecker
This public constant String represents the name of the property which is responsible for the list of excluded data.
PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.PseudoAtomChecker
This public constant String represents the name of the property which is responsible for the list of excluded pseudo atom labels
PROPERTY_KEY_EXPANDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker
This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups
PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Explicit connection count atom query property.
PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Explicit connection count checking property
PROPERTY_KEY_FACTORY_INSTANCE - Static variable in class chemaxon.marvin.util.codeassist.CodeAssistFactory
property key for factory instances
PROPERTY_KEY_H_CONNECTED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching H connected property
PROPERTY_KEY_H_CONNECTED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
H connected property
PROPERTY_KEY_HYDROGEN_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Hydrogen count atom query property.
PROPERTY_KEY_HYDROGEN_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Hydrogen count checking property
PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Implicit hydrogen count atom query property.
PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Implicit hydrogen count checking property
PROPERTY_KEY_IS_EXCLUSION_REGEXP - Static variable in class chemaxon.checkers.AttachedDataChecker
The name of the property, which is responsible for the decision if the excluded data should be treated as a regular expression instead of a (comma separated) list of strings.
PROPERTY_KEY_ISOTOPIC - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching isotopic explicit hydrogens in the molecule
PROPERTY_KEY_ISOTOPIC - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Isotopic property
PROPERTY_KEY_LONELY - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching lonely explicit hydrogens in the molecule
PROPERTY_KEY_LONELY - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Lonely property
PROPERTY_KEY_MAPPED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching mapped explicit hydrogens in the molecule
PROPERTY_KEY_MAPPED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Mapped property
PROPERTY_KEY_METAL_CONNECTED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Metal connected property
PROPERTY_KEY_NON_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker
Search for valence properties that are not equal to the default valence.
PROPERTY_KEY_POLYMER_END_GROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching Polymer end group property
PROPERTY_KEY_POLYMER_END_GROUP - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Polymer end group property
PROPERTY_KEY_PREFERRED_DESCRIPTION - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor
Property key for preferred service description
PROPERTY_KEY_PREFERRED_NAME - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor
Property key for preferred service name
PROPERTY_KEY_QUERY_ATOM - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction
Property key for serialization/deserialization an event changes for query atom (MolAtom value type)
PROPERTY_KEY_RADICAL - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching radical explicit hydrogens in the molecule
PROPERTY_KEY_RADICAL - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Radical property
PROPERTY_KEY_REPLACE_ATOM - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction
Property key for serialization/deserialization an event changes for replace atom (MolAtom value type)
PROPERTY_KEY_RING_BOND_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Ring bond count atom query property.
PROPERTY_KEY_RING_BOND_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Ring bond count checking property
PROPERTY_KEY_RING_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Ring count atom query property.
PROPERTY_KEY_RING_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Ring count checking property
PROPERTY_KEY_SEARCH_ALL - Static variable in class chemaxon.checkers.RatomChecker
This constant String represents the name of the property which is responsible for searching all ratoms in the molecule
PROPERTY_KEY_SEARCH_BRIDGEHEAD - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searchingBridgehead property
PROPERTY_KEY_SEARCH_CHARGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching charged explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_CONTRACTED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker
This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups
PROPERTY_KEY_SEARCH_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker
Search default valence property
PROPERTY_KEY_SEARCH_DISCONNECTED - Static variable in class chemaxon.checkers.RatomChecker
This constant String represents the name of the property which is responsible for searching disconnected ratoms in the molecule
PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker
This public constant String represents the name of the property which is responsible for the list of excluded groups
PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.AttachedDataChecker
 
PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.PseudoAtomChecker
 
PROPERTY_KEY_SEARCH_EXPANDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker
This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups
PROPERTY_KEY_SEARCH_GENERIC - Static variable in class chemaxon.checkers.RatomChecker
This constant String represents the name of the property which is responsible for searching generic ratoms in the molecule
PROPERTY_KEY_SEARCH_H_CONNECTED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching H connected property
PROPERTY_KEY_SEARCH_ISOTOPIC - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching isotopic explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_LINKER - Static variable in class chemaxon.checkers.RatomChecker
This private constant String represents the name of the property which is responsible for searching linker ratoms in the molecule
PROPERTY_KEY_SEARCH_LONELY - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching lonely explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_MAPPED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching mapped explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_NESTED - Static variable in class chemaxon.checkers.RatomChecker
This private constant String represents the name of the property which is responsible for searching nested ratoms in the molecule
PROPERTY_KEY_SEARCH_NON_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker
Search non default valence property
PROPERTY_KEY_SEARCH_POLYMER_END_GROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searchingPolymer end group property
PROPERTY_KEY_SEARCH_RADICAL - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching radical explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_SGROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searchingS-group property
PROPERTY_KEY_SEARCH_SGROUP_END - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searchingS-group end property
PROPERTY_KEY_SEARCH_VALENCE_ERROR - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searchingValence error property
PROPERTY_KEY_SEARCH_WEDGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the property which is responsible for searching wedged explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_WITH_REGEXP_EXCLUSION - Static variable in class chemaxon.checkers.AttachedDataChecker
 
PROPERTY_KEY_SGROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching S-group property
PROPERTY_KEY_SGROUP - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
S-group property
PROPERTY_KEY_SGROUP_END - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching S-group end property
PROPERTY_KEY_SGROUP_END - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
S-group end property
PROPERTY_KEY_SINGLE_UP_OR_DOWN_BOND - Static variable in class chemaxon.standardizer.actions.ClearStereoAction
Key of type for property change of mode
PROPERTY_KEY_SMALLEST_RING_SIZE - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Smallest ring size atom query property.
PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Smallest ring size checking property
PROPERTY_KEY_SMARTS_QUERY - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
SMARTS query property
PROPERTY_KEY_SMARTS_QUERY_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
SMARTS query checking property
PROPERTY_KEY_STEREO_GROUP - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Key of type for property change of mode
PROPERTY_KEY_SUBSTITUTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Substitution count atom query property.
PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Substitution count checking property
PROPERTY_KEY_TRADITIONAL_N_ALLOWED - Static variable in class chemaxon.checkers.ValenceErrorChecker
This public constant String represents the name of the configuration file property which is responsible for traditional N representation is allowed
PROPERTY_KEY_TYPE - Static variable in class chemaxon.checkers.AromaticityErrorChecker
This public constant String represents the name of the property which is responsible for using the given aromatization type during the check mechanism.
PROPERTY_KEY_TYPE - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Key of type for property change of mode
PROPERTY_KEY_TYPES - Static variable in class chemaxon.checkers.AtomTypeChecker
Types property
PROPERTY_KEY_UNSATURATION - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Unsaturation atom query property.
PROPERTY_KEY_UNSATURATION_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker
Unsaturation checking property
PROPERTY_KEY_USERSETTINGS - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor
Property key for optional client property UserSettings
PROPERTY_KEY_VALENCE_ERROR - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching Valence error property
PROPERTY_KEY_VALENCE_ERROR - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Valence error property
PROPERTY_KEY_VALID - Static variable in interface chemaxon.checkers.StructureChecker
This property key used to be the key of the property change event of valid property
PROPERTY_KEY_VALID - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor
Property key for editor validation state as Boolean
PROPERTY_KEY_WEDGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker
This public constant String represents the name of the configuration file property which is responsible for searching wedged explicit hydrogens in the molecule
PROPERTY_KEY_WEDGED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Wedged property
PROPERTY_TYPE_ALL - Static variable in class chemaxon.marvin.common.UserSettings
Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get all properties that are stored.
PROPERTY_TYPE_DEFAULT - Static variable in class chemaxon.marvin.common.UserSettings
Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the default properties.
PROPERTY_TYPE_PERSISTENT - Static variable in class chemaxon.marvin.common.UserSettings
Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the properties set by UserSettings.setProperty(String, String) method or by the setter methods.
PROPERTY_TYPE_TRANSIENT - Static variable in class chemaxon.marvin.common.UserSettings
Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the properties that are being stored temporary, and will not be saved to the properties file.
propertyChange(PropertyChangeEvent) - Method in class chemaxon.checkers.AbstractStructureChecker
 
propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Handles "ancestor" events or sets parameters if a bean property is changed.
propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.beans.MSketchPane
Handles property change events.
propertyChange(PropertyChangeEvent) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
propertyChangeSupport - Variable in class chemaxon.checkers.AbstractStructureChecker
property change support object bound to this
propertyContainer - Variable in class chemaxon.struc.MoleculeGraph
 
propertyCount() - Method in class chemaxon.struc.MolAtom
Returns the number of property (property key - property value) mappings of this atom.
propertyCount() - Method in class chemaxon.struc.MolBond
Returns the number of property (property key - property value) mappings of this bond.
propertyKeySet() - Method in class chemaxon.struc.MolAtom
Returns a set view of the property keys of this atom.
propertyKeySet() - Method in class chemaxon.struc.MolBond
Returns a set view of the property keys of this bond.
propertySet() - Method in class chemaxon.struc.MolAtom
Returns a collection view of the properties (property key - property value mappings) of this atom.
propertySet() - Method in class chemaxon.struc.MolBond
Returns a set view of the properties (property key - property value mappings) of this bond.
propToString(MProp) - Method in class chemaxon.marvin.io.MFieldAccessor
Converts a property to a string.
protectDoubleBondStereo() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Returns the adjusted double bond stereo protection flag.
protectTetrahedralStereo() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Returns the adjusted tetrahedral stereo protection flag.
PROTONATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Protonation Plugin Group
PSEUDO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with pseudo property could be converted to abbreviated group had found in the molecule
PSEUDO - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of a pseudoatom.
PSEUDO_NO_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with pseudo property had found in the molecule
PseudoAtomChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting pseudo atoms.
PseudoAtomChecker() - Constructor for class chemaxon.checkers.PseudoAtomChecker
Default constructor
PseudoAtomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.PseudoAtomChecker
 
Pt - Static variable in class chemaxon.core.ChemConst
 
Pu - Static variable in class chemaxon.core.ChemConst
 
PublicAPI - Annotation Interface in com.chemaxon.common.annotations
This annotation is used to mark types that are part of the ChemAxon public API.
put(int, float) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Stores the given value in the specified hitogram bin.
put(int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Stores the given value in the specified hitogram bin.
put(String, MProp) - Method in class chemaxon.struc.prop.MHashProp
Puts a value.
putBackLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Puts back the previous line to the input stream.
putBackLine() - Method in class chemaxon.marvin.io.PositionedInputStream
Puts back the last line into the stream.
putBackLine(int) - Method in class chemaxon.marvin.io.PositionedInputStream
Puts back the last line into the stream.
putColor(byte[]) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given color to the next place.
putColorComponent(byte) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given component (red-green-blue) of a color to the next place.
putFormattedTextToClipboard(Document, int, int) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Deprecated, for removal: This API element is subject to removal in a future version.
putImageToClipboard(Image) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Places the given Image to the clipboard.
putMoleculeToClipboard(Molecule, Properties) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Places a Molecule object to the clipboard which is represented as a Transferable being configured to support all the default Transfer types of Marvin.
putMoleculeToClipboard(Molecule, Properties, String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Places a Molecule object to the clipboard which is represented as a Transferable configured to support the transfer types of the specified format identifier.
putNormal(float[]) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given normal vector to the next place.
putNormal(float, float, float) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given normal vector to the next place.
putOLEToClipboard(Molecule, Properties) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
 
putPolygon(int[]) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given primitive to the next place.
putProperty(String, Object) - Method in class chemaxon.struc.MolAtom
Associates the specified value with the specified key at this atom.
putProperty(String, Object) - Method in class chemaxon.struc.MolBond
Associates the specified value with the specified key at this bond.
putStringToClipboard(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Places the given String to the clipboard as a StringSelection.
putTransferableToClipboard(Transferable) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
A generic way to put content to clipboard.
putTriangle(int, int, int) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given triangle to the next place.
putVertex(float[]) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given vertex to the next place.
putVertex(float, float, float) - Method in class chemaxon.marvin.space.SurfaceComponent
Puts the given vertex to the next place.

Q

qpropCheck() - Method in class chemaxon.struc.MolAtom
Query property checking.
qpropCheck(List<MolAtom>) - Method in class chemaxon.struc.MoleculeGraph
Check for query property errors.
QUADRIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Quadrivalent radical center.
query - Variable in class chemaxon.sss.search.MolComparator
 
QUERY_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with query properties had found in the molecule
QUERY_ATOMS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "queryAtoms".
QUERY_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that bond with query properties had found in the molecule
QueryAtomChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting generic atoms or ones having query properties.
QueryAtomChecker() - Constructor for class chemaxon.checkers.QueryAtomChecker
Default constructor
QueryBond - Class in chemaxon.struc
Chemical bond.
QueryBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.QueryBond
Construct an any bond between two atoms.
QueryBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.QueryBond
Construct an any bond between two atoms.
QueryBond(MolAtom, MolAtom, String) - Constructor for class chemaxon.struc.QueryBond
Construct a query bond between two atoms.
QueryBond(QueryBond) - Constructor for class chemaxon.struc.QueryBond
Copy constructor.
QueryBondChecker - Class in chemaxon.checkers
A descendant of BondChecker detecting query bonds.
QueryBondChecker() - Constructor for class chemaxon.checkers.QueryBondChecker
Default constructor
queryMol - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Query molecule (it is neither cloned nor modified).
querySearchData - Variable in class chemaxon.sss.search.MolComparator
 

R

r - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
 
R - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
 
R_GROUPS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "rgroupsVisible".
Ra - Static variable in class chemaxon.core.ChemConst
 
RA_IN_EXPAND - Static variable in class chemaxon.struc.Sgroup
Atom removal in expand.
RA_REMOVE_EXCEPT_RU - Static variable in class chemaxon.struc.Sgroup
Replace without duplicating.
RACEMATE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing asymmetric atom without specific stereo configuration.
RacemateChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting asymmetric tetrahedral atoms without specific stereochemistry.
RacemateChecker() - Constructor for class chemaxon.checkers.RacemateChecker
Creates a new RacemateChecker instance.
racemicStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the racemic tetrahedral stereogenic centers.
racemicStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the racemic tetrahedral stereogenic centers (with attached data).
RacemicTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral
Filter for racemic tetrahedral centers.
RacemicTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
 
RAD_COUNT_MASK - Static variable in class chemaxon.struc.MolAtom
Radical's free electron count bits in flags for valid radical values.
RAD_MASK - Static variable in class chemaxon.struc.MolAtom
Radical value bits in flags.
RAD_OFF - Static variable in class chemaxon.struc.MolAtom
Radical value offset in flags.
RAD1 - Static variable in class chemaxon.struc.MolAtom
Monovalent radical center.
RAD2 - Static variable in class chemaxon.struc.MolAtom
Divalent radical center.
RAD2_SINGLET - Static variable in class chemaxon.struc.MolAtom
Divalent radical center with singlet electronic configuration.
RAD2_TRIPLET - Static variable in class chemaxon.struc.MolAtom
Divalent radical center with triplet electronic configuration.
RAD3 - Static variable in class chemaxon.struc.MolAtom
Trivalent radical center.
RAD3_DOUBLET - Static variable in class chemaxon.struc.MolAtom
Trivalent radical center with doublet electronic configuration.
RAD3_QUARTET - Static variable in class chemaxon.struc.MolAtom
Trivalent radical center with quartet electronic configuration.
RAD4 - Static variable in class chemaxon.struc.MolAtom
Invalid value for radical center for students.
RADICAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with radical had found in the molecule
RADICAL_CHAR - Static variable in class chemaxon.struc.MolAtom
 
RADICAL_H - Static variable in class chemaxon.struc.MolAtom
Include radical Hydrogen atom(s).
RADICAL_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).
RADICAL_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).
RADICAL_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignore radical searching (radical information is ignored during searching).
RadicalChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting radical atoms.
RadicalChecker() - Constructor for class chemaxon.checkers.RadicalChecker
Default constructor
radicalCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
 
radicalMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
radicalMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether the radical information of atoms should be considered in search.
radicalMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
radicalState - Static variable in class chemaxon.struc.graphics.MEFlow
 
RADIUS_CONSTANT - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the atom property range a fix value
RADIUS_VDW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the atom property range the van der Waals radius
RADIUS_VDW_EXTENDED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the atom property range the van der Waals radius plus a fix value (for example the probe radius)
RAINBOW_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
randicIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
randomizeRotatableDihedrals(Molecule, Random) - Static method in class chemaxon.marvin.alignment.Alignment
Rotates rotatable bonds by a random dihedral angle value.
randomSeed - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Random seed (0 means using the current time).
RARE_ELEMENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that rare element had found in the molecule
RareElementChecker - Class in chemaxon.checkers
A descendant of AtomTypeChecker detecting structures containing elements which are usually rare in organic/drug molecules.
RareElementChecker() - Constructor for class chemaxon.checkers.RareElementChecker
Default constructor
RATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that the molecule contains R-atom.
RATOM - Static variable in class chemaxon.jep.context.ReactionContext
 
RatomChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting R-atoms.
RatomChecker() - Constructor for class chemaxon.checkers.RatomChecker
Creates a new anyChecker instance detecting all R-atoms.
RatomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RatomChecker
Creates a new anyChecker instance reading checking options from the params argument.
Rb - Static variable in class chemaxon.core.ChemConst
 
RC_CHANGE - Static variable in class chemaxon.struc.MolBond
The bond (order) has changed in the reaction.
RC_MAKE_AND_CHANGE - Static variable in class chemaxon.struc.MolBond
The bond is created and changed.
RC_MAKE_OR_BREAK - Static variable in class chemaxon.struc.MolBond
The bond is made or broken in the reaction.
RC_NOT_CENTER - Static variable in class chemaxon.struc.MolBond
The bond is not a reacting center.
RC_NOT_MODIFIED - Static variable in class chemaxon.struc.MolBond
The bond is not modified in the reaction.
RC_REACTING_CENTER - Static variable in class chemaxon.struc.MolBond
The bond is a reacting center.
RC_UNMAPPED - Static variable in class chemaxon.struc.MolBond
Unmapped bond in reacting center.
RDF - Static variable in class chemaxon.formats.MFileFormat
MDL RDfiles.
Re - Static variable in class chemaxon.core.ChemConst
 
REACTANT - Static variable in class chemaxon.jep.context.ReactionContext
 
REACTANTS - Static variable in class chemaxon.struc.RxnMolecule
"Reactant" structure type.
REACTING_CENTER_BOND_MARK - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule contains reacting center bond marks.
REACTING_CENTER_MASK - Static variable in class chemaxon.struc.MolBond
Mask for reacting center bits.
ReactingCenterBondMarkChecker - Class in chemaxon.checkers
Checker detects bonds with reacting center bond marks.
ReactingCenterBondMarkChecker() - Constructor for class chemaxon.checkers.ReactingCenterBondMarkChecker
Default constructor
REACTION_ERROR_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Deprecated, for removal: This API element is subject to removal in a future version.
As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
REACTION_SUPPORT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "reactionSupport".
reactionArrow - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The reaction arrow endpoints, null if not a reaction.
ReactionChecker - Class in chemaxon.checkers
Descendants of ReactionChecker detect reaction scheme problems.
ReactionChecker(StructureCheckerErrorType, StructureChecker) - Constructor for class chemaxon.checkers.ReactionChecker
Default constructor.
ReactionCheckerResult - Class in chemaxon.checkers.result
Deprecated, for removal: This API element is subject to removal in a future version. 
ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.ReactionCheckerResult
ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.ReactionCheckerResult
Deprecated.
Constructor which initialize all the properties.
ReactionContext - Class in chemaxon.jep.context
Expression evaluation context to evaluate reaction conditions.
ReactionContext() - Constructor for class chemaxon.jep.context.ReactionContext
Constructor.
ReactionContext(boolean) - Constructor for class chemaxon.jep.context.ReactionContext
Deprecated.
Copy feature is no longer required. Constructor.
ReactionContext(RxnMolecule) - Constructor for class chemaxon.jep.context.ReactionContext
Constructs a reaction context with specified reaction.
ReactionEditUtils - Class in chemaxon.marvin.modules.reaction
Extends ReactionUtils with some additional methods.
ReactionFingerprint - Class in chemaxon.descriptors
ReactionFingerprint class.
ReactionFingerprint() - Constructor for class chemaxon.descriptors.ReactionFingerprint
Creates a new, empty instance of ReactionFingerprint without allocating internal storage.
ReactionFingerprint(ReactionFingerprint) - Constructor for class chemaxon.descriptors.ReactionFingerprint
Copy constructor.
ReactionFingerprint(RFParameters) - Constructor for class chemaxon.descriptors.ReactionFingerprint
Creates a new instance of ReactionFingerprint according to the parameters given.
ReactionFingerprint(String) - Constructor for class chemaxon.descriptors.ReactionFingerprint
Creates a new instance of ReactionFingerprint according to the parameters given.
ReactionMapErrorChecker - Class in chemaxon.checkers
A descendant of ReactionChecker detecting reactions with invalid mapping.

Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.
ReactionMapErrorChecker() - Constructor for class chemaxon.checkers.ReactionMapErrorChecker
Default constructor
REACTOR - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Reactor
read() - Method in class chemaxon.formats.MolImporter
Read the next molecule.
read() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
 
read() - Method in class chemaxon.marvin.io.PositionedInputStream
Reads a character.
read() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Find the next structure in the source document and return it, or null when the end of the document has been reached.
read(byte[], int, int) - Method in class chemaxon.marvin.io.PositionedInputStream
Reads a byte array.
read(MolImporter) - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
 
read(Molecule) - Method in class chemaxon.formats.MolImporter
Deprecated.
as of Marvin 14.7.7. use MolImporter.read() instead
read16doubles(ObjectInput) - Method in class chemaxon.struc.CTransform3D
Reads the 4x4 matrix components as double precision floating point numbers.
read16floats(ObjectInput) - Method in class chemaxon.struc.CTransform3D
Reads the 4x4 matrix components as single precision floating point numbers.
readAttribute(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Reads an attribute from JAR manifest.
readDoc() - Method in class chemaxon.marvin.io.MRecordImporter
Reads the next document.
readDoc(MDocument, Molecule) - Method in class chemaxon.formats.MolImporter
Deprecated.
as of Marvin 14.7.7. useMolImporter.nextDoc() instead
readDoc(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane
 
readDocument(MDocument) - Method in class chemaxon.marvin.io.MolImportModule
Reads the next document.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MarvinPane
Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketch
Restores the sketcher's state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketchPane
Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MView
Restores the viewer's state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MViewPane
Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.struc.CTransform3D
Deserializes a transformation matrix.
readExternal(ObjectInput) - Method in class chemaxon.struc.DPoint3
Deserializes a 3D point.
readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextAttributes
 
readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextDocument
Restores the document.
readExternal(ObjectInput) - Method in class chemaxon.struc.MPropertyContainer
Restores the property container's state.
readFromString(String) - Method in class chemaxon.struc.graphics.MTextDocument
Reads the document from a string.
readFromXmlFile(File, boolean, boolean) - Method in class chemaxon.descriptors.MDParameters
Reads configuration from XML file.
readFromXmlString(String, boolean, boolean) - Method in class chemaxon.descriptors.MDParameters
Reads configuration from XML string.
readLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Reads the next line.
readLine() - Method in class chemaxon.marvin.io.PositionedInputStream
Reads a line.
readMetricParameters() - Method in class chemaxon.descriptors.MDParameters
Processes all ParametrizedMetric nodes in the DOM tree.
readMetricParameters() - Method in class chemaxon.descriptors.PFParameters
 
readMetricWeights(Element, int) - Method in class chemaxon.descriptors.MDParameters
 
readMetricWeights(Element, int) - Method in class chemaxon.descriptors.PFParameters
 
readMol(Molecule) - Method in class chemaxon.formats.MolImporter
Deprecated.
as of Marvin 14.7.7. use MolImporter.read() instead
readMol(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolImport
Reads a molecule from MDL mol/sdf/rxn file.
readMol(Molecule) - Method in class chemaxon.marvin.io.MolImportModule
Reads the next molecule.
readMol(Molecule) - Method in class chemaxon.marvin.io.MRecordImporter
Reads the next molecule.
readMol(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane
 
readMolMovie(MDocument) - Method in class chemaxon.marvin.io.MRecordImporter
Reads molecules as a movie.
readMultiSet(Molecule) - Method in class chemaxon.marvin.io.MRecordImporter
Reads molecules as one multi-set molecule.
readPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads a protein given as String.
readPropertyFile(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported feature.
readRecordAsText() - Method in class chemaxon.formats.MolImporter
Reads the next molecule in text format without creating a Molecule object.
readRecordAsText() - Method in class chemaxon.marvin.io.MRecordImporter
Reads the next record.
readResources(Class<?>, String) - Static method in class chemaxon.marvin.beans.MarvinPane
Reads resources from the specified file.
readSaltDictionary() - Static method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Reads the default salt dictionary.
readServiceDescriptors(InputStream) - Method in interface chemaxon.marvin.services.ServiceDescriptorReader
Returns a list of configured ServiceDescriptor objects from specified InputStream
readSolventDictionary() - Static method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Reads the default solvent dictionary.
readValues(boolean) - Method in class chemaxon.descriptors.BCUTParameters
Retrieves relavant parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.CDParameters
Picks parameter values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.CFParameters
Picks parameter values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.ECFPParameters
Picks parameter values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.MDParameters
Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.
readValues(boolean) - Method in class chemaxon.descriptors.PFParameters
 
readValues(boolean) - Method in class chemaxon.descriptors.RFParameters
Picks parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.scalars.HBParameters
Picks relevant parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.scalars.LDParameters
Picks parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.SDParameters
Reads attribute values form the XML configuration.
readValues(boolean) - Method in class chemaxon.descriptors.ShapeParameters
 
ready() - Method in class chemaxon.marvin.space.BoundingBox
It has to be called after passing all coordinates to the box.
RearomatizeFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which rearomatize the molecule
RearomatizeFixer() - Constructor for class chemaxon.fixers.RearomatizeFixer
 
RearrangeReactionAction - Class in chemaxon.standardizer.actions
 
RearrangeReactionAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RearrangeReactionAction
Initializes the action
rearrangeSgroups(int[]) - Method in class chemaxon.struc.Molecule
Orders S-groups in the vector of S-groups in the given order corresponding to the given new indexes.
RearrangeWedgesFixer - Class in chemaxon.fixers
Rearranges stereo wedge bonds according to IUPAC recommendations.
RearrangeWedgesFixer() - Constructor for class chemaxon.fixers.RearrangeWedgesFixer
 
rebuildStructures() - Method in class chemaxon.struc.RxnMolecule
For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow.
rebuildStructures(DPoint3[], int) - Method in class chemaxon.struc.RxnMolecule
Sets the reaction arrow.
recalcCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Recalculates and sets the coordinates of the central atom of this sgroup.
recalcReactionArrow() - Method in class chemaxon.struc.RxnMolecule
Recalculates the coordinates of the reaction arrow from the reactants and products, forced recalculation.
receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the current object that the coordinates of the given component have been changed.
receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
The molecule will notify the surface when its coordinates change.
receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Label
When the coordinates of the labeled object change, the label refreshes its coordinates relatively.
receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Gets notification from its selected components if their coordinates have been changed.
receiveNotificationOnCoordinateChange(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
Gets notification from its selected components if their coordinates have been changed.
receiveNotificationOnInvisibility(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the current object that the given component is not visible.
receiveNotificationOnInvisibility(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
If the component to that this monitor is assigned becomes hidden, this monitor will also behave so.
receiveNotificationOnSelection(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the current object that the given component became selected.
receiveNotificationOnUnSelection(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the current object that the given component became unselected.
receiveNotificationOnVisibility(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
Notifies the current object that the given component became visible.
receiveNotificationOnVisibility(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
If the component to that this monitor is assigned becomes visible, this monitor will also behave so.
recognizeOneLineFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil
Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
recognizeOneLineFormat(String, MFileFormat...) - Static method in class chemaxon.formats.MFileFormatUtil
Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
Recognizer - Class in chemaxon.formats.recognizer
File format recognizer.
Recognizer() - Constructor for class chemaxon.formats.recognizer.Recognizer
 
RecognizerFactory - Interface in chemaxon.formats.factory
Factory interface for Recognizers.
RecognizerList - Class in chemaxon.formats.recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
Not used, will be removed
reCreate() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
reCreate() - Method in class chemaxon.marvin.space.MoleculeComponent
 
RECURSIVE_UNGROUP - Static variable in class chemaxon.struc.Molecule
Ungroup and expand (if possible) the child S-groups.
RED - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Constant storing the red rgb value (the acidic pKa result color).
redo() - Method in class chemaxon.marvin.beans.MSketchPane
Invokes a redo command.
redraw() - Method in class chemaxon.marvin.space.GraphicScene
Redraws the entire scene.
refersTo(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Monitor
Retruns true if component is between the selected elements.
REFRACTIVITY_PLUGIN - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Refractivity Plugin
RefractivityPlugin - Class in chemaxon.marvin.calculations
Plugin class for refractivity calculation.
RefractivityPlugin() - Constructor for class chemaxon.marvin.calculations.RefractivityPlugin
Constructor.
refresh() - Static method in class chemaxon.license.LicenseManager
Re-reads licenses from the default locations.
refresh() - Method in class chemaxon.marvin.space.GraphicScene
 
refresh() - Method in class chemaxon.marvin.space.monitor.Label
The monitor refreshes its coordinates from the selected item's coordinates.
refresh() - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Deletes the position and the value of the measurement to recount.
refresh() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
The monitor refreshes its coordinates from the selected item's coordinates.
refresh() - Method in class chemaxon.marvin.space.MSpaceEasy
Makes all unprocessed event to be processed and makes the graphic canvas redraw.
refreshColoring() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
regenBonds() - Method in class chemaxon.struc.MoleculeGraph
Regenerates the bond vector: remove its elements, then put the bond objects from the atoms into it.
regenBonds() - Method in class chemaxon.struc.RgMolecule
Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
regenBonds() - Method in class chemaxon.struc.RxnMolecule
Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
regenBtab() - Method in class chemaxon.struc.MoleculeGraph
Regenerates the bond table.
regenBtab() - Method in class chemaxon.struc.SelectionMolecule
Regenerates the bond table.
regenCtab() - Method in class chemaxon.struc.MoleculeGraph
Regenerates the connection table.
regenCtab() - Method in class chemaxon.struc.SelectionMolecule
Regenerates the connection table.
regenGearch() - Method in class chemaxon.struc.MoleculeGraph
Recreate graph search results object.
registerFormat(MFileFormat) - Static method in class chemaxon.formats.MFileFormatUtil
Registers a user defined file format.
registerNativeNames() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Registers the Native names supported by the implementation.
registerNativeNames() - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
Registers the Native names supported by the implementation.
REGISTRATION_SYSTEM - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Structure Checker
REGULAR_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule
Regular double reaction arrow type.
REGULAR_SINGLE - Static variable in class chemaxon.struc.RxnMolecule
Regular single reaction arrow type.
RELATIVE_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecules having multiple stereogenic center groups
RelativeStereoChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting molecules having multiple stereogenic center groups
RelativeStereoChecker() - Constructor for class chemaxon.checkers.RelativeStereoChecker
Initializes relative stereo checker
relativeX - Variable in class chemaxon.marvin.space.monitor.Label
 
relativeY - Variable in class chemaxon.marvin.space.monitor.Label
 
releaseBaseMElectrons() - Method in class chemaxon.struc.graphics.MEFlow
 
releaseNewEMFGenerator() - Static method in class chemaxon.util.ImageExportUtil
Releases and disposes native resources needed by the .NET based EMF generator.
releasePermanentResources() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Releases all clipboard related native libraries and resources.
reload() - Method in class chemaxon.fixers.StructureFixerFactory
Deprecated.
Forces reload of configuration on next fixer list request.
reloadCodeCompletionData() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Forces all CodeAssist instances created with this factory to reload the code completion data.
reloadDefaultMap() - Static method in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Forces reload of factory data.
reloadDefaults() - Static method in class chemaxon.fixers.StructureFixerFactory
Deprecated.
Forces reload of factory defaults.
reloadParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Reloads previously stored parameters to parameter panel.
reloadParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Reloads previously stored parameters to parameter panel.
RemovalDate - Enum Class in com.chemaxon.common.annotations
Date values accepted by the SubjectToRemoval annotation.
remove() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator
Removes the next atom in the iteration.
remove() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
Removes the next bond in the iteration.
remove() - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
The remove operation is not supported by this Iterator implementation.
remove() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
The remove operation is not supported by this Iterator implementation.
remove() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
The remove operation is not supported by this Iterator implementation.
remove() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator
Removes the next s-group in the iteration.
remove(int) - Method in class chemaxon.struc.prop.MListProp
Removes an element.
remove(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Deletes a substring in the document.
remove(NameConverter) - Static method in class chemaxon.naming.NameConverters
Remove the converter from the converter list.
remove(MProp) - Method in class chemaxon.struc.MPropertyContainer
Removes a property.
remove(String) - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Removes the recognizer with the specified codename.
RemoveAbsoluteStereoAction - Class in chemaxon.standardizer.actions
Set absolute stereo standardizer action
RemoveAbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAbsoluteStereoAction
Initializes a remove absolute stereo action
removeAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Removes an action of the configuration
removeActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane
Removes an action listener.
removeActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions
Removes an action listener.
removeActions(Collection<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Removes actions of the configuration
RemoveAliasFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the alias information from the atoms of the molecule
RemoveAliasFixer() - Constructor for class chemaxon.fixers.RemoveAliasFixer
 
removeAll() - Method in class chemaxon.struc.Molecule
Removes all the atoms and bonds.
removeAll() - Method in class chemaxon.struc.MoleculeGraph
Removes all the atoms and bonds.
removeAll() - Method in class chemaxon.struc.RgMolecule
Remove all the atoms and bonds from the root structure, and from all the R-groups.
removeAll() - Method in class chemaxon.struc.RxnMolecule
Remove all the atoms and bonds from the root structure, and from all the R-groups.
removeAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "removed atom" list
removeAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "removed atom" list
removeAllAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Removes all attachment points of the Superatom s-group.
removeAllBonds() - Method in class chemaxon.struc.MolAtom
Removes all bonds.
removeAllBonds() - Method in class chemaxon.struc.Molecule
Removes all bonds.
removeAllBonds() - Method in class chemaxon.struc.MoleculeGraph
Removes all bonds.
removeAllBonds() - Method in class chemaxon.struc.RgMolecule
Remove all bonds from the root structure, and from all the R-groups.
removeAllBonds() - Method in class chemaxon.struc.RxnMolecule
Removes all bonds from the reactants, products and agents.
removeAllBonds() - Method in class chemaxon.struc.sgroup.SgroupAtom
Remove all edges.
removeAllBonds(boolean) - Method in class chemaxon.struc.MolAtom
Removes all bonds.
removeAllBonds(boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
Removes all edges.
removeAllComponents() - Method in class chemaxon.marvin.space.GraphicCell
Removes all components from the cell.
removeAllComponents() - Method in class chemaxon.marvin.space.GraphicScene
Removes all component from the scene and clears the selection panel.
removeAllComponents() - Method in class chemaxon.marvin.space.MSpaceEasy
Removes all components from the scene.
removeAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
Removes all component from the scene and clears the selection panel.
removeAllConstraints() - Method in class chemaxon.marvin.alignment.Alignment
 
removeAllExcept(long, long) - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Removes all recognizers except those with the specified flags.
removeAllExcept(String) - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Removes all recognizers except the specified.
removeAllFromDocument(MDocument) - Static method in class chemaxon.struc.NoStructure
Removes all NoStructure labels from the target document.
removeAllGroups() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Removes all group definitions from the group list of the action.
removeAllMolecules() - Method in class chemaxon.marvin.alignment.Alignment
before every new alignment the molecules have to be removed.
removeAllMolecules() - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
removeAllMolecules() - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
removeAllMolecules() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
removeAllPairs() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Removes all user defined atom pairs.
removeAllProperty() - Method in class chemaxon.marvin.common.UserSettings
Removes all property that are stored in this UserSettings object.
removeAllSalts() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Removes all salts from the salt list of the action.
removeAllSgroups() - Method in class chemaxon.struc.Molecule
Removes all S-groups.
removeAllSolvents() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Removes all solvents from the solvents list of the action.
removeAssociation(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
Removes the dependency of the given component from this component.
removeAtom(int) - Method in class chemaxon.struc.MoleculeGraph
Removes an atom and its bonds by index.
removeAtom(int) - Method in class chemaxon.struc.SelectionMolecule
Removes an atom and its bonds from the graph.
removeAtom(int) - Method in interface chemaxon.struc.WSmolecule
Removes an atom.
removeAtom(int, int) - Method in class chemaxon.struc.Molecule
Removes an atom and its bonds by index.
removeAtom(int, int) - Method in class chemaxon.struc.MoleculeGraph
Removes an atom and its bonds with extra clean-up options.
removeAtom(int, int) - Method in class chemaxon.struc.RgMolecule
Removes an atom and its bonds from the root structure.
removeAtom(int, int) - Method in class chemaxon.struc.RxnMolecule
Removes an atom from the reactants, products or agents.
removeAtom(MolAtom) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "removed atom" list.
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlow
 
removeAtom(MolAtom) - Method in class chemaxon.struc.MDocument
Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
removeAtom(MolAtom) - Method in class chemaxon.struc.MObject
Removes the atom from the corresponding molecule object.
removeAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Removes an atom and its bonds by reference.
removeAtom(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Removes an atom and its bonds.
removeAtom(MolAtom) - Method in class chemaxon.struc.Sgroup
Removes an atom and its bonds from the S-group.
removeAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "removed atom" list.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.MDocument
Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.Molecule
Removes an atom and its bonds by reference.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph
Removes an atom and its bonds with extra clean-up options.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.RgMolecule
Removes an atom and its bonds from the root structure and from all the R-groups.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.RxnMolecule
Removes an atom from the reactants, products or agents.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Removes an atom from the S-group.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.Sgroup
Removes an atom and its bonds from the S-group.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Removes an atom from the S-group.
removeAtom(Sgroup, MolAtom, int) - Static method in class chemaxon.struc.Sgroup
Wrapper method that calls Sgroup.removeAtom(MolAtom, int) of sg.
removeAtomAliases(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
RemoveAtomFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the atoms of the molecule signed in the result
RemoveAtomFixer() - Constructor for class chemaxon.fixers.RemoveAtomFixer
 
removeAtomFromChildren(Sgroup, MolAtom) - Method in class chemaxon.struc.Molecule
Removes the parameter atom from the parameter S-group and it's descendants.
removeAtomFromGraphs(MolAtom) - Method in class chemaxon.struc.MDocument
Removes the specified node from all molecule graphs.
RemoveAtomMapFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the atom maps from the molecule
RemoveAtomMapFixer() - Constructor for class chemaxon.fixers.RemoveAtomMapFixer
 
RemoveAtomQueryPropertyFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes query properties from the given atoms.
RemoveAtomQueryPropertyFixer() - Constructor for class chemaxon.fixers.RemoveAtomQueryPropertyFixer
 
RemoveAtomValueFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the atom value from the molecule
RemoveAtomValueFixer() - Constructor for class chemaxon.fixers.RemoveAtomValueFixer
 
RemoveAtomValuesAction - Class in chemaxon.standardizer.actions
Remove Atom Values standardizer action
RemoveAtomValuesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAtomValuesAction
Initializes the action
RemoveAttachedDataAction - Class in chemaxon.standardizer.actions
Remove Attached Data standardizer action
RemoveAttachedDataAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAttachedDataAction
Initializes the action
RemoveAttachedDataFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the attached data from the molecule.
RemoveAttachedDataFixer() - Constructor for class chemaxon.fixers.RemoveAttachedDataFixer
 
removeAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Removes the attachment point with the given order.
removeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Removes all attachment points of the given attachment atom.
removeBond(int) - Method in class chemaxon.struc.MolAtom
Removes a bond.
removeBond(int) - Method in class chemaxon.struc.MoleculeGraph
Removes a bond by index.
removeBond(int) - Method in class chemaxon.struc.SelectionMolecule
Removes a bond from the graph.
removeBond(int) - Method in interface chemaxon.struc.WSmolecule
Removes a bond.
removeBond(int, boolean) - Method in class chemaxon.struc.MolAtom
Removes a bond.
removeBond(int, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
Removes a bond.
removeBond(int, int) - Method in class chemaxon.struc.Molecule
Removes a bond by index.
removeBond(int, int) - Method in class chemaxon.struc.MoleculeGraph
Removes a bond by index.
removeBond(int, int) - Method in class chemaxon.struc.RgMolecule
Remove a bond from the root structure.
removeBond(int, int) - Method in class chemaxon.struc.RxnMolecule
Removes an edge from a reactant, agent or product.
removeBond(MolBond) - Method in class chemaxon.struc.MolAtom
Removes a bond by reference.
removeBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Removes a bond by reference.
removeBond(MolBond) - Method in class chemaxon.struc.SelectionMolecule
Removes a bond by reference.
removeBond(MolBond) - Method in class chemaxon.struc.Sgroup
Removes a bond from the S-group.
removeBond(MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Removes a the given bond from the S-group.
removeBond(MolBond, boolean) - Method in class chemaxon.struc.MolAtom
Removes a bond by reference.
removeBond(MolBond, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
Removes a bond by reference.
removeBond(MolBond, int) - Method in class chemaxon.struc.Molecule
Removes a bond by reference.
removeBond(MolBond, int) - Method in class chemaxon.struc.MoleculeGraph
Removes a bond by reference.
removeBond(MolBond, int) - Method in class chemaxon.struc.RgMolecule
Remove a bond from the root structure, and from all the R-groups.
removeBond(MolBond, int) - Method in class chemaxon.struc.RxnMolecule
Removes a bond from the reactants, products or agents.
RemoveBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the bonds of the molecule signed by the result
RemoveBondFixer() - Constructor for class chemaxon.fixers.RemoveBondFixer
 
removeBonds() - Method in class chemaxon.struc.Sgroup
Removes the edge references.
RemoveBondTopologyFixer - Class in chemaxon.fixers
Fixer removes reactiong center bond marks from bonds.
RemoveBondTopologyFixer() - Constructor for class chemaxon.fixers.RemoveBondTopologyFixer
 
RemoveBracketsFixer - Class in chemaxon.fixers
Removes brackets from molecule by ungrouping S-groups surrounded by brackets.
RemoveBracketsFixer() - Constructor for class chemaxon.fixers.RemoveBracketsFixer
 
removeChild(MObject) - Method in class chemaxon.struc.graphics.MPolyline
 
removeChild(MObject) - Method in class chemaxon.struc.graphics.MRectangle
 
removeChild(MObject) - Method in class chemaxon.struc.MObject
Removes a child object.
removeChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup
Removes an S-group from the children list.
RemoveChiralFlagFixer - Class in chemaxon.fixers
A StructureFixer implementation which removes absolute stereo property from the molecule.
RemoveChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveChiralFlagFixer
 
removeColorsFromMolecules() - Method in class chemaxon.struc.MDocument
Removes coloring from all molecular objects in the document.
removeComparator(MolComparator) - Method in class chemaxon.sss.search.MolSearch
Delete a comparator from the search object.
removeComponent(int) - Method in class chemaxon.marvin.space.GraphicCell
Removes the component which has the given index, and all of its associated components from the cell.
removeComponent(int, int) - Method in class chemaxon.struc.RxnMolecule
Removes a reactant, product or agent.
removeComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Removes the component and all associated components from the cell.
removeComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Removes a component from the scene.
removeComponent(GraphicComponent) - Method in class chemaxon.marvin.space.MSpaceEasy
Activates the container cell of the component, removes it from the scene, and also from the selection panel if that exists.
removeComponent(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Removes a component from the scene.
removeComponent(Class) - Method in class chemaxon.marvin.space.GraphicCell
 
removeCTflagFromSmallRings(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Remove CIS|TRANS flag from bonds in rings smaller than size 8.
removeDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule
Removes the dependent R-group definition of the referenced R-group definition.
removeElectronsOf(MolAtom) - Method in class chemaxon.struc.MDocument
Removes the Electron containers belongs to targetAtom,
removeElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
removeEmptyComponents() - Method in class chemaxon.struc.RxnMolecule
Checks all the componentes and removes those that are empty (node count is zero).
RemoveExplicitHydrogenFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which implicitize the hydrogens in the molecule
RemoveExplicitHydrogenFixer() - Constructor for class chemaxon.fixers.RemoveExplicitHydrogenFixer
 
RemoveExplicitHydrogensAction - Class in chemaxon.standardizer.actions
Remove explicit H standardizer action
RemoveExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Initializes the remove explicit H action
removeExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
RemoveFragmentAction - Class in chemaxon.standardizer.actions
Removal standardizer action
RemoveFragmentAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveFragmentAction
Initializes the action with parameters
RemoveFragmentAction.Measurement - Enum Class in chemaxon.standardizer.actions
Type of measurement
RemoveFragmentAction.Method - Enum Class in chemaxon.standardizer.actions
Type of removal methods
removeFromDocument(NoStructure, MDocument) - Static method in class chemaxon.struc.NoStructure
Removes the given NoStructre from the target document.
removeFunction(String) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The function table will become unmodifiable. Configure the Evaluator instead before creating the ChemJEP.
removeGraphicComponent(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
 
removeGroup(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Removes a group definition from the group list of the action
removeGroupedAtom(MoleculeGraph, MolAtom, MolBond[], int) - Static method in class chemaxon.struc.Sgroup
Removes an atom from the molecule and remove its specified bonds.
removeHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
removeHAtoms(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
removeHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
removeHAtoms(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
removeInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil
Removes the Standardizer tasks specified in the configuration parameter from the inactive tasks list.
RemoveInvalidChiralFlagFixer - Class in chemaxon.fixers
A StructureFixer implementation which removes absolute stereo property from the molecule.
RemoveInvalidChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveInvalidChiralFlagFixer
 
removeIsolatedAtoms() - Method in class chemaxon.struc.MoleculeGraph
Removes the null atom entries in the atoms array and sets the index fields appropriately.
removeIsolatedBonds() - Method in class chemaxon.struc.MoleculeGraph
Removes the null bond entries in the bonds array and sets the index fields appropriately.
REMOVELARGEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Remove largest fragment
removeListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage
Removes a listener.
removeLonePairs(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
removeLonePairs(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated, for removal: This API element is subject to removal in a future version.
removeMolecules() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MEFlow
 
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint
Point removed from a document.
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MPolyline
 
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint
Point removed from a document.
removeNotify(MDocument) - Method in class chemaxon.struc.MObject
Called when the object is removed from a document.
removeObject(int) - Method in class chemaxon.struc.MDocument
Removes an object from the document.
removeObject(int) - Method in class chemaxon.struc.MSelectionDocument
Removes an object from the document.
removeObject(MObject) - Method in class chemaxon.struc.MDocument
Removes an object from the document or from the chemical structure of the document.
removeObject(MObject) - Method in class chemaxon.struc.Molecule
 
removeObject(MObject) - Method in class chemaxon.struc.MSelectionDocument
Removes an object from the document.
removeObject(MObject) - Method in class chemaxon.struc.RgMolecule
 
removeObject(MObject) - Method in class chemaxon.struc.RxnMolecule
Removes a graphical object from this.
removeObject(MObject) - Method in class chemaxon.struc.Sgroup
Removes the specified MObject from this Sgroup.
removeOLESupport() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Removing the support of OLE transfer format.
removeOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Removes an owner.
removePharmacophorePoint(ComponentElement) - Method in class chemaxon.marvin.space.GraphicScene
 
removeProperty(String) - Method in class chemaxon.struc.MolAtom
Removes the mapping for this property key from this atom if present.
removeProperty(String) - Method in class chemaxon.struc.MolBond
Removes the mapping for this property key from this bond if present.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
 
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Remove a property change listener
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction
Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction
Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Remove a PropertyChangeListener for a specific property.
RemoveRadicalFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes the radicals from the atoms of the molecule
RemoveRadicalFixer() - Constructor for class chemaxon.fixers.RemoveRadicalFixer
 
RemoveReactingCenterBondMarkFixer - Class in chemaxon.fixers
Fixer removes reactiong center bond marks from bonds.
RemoveReactingCenterBondMarkFixer() - Constructor for class chemaxon.fixers.RemoveReactingCenterBondMarkFixer
 
removeReactionArrow() - Method in class chemaxon.struc.RxnMolecule
Removes the reaction arrow of this reacion.
removeRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Removes an atom from the list of paradigmatic repeating unit atoms.
removeRestH(int) - Method in class chemaxon.struc.RgMolecule
Removes the restH condition from an R-group definition.
removeRgroup(int) - Method in class chemaxon.struc.RgMolecule
Removes an R-group.
removeRgroupBridge(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule
Removes an R-group bridge.
removeRgroupBridgeMember(RgroupBridgeId, int) - Method in class chemaxon.struc.RgMolecule
Removes a definition member of an R-group bridge.
RemoveRGroupDefinitionsAction - Class in chemaxon.standardizer.actions
Remove R-group definition standardizer action
RemoveRGroupDefinitionsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveRGroupDefinitionsAction
Initializes the action
removeRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule
Removes an R-group definition member.
removeRgroupMembers(int, int[]) - Method in class chemaxon.struc.RgMolecule
Removes R-group members.
removeSalt(int) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Removes a salt from the salt list of the action
removeSalts(int...) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Removes a salt from the salt list of the action
removeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Removes all selected components and all associated components from the cell.
removeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Removes all selected components from the active cell with all related components (connected monitors, surface of a molecule).
removeSelectedFrom(MDocument) - Static method in class chemaxon.struc.NoStructure
Removes the selected NoStructres from the document.
removeSgroupFromList(Sgroup) - Method in class chemaxon.struc.Molecule
Removes an S-group from the sgroupVector.
removeSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule
Removes S-groups from this object and its parent.
removeSgroupsOf(Molecule, int) - Method in class chemaxon.struc.Molecule
Removes S-groups that are contained in a given molecule but not contained in another molecule.
removeSketchRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings
Remove a file from marvinsketch's recent file list
REMOVESMALLEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Remove smallest fragment
removeSolvent(int) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Removes a solvent from the solvent list of the action
removeSolvents(int...) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Removes a solvent from the solvent list of the action
RemoveSolventsAction - Class in chemaxon.standardizer.advancedactions
Remove solvents standardizer action.
RemoveSolventsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Initializes remove solvents action
removeStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Changes terminal star atoms (*) to carbon atoms (C).
RemoveStereoCareBoxAction - Class in chemaxon.standardizer.actions
Remove Stereo Care Box standardizer action
RemoveStereoCareBoxAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveStereoCareBoxAction
Initializes the action
RemoveStereoCareBoxFixer - Class in chemaxon.fixers
Fixer for molecules containing Stereo Care Boxes.
RemoveStereoCareBoxFixer() - Constructor for class chemaxon.fixers.RemoveStereoCareBoxFixer
 
RemoveStereoInversionRetentionMarkFixer - Class in chemaxon.fixers
Removes stereo inversion retention marks.
RemoveStereoInversionRetentionMarkFixer() - Constructor for class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer
 
removeTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Removes a TransferableDescriptor to the MTransferable Registry.
removeTransferable(String) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Removes a TransferableDescriptor to the MTransferable Registry by name.
RemoveUnreferencedRgroupDefinitionsFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer that removes unused R-group definitions.
RemoveUnreferencedRgroupDefinitionsFixer() - Constructor for class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer
 
removeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Removes all unselected components and all associated components from the cell.
removeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Removes all unselected components from the active cell with all related components (connected monitors, surface of a molecule).
removeUnSelectedFrom(MDocument) - Static method in class chemaxon.struc.NoStructure
Removes the non-selected NoStructures from the document.
removeUnselectedMonitors() - Method in class chemaxon.marvin.space.GraphicCell
Removes all unsselected monitor components from the cell.
removeUnselectedMonitors() - Method in class chemaxon.marvin.space.GraphicScene
Removes all unselected monitor component from the scene.
RemoveValencePropertyFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which removes valence properties from the given atoms.
RemoveValencePropertyFixer() - Constructor for class chemaxon.fixers.RemoveValencePropertyFixer
 
removeVariable(String) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.
removeViewRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings
Remove a file from marvinview's recent file list
removeWhitespace(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Removes whitespace characters from the given string.
REMOVEZCOORDINATE - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Convert 3D to 2D
RemoveZCoordinateFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which sets the z-coordinates of atoms to zero.
RemoveZCoordinateFixer() - Constructor for class chemaxon.fixers.RemoveZCoordinateFixer
 
RENDERING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "rendering".
RENDERING_QUALITY_HIGH - Static variable in class chemaxon.marvin.space.GraphicComponent
Highest though slowest drawing quality indicator.
RENDERING_QUALITY_LOW - Static variable in class chemaxon.marvin.space.GraphicComponent
Lowest but fastest drawing quality indicator.
RENDERING_QUALITY_MEDIUM - Static variable in class chemaxon.marvin.space.GraphicComponent
Medium drawing quality indicator.
renderingQuality - Variable in class chemaxon.marvin.space.GraphicComponent
The actual rendering quality.
reparentSgroups(Molecule) - Method in class chemaxon.struc.Molecule
Change parents of all S-groups in this molecule.
RepeatingUnitSgroup - Class in chemaxon.struc.sgroup
Source-based and structure-based representation of repeating unit groups (polymers and repeating units with repetition ranges).
RepeatingUnitSgroup(Molecule, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
Constructs an SRU S-group.
RepeatingUnitSgroup(Molecule, String, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
Constructs an SRU S-group with connectivity.
RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
Copy constructor.
RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup
Copy constructor.
replace(int, int, String) - Method in class chemaxon.struc.graphics.MTextDocument
Replaces a substring in the document.
replace(MolAtom, MolAtom, Molecule) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Replaces an atom to the replace atom in the target molecule
replace(MProp, MProp) - Method in class chemaxon.struc.MPropertyContainer
Replaces or removes a property.
replace(MProp, MProp) - Method in class chemaxon.struc.prop.MCollectionProp
Replaces or removes a property.
replace(MProp, MProp) - Method in class chemaxon.struc.prop.MHashProp
Replaces or removes a property.
replace(MProp, MProp) - Method in class chemaxon.struc.prop.MListProp
Replaces or removes a property.
REPLACE_COORDINATE_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
Replace coordinate bonds to multicenter atoms with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).
replaceAtom(int, MolAtom) - Method in class chemaxon.struc.Molecule
Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.
replaceAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.MObject
Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.Sgroup
Replace an existing atom by a new one in this S-group and its parent (recursively).
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
 
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Replace an existing atom by a new one.
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.Sgroup
Replace an existing atom by a new one in this S-group and its parent (recursively).
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Replace an existing atom by a new one.
ReplaceAtomsAction - Class in chemaxon.standardizer.actions
Replace atoms standardizer action
ReplaceAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ReplaceAtomsAction
Initializes a replace atom standardizer action
replaceAtomsWithNewRgroup(SelectionMolecule, int) - Method in class chemaxon.struc.RgMolecule
Replaces selected atoms with a new R-group.
replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RgMolecule
Deprecated.
as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.
replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RxnMolecule
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.
replaceMulticenterAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 2014.08.25.0, use MulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom) instead
replaceSgroup(Sgroup, Sgroup) - Method in class chemaxon.struc.Molecule
Replaces an S-group with a new sgroup in the molecule.
reportFormat - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the report file
reportPath - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the report file
reportPattern - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the report file
reportProperty - Variable in class chemaxon.checkers.StructureCheckOptions
The name of the report property, in the output structure file(s)
REPUNIT - Static variable in class chemaxon.sss.search.MarkushFeature
Deprecated.
Expansion type: repeating unit.
requireBinaryVector() - Method in class chemaxon.descriptors.ECFP
Checks the binary vector storage and generates it from the identifier list if necessary.
reset() - Method in class chemaxon.marvin.io.PositionedInputStream
Repositions this stream to the position at the time the mark method was last called on this input stream.
reset() - Method in class chemaxon.marvin.space.SurfaceColoring
Resets all parameters to the default.
reset(int) - Method in interface chemaxon.struc.WSmolecule
Clears the molecule and sets the array flags.
resetAll() - Method in class chemaxon.marvin.space.GraphicScene
Resets view settings of all cells including rotation, zoom and shifting.
resetAll() - Method in class chemaxon.marvin.space.MSpaceEasy
Resets view settings of all cells including rotation, zoom and shifting.
resetBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow
 
resetCtab() - Method in class chemaxon.struc.MoleculeGraph
An operation performed that changed the connection table and the graph invariants.
resetFilePointer() - Method in class chemaxon.marvin.io.PositionedInputStream
Resets file pointer to zero.
resetGrinvInParents() - Method in class chemaxon.struc.MoleculeGraph
Graph invariants must be recalculated for this graph and all parent graphs.
resetMap() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
resetSettings() - Method in class chemaxon.marvin.space.GraphicScene
Sets all draw properties to the default value and resets view.
resetView() - Method in class chemaxon.marvin.space.GraphicCell
 
resetView() - Method in class chemaxon.marvin.space.GraphicScene
Resets view settings of the active cell including rotation, zoom and shifting.
resetZoom() - Method in class chemaxon.marvin.space.GraphicCell
 
reshape(GLAutoDrawable, int, int, int, int) - Method in class chemaxon.marvin.space.GraphicScene
Called by the drawable during the first repaint after the component has been resized.
residueSymbolOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the name of a residue.
residueSymbolOf(int) - Static method in class chemaxon.struc.Molecule
Gets the name of a residue.
residueTypeOf(String) - Static method in class chemaxon.struc.MolAtom
Gets the residue identifier for a residue name.
residueTypeOf(String) - Static method in class chemaxon.struc.Molecule
Gets the residue identifier for a residue name.
resize(double, double, double) - Method in class chemaxon.marvin.space.GraphicComponent
Resizes the component according to the given factors in each directions.
resize(double, double, double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Resizes the component according to given factors.
resize(double, double, double) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Resizes the component according to the given factors in each direction.
resize(double, double, double) - Method in class chemaxon.marvin.space.PharmacophorePoint
Resizes the component according to given factors.
ResizeControl - Class in chemaxon.marvin.space.monitor
This control is to change the size of a GraphicComponent by changing the coordinates.
ResizeControl(Monitor) - Constructor for class chemaxon.marvin.space.monitor.ResizeControl
Creates a new instance of ResizeControl
RESONANCE - Static variable in class chemaxon.struc.RxnMolecule
Resonance arrow, the same as the two-headed single reaction arrow.
RESONANCE_ALL - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
RESONANCE_CANONICAL - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
RESONANCE_MAJORCONTRIBUTORS - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
ResonancePlugin - Class in chemaxon.marvin.calculations
Plugin class for finding resonant structures.
ResonancePlugin() - Constructor for class chemaxon.marvin.calculations.ResonancePlugin
Constructor.
RESSEQ_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum residue sequence number is currently 8191.
restoreCache(int) - Method in class chemaxon.struc.MoleculeGraph
Restores caches like connection table, bond table, etc.
restoreCoords(MoleculeGraph, double[]) - Static method in class chemaxon.marvin.util.CleanUtil
Restores atomic coordinates.
restoreDefaultParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Restores default parameters to parameter panel.
restoreDefaultParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Restores default parameters to parameter panel.
restoreExplicitHydrogens(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
When the input molecule is set, the explicit H-s may be stored CalculatorPlugin.setMolecule(Molecule, boolean, boolean, boolean) The parameter should be topologically equal to the input molecule for a successfull restore.
RESTYPE_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum residue type is currently 63.
resultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Returns an iterator that will wrap the specified iterator and standardizes all molecules.
resultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String, boolean) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Returns an iterator that will wrap the specified iterator and standardizes all molecules.
resultMolList - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The result molecules to be displayed.
resultValues - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The result values to be displayed in MarvinSpace.
RETROSYNTHETIC - Static variable in class chemaxon.struc.RxnMolecule
Retrosynthetic arrow, the same as the regular double reaction arrow.
returnOptionString(boolean) - Method in class chemaxon.sss.search.SearchOptions
 
ReusablePluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent
Work unit performing plugin calculation.
ReusablePluginWorkUnit() - Constructor for class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Constructor.
reuseAtom(int, int) - Method in class chemaxon.struc.Molecule
Reuse an atom or create a new one.
reuseAtom(int, int) - Method in class chemaxon.struc.RgMolecule
Reuse an atom or create a new one.
reuseFont(String, int, double) - Method in class chemaxon.struc.graphics.MTextDocument
 
revalidateCoordDependentProps() - Method in class chemaxon.struc.MoleculeGraph
Revalidate coordinate dependent properties.
revalidateCoordDependentProps() - Method in class chemaxon.struc.RgMolecule
Revalidate coordinate dependent properties.
revalidateCoordDependentProps() - Method in class chemaxon.struc.RxnMolecule
Revalidate coordinate dependent properties.
reverse() - Method in class chemaxon.struc.graphics.MPolyline
Reverses the order of points.
REVERSIBLE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.2, use Expandable.LEAVE_COORDS_UNCHANGED instead
Rf - Static variable in class chemaxon.core.ChemConst
 
RFGenerator - Class in chemaxon.descriptors
Generator class for the ReactionFingerprint descriptor.
RFGenerator() - Constructor for class chemaxon.descriptors.RFGenerator
 
RFParameters - Class in chemaxon.descriptors
Manages reaction fingerprint parameters.
RFParameters() - Constructor for class chemaxon.descriptors.RFParameters
Creates an empty object.
RFParameters(File) - Constructor for class chemaxon.descriptors.RFParameters
Creates a new object based on a given configuration file.
RFParameters(String) - Constructor for class chemaxon.descriptors.RFParameters
Creates a new object based on a given configuration string.
Rg - Static variable in class chemaxon.core.ChemConst
 
RG_ID_MASK - Static variable in class chemaxon.struc.RgMolecule
R-group id mask in R-logic.
RG_ID2_FLAG - Static variable in class chemaxon.struc.RgMolecule
Other R-group ID's presence flag in R-logic.
RG_ID2_MASK - Static variable in class chemaxon.struc.RgMolecule
Mask of the other R-group's id in R-logic.
RG_ID2_OFF - Static variable in class chemaxon.struc.RgMolecule
Offset of the other R-group's id in R-logic.
RG_RESTH - Static variable in class chemaxon.struc.RgMolecule
The RestH flag in R-logic.
RgComponentIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
Constructs an iterator to process the rgroup definition components, if the specified molecule in the factory is an RgMolecule, the iterator is empty otherwise.
RgMolecule - Class in chemaxon.struc
A molecule or reaction containing R-groups.
RgMolecule() - Constructor for class chemaxon.struc.RgMolecule
Creates a 2 dimensional RgMolecule.
RgMolecule(Molecule) - Constructor for class chemaxon.struc.RgMolecule
Creates an RgMolecule with the given root structure.
RGROUP - Static variable in class chemaxon.sss.search.MarkushFeature
Deprecated.
Expansion type: R-grgoup.
RGROUP - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the Rgroup query "atom".
RGROUP_ATTACHMENT - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of an ordered R-group attachment point.
RGROUP_ATTACHMENT_ERROR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing invalid attachments in R-group definitions.
RGROUP_BRIDGE_RATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing invalid R-atoms corresponding to R-group bridge definitions.
RGROUP_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum R-group number (32767).
RGROUP_MAX - Static variable in interface chemaxon.struc.Smolecule
Maximum R-group index (32767).
RgroupAttachmentCountFilter(int) - Constructor for class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter
Contructor.
RgroupAttachmentErrorChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting invalid attachments in R-group definitions.
RgroupAttachmentErrorChecker() - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker
Creates a new RgroupAttachmentErrorChecker instance.
RgroupAttachmentErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker
Parameterized constructor.
RgroupAttachmentFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer that can fix attachment errors in R-group definition members.
RgroupAttachmentFixer() - Constructor for class chemaxon.fixers.RgroupAttachmentFixer
 
RgroupBridgeRatomChecker - Class in chemaxon.checkers
Checker for R-atoms that form R-group bridges: One R-group can be involved in at most one bridge. Two R-atoms that represent a bridge must be in the scaffold or in the same R-group definition member. The R-group number that represents an R-group bridge cannot represent an ordinary R-group.
RgroupBridgeRatomChecker() - Constructor for class chemaxon.checkers.RgroupBridgeRatomChecker
 
RgroupCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult providing information of R-group issues.
RgroupCheckerResult(StructureChecker, StructureCheckerErrorType, List<MolAtom>, List<MolBond>, List<Integer>, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.RgroupCheckerResult
Constructor which initialize all the properties.
RGROUPED - Static variable in class chemaxon.struc.RxnMolecule
Add R-groups to component structure.
rgroupIdOf(MolAtom) - Method in class chemaxon.struc.RgMolecule
Finds the ID of the R-group (the number in R#) that contains the specified atom.
rgroupIndexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule
Finds the index of the R-group (the number in R#) that contains the specified atom.
Rh - Static variable in class chemaxon.core.ChemConst
 
Ring - Class in chemaxon.calculations
The ring class provides information of the ring types in a molecule.
Ring() - Constructor for class chemaxon.calculations.Ring
 
ringAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of ring atoms in the molecule.
ringAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringAtomCount()
ringBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of ring bonds in the molecule.
ringBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringBondCount()
ringCount() - Method in class chemaxon.calculations.Ring
Calculates the number of rings (SSSR smallest set of smallest rings) in the molecule.
ringCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringCount()
ringCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
ringCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringCount(int)
ringCountOfAtom(int) - Method in class chemaxon.calculations.Ring
Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
ringCountOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringCountOfAtom(int)
ringHandlingMode(RingHandlingMode) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets how rings should be handled during the search.
RingHandlingMode - Enum Class in com.chemaxon.search.mcs
Enum type for the ring handling modes of MaxCommonSubstructure (MCS) algorithms.
ringHasOnlyOneNeighbour(int[], Molecule, MolAtom) - Static method in class chemaxon.checkers.StructureCheckerHelper
This function determines if the ring (indexed with idx parameter) has only one neighbour (and this neighbour is the the atom parameter) or not.
rings() - Method in class chemaxon.calculations.Ring
Identifies the rings in the molecule.
rings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.rings()
rings(int) - Method in class chemaxon.calculations.Ring
Identifies rings in the molecule having a given size.
rings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.rings(int)
RingStrainErrorChecker - Class in chemaxon.checkers
RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.
RingStrainErrorChecker() - Constructor for class chemaxon.checkers.RingStrainErrorChecker
Default constructor
RingStrainErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RingStrainErrorChecker
Parameterized constructor.
If params contains "transDoubleBond"/"cumulatedDoubleBond"/"tripelBond" key with value "true" then trans double bonds/cummulated double bonds/triple bonds will be checked.
ringSystemCount() - Method in class chemaxon.calculations.Ring
Calculates the number of ring systems.
ringSystemCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringSystemCount()
ringSystemCount(int) - Method in class chemaxon.calculations.Ring
Identifies ring systems having a given size (number of rings) in the molecule.
ringSystemCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringSystemCount(int)
ringSystems() - Method in class chemaxon.calculations.Ring
Identifies the ring systems in the molecule.
ringSystems() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringSystems()
ringSystems(int) - Method in class chemaxon.calculations.Ring
Indentifies the ring systems in the molecule having a given size (number of rings).
ringSystems(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.ringSystems(int)
RLOGIC_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "RLogicVisible" or "RLogic".
rm - Variable in class chemaxon.marvin.space.GraphicComponent
Rotation matrix as a GeomCalc matrix.
RMCLEANUP_ALL - Static variable in class chemaxon.struc.MoleculeGraph
Perform all clean-up methods when removing an atom or a bond.
RMCLEANUP_EDGES - Static variable in class chemaxon.struc.MoleculeGraph
When removing an atom or a bond, also remove the bond(s) from the atom object(s).
RMCLEANUP_FIXCOMPONENT - Static variable in class chemaxon.struc.MoleculeGraph
Remove called from RxnMolecule.fixComponent.
RMCLEANUP_FROMSGROUPS - Static variable in class chemaxon.struc.Molecule
Remove atoms from S-groups.
RMCLEANUP_MOBJECT - Static variable in class chemaxon.struc.MoleculeGraph
Remove graphics objects containing the removed atom.
RMCLEANUP_NONE - Static variable in class chemaxon.struc.MoleculeGraph
Do not perform any clean-up methods when removing an atom or a bond.
RMCLEANUP_PARENTDOC - Static variable in class chemaxon.struc.MoleculeGraph
Remove atom from parent document.
RMCLEANUP_SGROUPATOMS - Static variable in class chemaxon.struc.Molecule
Remove S-groups of removed superatoms.
RMCLEANUP_STEREO - Static variable in class chemaxon.struc.MoleculeGraph
When removing a H atom, keep stereo information unchanged.
rmsd() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
calculates the rmsd value
rmsd() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
Root mean square deviation from the reference molecule.
RMSG_DEFAULT - Static variable in class chemaxon.struc.Molecule
Remove S-group's children and remove S-group from its parent.
RMSG_KEEP_CHILDREN - Static variable in class chemaxon.struc.Molecule
Do not remove S-group's children.
RMSG_KEEP_MULTICENTER - Static variable in class chemaxon.struc.Molecule
Do not remove central atom of multicenter S-groups.
RMSG_KEEP_PARENT - Static variable in class chemaxon.struc.Molecule
Do not remove S-group from its parent.
Rn - Static variable in class chemaxon.core.ChemConst
 
RNA - Static variable in class chemaxon.formats.MFileFormat
RNA sequence.
rotatableBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of rotatable bonds in the molecule.
RotatableBondDetector - Class in chemaxon.marvin.alignment
 
RotatableBondDetector(Molecule, boolean) - Constructor for class chemaxon.marvin.alignment.RotatableBondDetector
 
rotate(double, double, double) - Method in class chemaxon.marvin.space.GraphicCell
 
rotate(double, double, double) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given rotation factor in the active cell or in every cells in case of synchronous mode.
rotate(float[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Rotates the component by changing its coordinates, and not just the view.
rotate(float[], float[]) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Rotates its selected ligand by changing its coordinates, and not just the view.
rotate(float[], float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
Rotates the molecule with parameter center as an origin.
rotate(float[], float[]) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Rotates the component around the 3 axis, x, y, z, and given center.
rotate(float[], float[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Rotates the given p point by changing its coordinates.
rotate(int, float[], float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Rotates the given p point by changing its coordinates.
rotate(DPoint3, double, DPoint3) - Static method in class chemaxon.struc.graphics.MPolyline
Deprecated, for removal: This API element is subject to removal in a future version.
rotateBy(double, int, int, int, int) - Method in class chemaxon.marvin.alignment.DihedralRotator
Rotates the selected dihedral by the defined angle
rotatedAndReferenceFused() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
Fuse the rotated and the reference molecule.
rotatedMolecule() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
The rotated molecule.
rotateTo(double, int, int, int, int) - Method in class chemaxon.marvin.alignment.DihedralRotator
Sets the dihedral defined by the atoms a1-a4 to the angle
rotateTo(float[]) - Method in class chemaxon.marvin.space.GraphicScene
Sets the matrix of rotation explicitly in the active cell or in every cells in case of synchronous mode.
roundTo(int) - Method in class chemaxon.struc.DPoint3
Rounds the represented value to the given decimal precision.
ROWS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "rows".
Ru - Static variable in class chemaxon.core.ChemConst
 
run() - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
run() - Method in class chemaxon.marvin.calculations.ChargePlugin
Runs the charge calculation.
run() - Method in class chemaxon.marvin.calculations.ConformerPlugin
Runs the conformer calculation.
run() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Runs the tool.
run() - Method in class chemaxon.marvin.calculations.GeometryPlugin
Runs the tool.
run() - Method in class chemaxon.marvin.calculations.HBDAPlugin
Runs the charge calculation.
run() - Method in interface chemaxon.marvin.calculations.HlbPlugin
Run the calculation.
run() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Runs the Huckel analysis calculation.
run() - Method in class chemaxon.marvin.calculations.IonChargePlugin
Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH.
run() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Runs the isoelectric point and charge distribution calculations.
run() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
run() - Method in class chemaxon.marvin.calculations.logDPlugin
Runs the logD calculation.
run() - Method in class chemaxon.marvin.calculations.logPPlugin
Runs the logP calculation.
run() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Stores the input molecule with ungrouped sgroups.
run() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Creates enumerated structures.
run() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Runs the tool.
run() - Method in class chemaxon.marvin.calculations.MSAPlugin
Runs the surface area calculation.
run() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Runs the orbital electornegativity calculation.
run() - Method in class chemaxon.marvin.calculations.pKaPlugin
Runs the macro pKa calculation.
run() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Runs the charge calculation.
run() - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Runs the refractivity calculation.
run() - Method in class chemaxon.marvin.calculations.ResonancePlugin
Calculates the resonant structures.
run() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Runs the plugin.
run() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Run calculation
run() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Calculates the tautomers.
run() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Runs the tool.
run() - Method in class chemaxon.marvin.calculations.TPSAPlugin
Runs the surface area calculation.
run() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Runs the tool.
run(String[]) - Method in class chemaxon.checkers.StructureCheck
This method runs the command line parameterized by the args array of String
runScript(String) - Method in class chemaxon.jep.Evaluator
Runs a script, variables will be added to the base variable table and can be referenced by chemical expressions.
RXN - Static variable in class chemaxon.formats.MFileFormat
MDL Rxnfiles.
RXN_V3_OUT - Static variable in class chemaxon.formats.MFileFormat
MDL Extended Rxnfiles.
RxnComponentIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
Constructs an iterator to process the components (reactant, product and agent components), if the specified molecule in the factory is an RxnMolecule, the iterator is empty otherwise.
RxnMolecule - Class in chemaxon.struc
Reaction.
RxnMolecule() - Constructor for class chemaxon.struc.RxnMolecule
Create a reaction.
RXNSTEREO_INVERSION - Static variable in class chemaxon.struc.MolAtom
The stereo configuration of the atom is inverted during the reaction.
RXNSTEREO_NONE - Static variable in class chemaxon.struc.MolAtom
The stereo configuration of the atom is not considered during the reaction.
RXNSTEREO_RETENTION - Static variable in class chemaxon.struc.MolAtom
The stereo configuration of the atom is retained during the reaction.

S

s - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
 
S - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
 
S - Static variable in class chemaxon.core.ChemConst
 
SAFE - Enum constant in enum class com.chemaxon.calculations.admet.HergClass
 
SALT_ID_PROPERTY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
Property key for salt ID
SALT_LIST_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
Property key for salt list modification
SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
 
save(String) - Method in class chemaxon.marvin.common.UserSettings
Save the persistent properties to the config file set by the constructor.
save(String, String) - Method in class chemaxon.marvin.common.UserSettings
Save the persistent properties to the file given as the first parameter.
SAVE_PROPERTIES - Static variable in class chemaxon.marvin.common.ParameterConstants
 
saveAsMacro() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Shows the modal macro manager dialog, setting current selection as new macro
saveCache(int) - Method in class chemaxon.struc.MoleculeGraph
Saves caches like connection table, bond table, etc.
saveCoords(MoleculeGraph, double[]) - Static method in class chemaxon.marvin.util.CleanUtil
Saves atomic coordinates.
saveParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Saves parameters from parameter panel.
saveParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Saves parameters from parameter panel.
saveParameterSettings() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
saveParameterSettings() - Method in class com.chemaxon.calculations.gui.PluginFactory
Saves plugin parameter settings to file $HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or $HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).
Sb - Static variable in class chemaxon.core.ChemConst
 
Sc - Static variable in class chemaxon.core.ChemConst
 
scalar(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Calculates the scalar product of the two vectors
SCALAR - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
 
ScalarDescriptor - Class in chemaxon.descriptors
Base class for all scalar descriptors.
ScalarDescriptor() - Constructor for class chemaxon.descriptors.ScalarDescriptor
Creates a new, empty instance of ScalarDescriptor.
ScalarDescriptor(ScalarDescriptor) - Constructor for class chemaxon.descriptors.ScalarDescriptor
Copy constructor.
ScalarDescriptor(SDParameters) - Constructor for class chemaxon.descriptors.ScalarDescriptor
Creates a new instance of ScalarDescriptor according to the parameters given.
ScalarDescriptor(String) - Constructor for class chemaxon.descriptors.ScalarDescriptor
Creates a new instance of ScalarDescriptor according to the parameters given.
scale(double) - Method in class chemaxon.struc.DPoint3
Scales the vector with the given factor.
SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "scale".
SCALED_BALLS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
scaledAsymmetricTanimoto(float[], float[], float[], float, float) - Static method in class chemaxon.descriptors.Metrics
Calculates the scaled asymmetric Tanimoto dissimilarity for floating point values.
scaledAsymmetricTanimoto(int[], int[], float[], float, float) - Static method in class chemaxon.descriptors.Metrics
Calculates the scaled asymmetric Tanimoto dissimilarity for floating point values.
scaledBalls - Variable in class chemaxon.marvin.space.MoleculeComponent
 
scaledTanimoto(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the scaled Tanimoto dissimilarity for floating point values.
scaledTanimoto(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the scaled Tanimoto dissimilarity for floating point values.
scaleFactors - Variable in class chemaxon.descriptors.MDParameters
scale factor of scalable parametrized metrics
scaleShift(double) - Method in class chemaxon.calculations.nmr.Shift
Scales the stored chemical shift and shift standard deviation values.
scanFinished(BondInfo) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when dihedral scan finished.
SCENE_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
scheduler - Variable in class chemaxon.marvin.view.swing.TableSupport
Record access task scheduler.
SCN_EITHER_UNKNOWN - Static variable in class chemaxon.struc.Sgroup
Either unknown S-group connectivity.
SCN_HEAD_TO_HEAD - Static variable in class chemaxon.struc.Sgroup
Head-to-head S-group connectivity.
SCN_HEAD_TO_TAIL - Static variable in class chemaxon.struc.Sgroup
Head-to-tail S-group connectivity.
score() - Method in class chemaxon.calculations.bbb.BBB.Property
 
score() - Method in class chemaxon.calculations.bbb.BBB
Calculates the BBB score from properties.
score() - Method in class chemaxon.calculations.cnsmpo.CnsMpo.Property
 
score() - Method in class chemaxon.calculations.cnsmpo.CnsMpo
Calculates the CNS MPO score from properties.
SCREEN - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Screen
SCREEN3D - Static variable in class chemaxon.license.LicenseManager
Identifier of product: 3D Screen
screeningConfigurationNode - Variable in class chemaxon.descriptors.MDParameters
 
SCRIPT - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "script".
SDF - Static variable in class chemaxon.formats.MdlCompressor
 
SDF - Static variable in class chemaxon.formats.MFileFormat
MDL SDfiles.
SDParameters - Class in chemaxon.descriptors
Manages ScalarDescriptor parameters.
SDParameters() - Constructor for class chemaxon.descriptors.SDParameters
Creates an empty object.
SDParameters(File) - Constructor for class chemaxon.descriptors.SDParameters
Creates a new object from the given configuration file.
SDParameters(String) - Constructor for class chemaxon.descriptors.SDParameters
Creates a new object from the given configuration string.
Se - Static variable in class chemaxon.core.ChemConst
 
Search - Class in chemaxon.sss.search
Abstract base class of all structural search classes.
Search() - Constructor for class chemaxon.sss.search.Search
 
SEARCH_MODE_NAMES - Static variable in interface chemaxon.sss.SearchConstants
Deprecated, for removal: This API element is subject to removal in a future version.
As of JChem 5.12, replaced by SearchConstants.SEARCH_TYPE_NAMES.
SEARCH_OPTIONS_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction
Key of search options for parsing and property change
SEARCH_TYPE_NAMES - Static variable in interface chemaxon.sss.SearchConstants
The names of the search types.
SearchConstants - Interface in chemaxon.sss
Constants for structure searching
SearchException - Exception in chemaxon.sss.search
Exception denoting errors during the search process.
SearchException() - Constructor for exception chemaxon.sss.search.SearchException
Constructs a new exception with null as its detail message.
SearchException(String) - Constructor for exception chemaxon.sss.search.SearchException
Constructs a new exception with the specified detail message.
SearchException(String, Throwable) - Constructor for exception chemaxon.sss.search.SearchException
Constructs a new exception with the specified detail message and cause.
SearchException(Throwable) - Constructor for exception chemaxon.sss.search.SearchException
Constructs a new exception with the specified cause and a detail message of (cause==null ? null : cause.toString()) (which typically contains the class and detail message of cause).
SearchHit - Class in chemaxon.sss.search
Search hit object.
SearchHit(int[]) - Constructor for class chemaxon.sss.search.SearchHit
Constructor: creates a hit object from a single (1 dimensional) hit mapping array.
SearchHit(int[][]) - Constructor for class chemaxon.sss.search.SearchHit
Constructor: creates a hit object from a group (2 dimensional) hit mapping array.
searchMode - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Search mode.
SearchMode - Enum Class in com.chemaxon.search.mcs
Enum type for search modes of MaxCommonSubstructure (MCS) algorithms.
searchOptions - Variable in class chemaxon.sss.search.MolComparator
 
searchOptions - Variable in class chemaxon.sss.search.Search
Object to store all search parameters.
SearchOptions - Class in chemaxon.sss.search
Class to encapsulate common search parameters.
SearchOptions(int) - Constructor for class chemaxon.sss.search.SearchOptions
Creates a SearchOptions object while setting different search options according to a predefined search type.
searchOpts - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Search options.
secondaryAtomIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated, for removal: This API element is subject to removal in a future version.
secondaryBonds - Variable in class chemaxon.util.iterator.IteratorFactory.BondIterator
Secondary bonds that replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).
secondaryBonds - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Secondary bonds that replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).
Section(int, String) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section
Constructs a text section.
Section(int, String, MTextAttributes) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section
Constructs a text section.
Section(MTextDocument.Section) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section
Copy constructor.
SECTION - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the section of the document where the structure was found.
seek(long, int) - Method in class chemaxon.marvin.io.PositionedInputStream
Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
seek(long, int, int) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
seek(long, int, int) - Method in class chemaxon.marvin.io.MRecordImporter
Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
seek(long, int, int) - Method in interface chemaxon.marvin.io.MRecordReader
Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
seekForward(int, MProgressMonitor, int, Runnable) - Method in class chemaxon.marvin.io.MDocSource
Seeks in forward direction.
seekRecord(int, MProgressMonitor) - Method in class chemaxon.formats.MolImporter
Seek the specified record.
seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.io.ArrayMDocSource
Seeks the specified record.
seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.io.MDocSource
Seeks the specified record.
seekRecordAtFraction(double, int, int, int, MProgressMonitor) - Method in class chemaxon.marvin.io.MDocSource
Seeks an approximate file position.
seekVisitedRecord(int) - Method in class chemaxon.formats.MolImporter
Seeks an already visited position in case of rewindable input.
seekVisitedRecord(int) - Method in class chemaxon.marvin.io.ArrayMDocSource
Seeks an already visited position in case of rewindable input.
seekVisitedRecord(int) - Method in class chemaxon.marvin.io.MDocSource
Seeks an already visited position in case of rewindable input.
select() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the component to be selected.
select() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
select() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets all visualizers to be selected.
select() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
select() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the whole component to be selected.
select() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
When the monitor is selected, a DihedralControl is created or changes its direction if it was alredy created.
select() - Method in class chemaxon.marvin.space.monitor.Label
The color of the label changes by selection.
select() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the component to be selected.
select() - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the component to be selected.
select(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the specific part of the component to be selected.
SELECTABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "selectable".
selectAllAtoms() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets all atoms to be selected.
selectAllConnectedObjects(boolean) - Method in class chemaxon.struc.MDocument
Selects or unselects all objects in this document and objects that belong to the chemical structure of this document.
selectAllObjects(boolean) - Method in class chemaxon.struc.MDocument
Selects or unselects all objects.
selectAllObjects(boolean) - Method in class chemaxon.struc.Molecule
 
selectAllObjects(boolean) - Method in class chemaxon.struc.RgMolecule
 
selectAllObjects(boolean) - Method in class chemaxon.struc.RxnMolecule
 
selectAllObjects(boolean) - Method in class chemaxon.struc.Sgroup
Sets the selection state of the MObject-s that belong to this Sgroup.
selectAtom(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
selectAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the atom with the given index to be selected.
selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.GraphicCell
Sets all components lying inside the given box to be selected.
selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.GraphicComponent
The component will be selected if it is inside the given box.
selectComponentElementsInside(BoundingBox) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Visualizers lying in the given box will be selected.
selectComponentElementsInside(BoundingBox) - Method in class chemaxon.marvin.space.MoleculeComponent
Atoms lying in the given box will be selected.
SELECTED_INDEX - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "selectedIndex".
selectedAtomCount() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
selectedAtomCount() - Method in class chemaxon.marvin.space.MoleculeComponent
Returns the number of atoms being selected.
selectedAtoms - Variable in class chemaxon.marvin.space.MoleculeComponent
 
selectedItemCoordinates - Variable in class chemaxon.marvin.space.monitor.Monitor
 
selectedItems - Variable in class chemaxon.marvin.space.monitor.Monitor
Storage of the items of monitoring.
SELECTION - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "selection".
selectionBar - Variable in class chemaxon.marvin.space.MSpaceEasy
 
selectionBeforeInit - Variable in class chemaxon.marvin.space.MoleculeComponent
 
SelectionMolecule - Class in chemaxon.struc
A selection object which can contain atoms and bonds without real parent relationship (the real parent of atoms and bonds is another MoleculeGraph ancestor).
SelectionMolecule() - Constructor for class chemaxon.struc.SelectionMolecule
 
selectionPointer - Variable in class chemaxon.marvin.space.monitor.Monitor
Points to the next empty space in selectedItems.
selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.Label
Parameter item will be the selected item of the monitor.
selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Puts the item to the selection and clears its description.
selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.Monitor
Puts item to the selection.
selectItem(ComponentElement) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Parameter item will be the selected item of the monitor.
selectItem(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Label
The given component will be the selected item of the Label.
selectItem(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
The given component will be the selected item of the monitor.
Separated - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
Indicates, that the structure checker puts valid or fixed structures to the output file, the others to the discarded file.
separator - Variable in class com.chemaxon.calculations.cli.CalculatorPluginOutput
The separator string separating the results for different result types.
SEPARATOR - Static variable in enum class chemaxon.descriptors.MetricsType
 
SEPARATOR - Static variable in class chemaxon.descriptors.SimilarityCalculatorFactory
This character is used to separate fields of the parameter string.
SEPARATOR - Static variable in class com.chemaxon.calculations.gui.PluginFactory
Menuitem separator in Tools menu: if present then separator will be added to the Tools menu after the plugin menuitem.
seqCis - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
 
seqTrans - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
 
SERVICE - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Property key for service name as String
SERVICE_CONFIGURATION_PATH_PROPERTY_KEY - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
Java System Property key to globally override default configuration path.
SERVICE_DIALOG_PROVIDER_CLASS_NAME_PROPERTY_KEY - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
Java System Property key to globally override default Service Dialog Provider class with custom implementation.
ServiceArgument<T> - Class in chemaxon.marvin.services
Describes an argument passed to services
ServiceArgument(Class<T>, T) - Constructor for class chemaxon.marvin.services.ServiceArgument
Constructs a service argument with specified type and value
ServiceArgument(Class<T>, T, boolean) - Constructor for class chemaxon.marvin.services.ServiceArgument
Constructs a service argument with specified type and value
ServiceDescriptorEditor<T extends chemaxon.marvin.services.ServiceDescriptor> - Interface in chemaxon.marvin.services
Provides editor suport for ServiceDescriptor
ServiceDescriptorEditorProvider - Interface in chemaxon.marvin.services
Provides ServiceDescriptorEditor instances based on ServiceDescriptor classes.
ServiceDescriptorReader - Interface in chemaxon.marvin.services
Reader for ServiceDescriptors
ServiceDescriptorTools - Class in chemaxon.marvin.services
Helper class for accessing ServiceDescriptorReader, ServiceDescriptorWriter and ServiceDialogProvider implementations and various configuration data for services.
ServiceDescriptorTools() - Constructor for class chemaxon.marvin.services.ServiceDescriptorTools
 
ServiceDescriptorWriter - Interface in chemaxon.marvin.services
Writer for ServiceDescriptors
ServiceDialogProvider - Interface in chemaxon.marvin.services
Provides Dialog instances to provide argument editor and result view for ServiceDescriptor
ServiceException - Exception in chemaxon.marvin.services
Exception for failure indication for services.
ServiceException(String) - Constructor for exception chemaxon.marvin.services.ServiceException
Creates a ServiceException with specified message
ServiceException(String, Throwable) - Constructor for exception chemaxon.marvin.services.ServiceException
Creates a ServiceException with specified message and cause
ServiceException(Throwable) - Constructor for exception chemaxon.marvin.services.ServiceException
Creates a ServiceException with specified cause
ServiceHandler<DT extends chemaxon.marvin.services.ServiceDescriptor> - Class in chemaxon.marvin.services
Manages service calls.
ServiceHandler keeps track of the previous call and if it is not yet finished cancels it.
ServiceHandler() - Constructor for class chemaxon.marvin.services.ServiceHandler
 
set(float) - Method in class chemaxon.descriptors.ScalarDescriptor
Set the value of the descriptor.
set(float, float, float, float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the minimum and maximum coordinates of the box.
set(int, float) - Method in class chemaxon.descriptors.CustomDescriptor
Sets the value of one cell of the descriptor.
set(int, float[]) - Method in class chemaxon.descriptors.CustomDescriptor
Sets values of the descriptor.
set(int, int) - Method in class chemaxon.descriptors.CustomDescriptor
Sets the value of one cell of the descriptor.
set(int, int[]) - Method in class chemaxon.descriptors.CustomDescriptor
Sets values of the descriptor.
set(int, GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Sets the group definition at specified index, and returns the previous value.
set(int, MProp) - Method in class chemaxon.struc.prop.MListProp
Sets an element.
set(CTransform3D) - Method in class chemaxon.struc.CTransform3D
Copy.
set(DPoint3) - Method in class chemaxon.struc.DPoint3
Set coordinates.
set(MolAtom) - Method in class chemaxon.struc.MolAtom
Set all atom properties except the coordinates.
set(MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
Set properties of this S-group superatom.
set(String, MProp) - Method in class chemaxon.struc.MPropertyContainer
Sets a property object.
set(String, MProp, int) - Method in class chemaxon.struc.MPropertyContainer
Sets a property object.
SET_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "setColoringEnabled".
setAbbreviation(int, String) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Sets the abbreviation of the group at the provided index
setAbbreviation(String) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Sets the abbreviation of the group.
setAbsoluteLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Set 'Absolute' label visibility.
setAbsoluteLabelVisible(String) - Method in class chemaxon.marvin.common.UserSettings
Show or hide Abolute labels
setAbsolutePlacement(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets whether the placement of this attached data is absolute or relative to the objects it is attached.
SetAbsoluteStereoAction - Class in chemaxon.standardizer.actions
Set absolute stereo standardizer action
SetAbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.SetAbsoluteStereoAction
Initializes a set absolute stereo action
setAbsoluteXY(double, double) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
setAbsoluteXY(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
setAbsStereo(boolean) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Sets the absoluteLegacy value of the action
setAbsStereo(boolean) - Method in class chemaxon.struc.MoleculeGraph
Sets the absolute stereoconfiguration flag.
setAbsStereo(boolean) - Method in class chemaxon.struc.RgMolecule
Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
setAbsStereo(boolean) - Method in class chemaxon.struc.RxnMolecule
Sets the absolute stereoconfiguration flag for all the structures.
setAcceptor(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the acceptor property of the PharmacophorePoint.
setAccuracyMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
setAcidicpKaUpperLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the maximum acidic pKa (default: 20).
setAction(StandardizerAction) - Method in class chemaxon.standardizer.Changes
Sets the base StandardizerAction of the changes
setActionB(int, String) - Method in class chemaxon.marvin.beans.MViewPane
Sets the action string (URL or JavaScript expression) of a button in a GridBagView table.
setActionC(int, String) - Method in class chemaxon.marvin.beans.MViewPane
Sets one of the two action strings (JavaScript expressions) of a checkbox in a GridBagView table.
setActionMap(ActionMap) - Method in class chemaxon.struc.graphics.MTextBox
Sets the ActionMap to map.
setActionsEnabled(boolean) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Enables / disables action buttons.
setActionStringTokens(String[]) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the action string token of the checker
setActionStringTokens(String[]) - Method in class chemaxon.fixers.StructureFixerDescriptor
Sets the action string token of the fixer
setActionStringTokens(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the action string tokens of the action
setActive() - Method in class chemaxon.marvin.space.GraphicCell
Sets this cell to the active cell of the scene.
setActive(boolean) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
setActive(boolean) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
setActive(boolean) - Method in interface chemaxon.standardizer.StandardizerAction
Sets whether the action is active, and can be used
setActiveCell(int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the ith cell to be the active cell of the scene.
setActiveGroups(String[]) - Method in class chemaxon.standardizer.Standardizer
setAddServices(boolean) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the services display
setAdvancedSave(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets wether the user prefers advanced svae or not.
setAlias(String) - Method in class chemaxon.marvin.services.ServiceArgument
Sets the argument alias.
setAliasstr(String) - Method in class chemaxon.struc.MolAtom
Sets the alias string or pseudo atom type string for pseudo atoms.
setAlignScaffold(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets the scaffold aligning mode.
setAllowExperimentalFeatures(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setAllowTraditionalNitrogen(boolean) - Method in class chemaxon.checkers.ValenceErrorChecker
Sets if the checker should allow traditional N representation
setAllowUndeclared(boolean) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Undeclared variables will always be allowed in the future, changing this will no longer be supported.
setAllowValenceError(boolean) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Sets replace should be applied even in case of invalid valence in the result
setAminoAcid(boolean) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Sets whether the group represents an amino-acid
setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets wether the user uses peptide bridge coloring or not.
setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets peptide bridge coloring enabled.
setAnalysisBoxTerms(String) - Method in class chemaxon.marvin.common.UserSettings
 
setAnalysisBoxWarning() - Method in class chemaxon.marvin.common.UserSettings
 
setAnimated(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Starts or stops animation in each cells of the table or in the simple viewer.
setAnimated(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane
Sets animation of a cell of the table.
setAnimDelay(double) - Method in class chemaxon.marvin.beans.MViewPane
Sets the repeat delay for animations.
setAnimFPS(double) - Method in class chemaxon.marvin.beans.MViewPane
Sets the frames per second for animations.
setAnimSync(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Sets the animation synchronization.
setAnionic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the anionic property of the PharmacophorePoint.
setAnnotatedOutput(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Set the destination file where an annotated version of the source document should be written.
setAnnotatedOutput(OutputStream) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Set the destination output stream where an annotated version of the source document should be written.
setAnnotatedOutputDirectory(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Set the directory where the annotated document and associated resources will be placed.
setAnnotatedOutputDirectory(File, boolean) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Set the directory where the annotated document and associated resources will be placed.
setAntialias(boolean) - Method in class chemaxon.marvin.space.GraphicCell
Switches the full scene anti-aliasing on/off.
setAntialias(boolean) - Method in class chemaxon.marvin.space.GraphicScene
Enables/disables full scene anti-aliasing.
setAnyBondStyles(String) - Method in class chemaxon.marvin.MolPrinter
Sets the any bond style.
setArcAngle(double) - Method in class chemaxon.struc.graphics.MPolyline
Sets the central angle of the arc.
setArcHeight(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
setArcWidth(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
setAromatic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the aromatic property of the PharmacophorePoint.
setAromaticityChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects aromaticity atom query properties or not.
setAromatizationMethod(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Sets the aromatization method.
setAromatize(boolean) - Method in class chemaxon.marvin.alignment.MinMaxDistance
Deprecated, for removal: This API element is subject to removal in a future version.
setAromatize(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
The original input structure is not aromatized. No need to use.
setAromatizeMethod(int) - Method in class chemaxon.marvin.common.UserSettings
Sets the aromatize method.
setArrow(boolean) - Method in class chemaxon.struc.graphics.MPolyline
Sets or unsets arrow mode.
setArrowFlags(int, int) - Method in class chemaxon.struc.graphics.MPolyline
Sets the flags.
setArrowLength(int, double) - Method in class chemaxon.struc.graphics.MPolyline
Sets the arrow head length.
setArrowWidth(int, double) - Method in class chemaxon.struc.graphics.MPolyline
Sets the arrow head width.
setAssigned(int, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
setAsymmetryFactor(float) - Method in class chemaxon.descriptors.MDParameters
Sets the value of the asymmetry factor of the current parametrized metric.
setAtno(int) - Method in class chemaxon.struc.MolAtom
Sets the atomic number.
setAtom(int) - Method in class chemaxon.jep.context.AtomContext
Sets the input atom.
setAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(int) for atom removal and MoleculeGraph.add(MolAtom) for adding new atoms.
setAtom(int, MolAtom) - Method in class chemaxon.struc.RgMolecule
Deprecated.
as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RgMolecule.add(MolAtom) to modify the structure.
setAtom(int, MolAtom) - Method in class chemaxon.struc.RxnMolecule
Deprecated.
As of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RxnMolecule.add(MolAtom) to modify the structure.
setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Sets the specified atom in the S-group graph.
setAtom(int, MolAtom) - Method in class chemaxon.struc.Sgroup
Sets the specified atom in the S-group graph.
setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Sets the specified atom in the S-group graph.
setAtom0(int, MolAtom) - Method in class chemaxon.struc.Molecule
Sets the atom at the specified index.
setAtom0(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Sets the atom at the specified index.
setAtom0(int, MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Sets the atom at the specified index.
setAtom1(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom
Sets the first atom of a bond.
setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom
Sets the first node of an edge.
setAtom2(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom
Sets the second atom of a bond.
setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom
Sets the second node of an edge.
setAtomFont(Font) - Method in class chemaxon.marvin.common.UserSettings
Sets the atom symbol font name.
setAtomIndex(int) - Method in class chemaxon.calculations.nmr.Shift
Sets the atom index.
setAtomIndexMap(int[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
setAtomMap(int) - Method in class chemaxon.struc.MolAtom
Sets the atom-atom mapping number.
setAtomMap(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the atom-atom mapping number.
setAtomMappingMethod(int) - Method in class chemaxon.marvin.common.UserSettings
Sets the atom mapping method.
setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Shows or hides the atom mapping.
setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the atom mapping visibility.
setAtomNumberingType(int) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the atom numbering.
setAtomNumberingType(int) - Method in class chemaxon.marvin.common.UserSettings
Sets the atom numbering type.
setAtomNumberingType(int) - Method in class chemaxon.marvin.MolPrinter
sets atom numbering type.
setAtomNumbersVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
in 6.2.0. Use setAtomNumberingType() instead
setAtomNumbersVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
in 6.2.0. Use setAtomNumberingType() instead.
setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets atom properties visibility.
setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Set the atom properties visibility
setAtomPropertyList(ArrayList) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets a list of atomic properties that can be mapped as coloring on the surface.
setAtomRadiusExtension(float) - Method in class chemaxon.marvin.space.SurfaceColoring
In case of {#RADIUS_VDW_EXTENDED} mode the extension can be set.
setAtomRefs(CloneStateMapper) - Method in class chemaxon.struc.StereoActivePart
 
setAtoms(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
Sets 2 atoms as the 2 end of the torsion bond.
setAtoms(MolAtom[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Sets the atoms.
setAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
setAtoms(List<MolAtom>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
This method sets the atoms property
setAtomSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the color of an atom set.
setAtomSetColorMode(int, int) - Method in class chemaxon.struc.MDocument
Sets the atom set coloring mode.
setAtomSetFont(int, MFont) - Method in class chemaxon.struc.MDocument
Sets the font of an atom set.
setAtomSetRGB(int, int) - Method in class chemaxon.struc.MDocument
Sets the color of an atom set.
setAtomSetSeq(int, int, int) - Method in class chemaxon.marvin.beans.MViewPane
Sets the set sequence number of the atom.
setAtomSetSeq(int, String, int, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets the atom set sequence number of an atom.
setAtomSetSeq(int, String, String, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets atom set sequence numbers.
setAtomSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph
Sets the set sequence number of all atoms.
setAtomSetSeqs(int, String, int[]) - Method in class chemaxon.marvin.view.MDocStorage
Sets atom set sequence numbers.
setAtomsize(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the atom size.
setAtomsize(double) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.2, replaced by MolPrinter.setAtomSize(double).
setAtomSize(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the atom size in C-C bond length units.
setAtomSize(double) - Method in class chemaxon.marvin.MolPrinter
Sets the size of displayed atoms in units of regular bond length.
setAtomStereo(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets atom stereo properties.
setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Shows or hides the atom symbols in 3D.
setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets atom symbol visibility in 3D mode.
setAttach(int) - Method in class chemaxon.struc.MolAtom
setAttach(int, Sgroup) - Method in class chemaxon.struc.MolAtom
setAttachedDataMatch(int) - Method in class chemaxon.sss.search.SearchOptions
Sets whether attached data (in data sgroups) should be used when comparing structures.
setAttachedDataPrefixes(String) - Method in class chemaxon.sss.search.SearchOptions
Sets the prefixes of the names of those data sgroups that will be used during structure comparison.
setAttachmentPointOrder(MolAtom, int, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Sets a new order for the given attachment point.
setAttachmentPointsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the attachment points visibility.
setAttachParentSgroup(Sgroup) - Method in class chemaxon.struc.MolAtom
Sets the attach parent s-group information to the extra atom properties
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MBracket
Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MEFlow
 
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MPolyline
Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRectangle
Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRoundedRectangle
Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MTextBox
Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.MObject
Sets the value of an attribute.
setAttributes(int, int, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
Sets attributes of selected text.
setAutoCheckStructure(boolean) - Method in class chemaxon.marvin.common.UserSettings
Turn on automatic Structure checking
setAutoHeight(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Turns on/off automatic height calculation.
setAutomaticFogEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets the fog to automatic calculation mode.
setAutomaticReactionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets the calculation of reaction plus signs to automatic.
setAutoPopup(boolean) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the auto popup behaviour
setAutoScale(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the autoscale property.
setAutoSize(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Turns on/off automatic size calculation.
setAutoTabScale(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Allows or disallows automatic changing of tab scale.
setBackground(Color) - Method in class chemaxon.struc.MObject
Sets the background color of the object.
setBackgroundColor(float[]) - Method in class chemaxon.marvin.space.GraphicCell
Sets the background color of the cell used by drawing smooth background.
setBackgroundColor(float[]) - Method in class chemaxon.marvin.space.GraphicScene
 
setBackgroundColor(Color) - Method in class chemaxon.marvin.MolPrinter
Sets the background color.
setBackgroundColor(Color) - Method in class chemaxon.marvin.space.GraphicCell
Sets the background color of the cell used by drawing smooth background.
setBackgroundColor(Color) - Method in class chemaxon.marvin.space.GraphicScene
Sets the background color of the scene and an alpha value of 0 (transparent background).
setBackgroundColor(Color) - Method in class chemaxon.marvin.space.monitor.Label
Sets the background color of the label.
setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer
Sets the background color for the current cell based on selection.
setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer
Sets the background color for the current cell based on selection.
setBackgroundColor(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor
Sets the background color for the current cell based on selection.
setBackgroundColorMode(int) - Method in class chemaxon.marvin.space.monitor.Label
Sets the coloring mode of the background.
setBallRadius(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the ball radius in units of covalent radius.
setBallRadius(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the ball radius for ball and stick mode.
setBallRadius(double) - Method in class chemaxon.marvin.MolPrinter
Sets the ball radius for "ball and stick" mode.
setBarrierLimit(double) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Set the energy barrier limit.
setBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow
 
setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlow
 
setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlow
 
setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
setBaseFontFamily(String) - Method in class chemaxon.struc.graphics.MTextBox
Sets the base font family.
setBaseFontStyle(int) - Method in class chemaxon.struc.graphics.MTextBox
Sets the base font style.
setBasicpKaLowerLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the minimum basic pKa (default: -10).
setBestLigandPosition(MolAtom, MolAtom) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates and sets an optimal position for a ligand atom.
setBestLigandPosition(MolAtom, MolAtom, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates and sets an optimal position for a ligand atom.
setBicycloStereo(BicycloStereoDescriptor[]) - Method in class chemaxon.struc.MolAtom
Registers the bicyclo stereo information for this atom.
setBitCount(int) - Method in class chemaxon.descriptors.CFParameters
Sets the bit count (number of fingerprint bits to be set to 1) parameter.
setBitCount(int) - Method in class chemaxon.descriptors.RFParameters
Sets the bit count (number of fingerprint bits to be set to 1) parameter.
setBoldBondWidth(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the bold bond width.
setBoldBondWidth(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the bold bond width in pt.
setBoldBondWidth(double) - Method in class chemaxon.marvin.MolPrinter
Sets the bold bond with.
setBond(int, MolBond) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
setBond(int, MolBond) - Method in class chemaxon.struc.RgMolecule
Deprecated.
as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.
setBond(int, MolBond) - Method in class chemaxon.struc.RxnMolecule
Deprecated.
as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.
setBond(int, MolBond) - Method in class chemaxon.struc.SelectionMolecule
Deprecated.
as of Marvin 6.2. Use SelectionMolecule.removeBond(MolBond) for bond removal and SelectionMolecule.add(MolBond) for adding a new bond to the molecule.
setBondCorrespondence(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the crossing bonds (head and tail) of a ladder-type polymer.
setBondCount(int) - Method in class chemaxon.descriptors.CFParameters
Sets the path length (number of adjacent bonds) parameter.
setBondCount(int) - Method in class chemaxon.descriptors.RFParameters
Sets the path length (number of adjacent bonds) parameter.
setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the visibility of the currently used bond at the mouse cursor.
setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets the visibility of the currently used bond at the mouse cursor.
setBondHashSpacing(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the bond hash spacing.
setBondHashSpacing(double) - Method in class chemaxon.marvin.MolPrinter
Sets the bond hash spacing that is the distance the hashes in a hashed bond.
setBondIndex(int, int, int) - Method in class chemaxon.core.util.BondTable
Sets the index of the bond connecting two atoms.
setBondLength(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the bond length.
setBondLength(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the bond length in pt.
setBondLength(double) - Method in class chemaxon.marvin.MolPrinter
Sets the bond length in pt.
setBondLengthVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the bond length display option.
setBondLengthVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the bond length visibility
setBonds(List<MolBond>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
setBonds(List<MolBond>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
This method sets the bonds property
setBondSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the color of a bond set.
setBondSetColorMode(int, int) - Method in class chemaxon.struc.MDocument
Sets the bond set coloring mode.
setBondSetRGB(int, int) - Method in class chemaxon.struc.MDocument
Sets the color of a bond set.
setBondSetSeq(int, String, int, int, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets bond set sequence numbers.
setBondSetSeq(int, String, String, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets bond set sequence numbers.
setBondSetSeqAll(int, String, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets all bond set sequence numbers.
setBondSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph
Sets the set sequence number of all bonds.
setBondSetSeqs(int, String, List<int[]>) - Method in class chemaxon.marvin.view.MDocStorage
Sets bond set sequence numbers.
setBondSetThickness(int, double) - Method in class chemaxon.struc.MDocument
Sets the thickness of a bond set.
setBondSpacing(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the bond spacing.
setBondSpacing(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the double bond spacing.
setBondSpacing(double) - Method in class chemaxon.marvin.MolPrinter
Sets the double bond spacing that is the distance of the two lines representing a double bond.
setBondWidth(double) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 4.1, replaced by MarvinPane.setBondSpacing(double)
setBondWidth(double) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 4.1, replaced by MolPrinter.setBondSpacing(double)
setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer
Sets the border for the current cell based on selection.
setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer
Sets the border for the current cell based on selection.
setBorder(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor
Sets the border for the current cell based on selection.
setBorderColor(Color) - Method in class chemaxon.marvin.space.monitor.Label
Sets the border color of the label.
setBorderColorMode(int) - Method in class chemaxon.marvin.space.monitor.Label
Sets the coloring mode of the border.
setBorderWidth(int) - Method in class chemaxon.marvin.beans.MViewPane
Sets the width of the border between cells.
setBoundingBox() - Method in class chemaxon.marvin.space.MoleculeComponent
Computes the bounding box of the visible atoms of the molecule, and adds 2 angstroms to each side.
setBounds(int, int, int, int) - Method in class chemaxon.marvin.space.GraphicScene
Moves and resizes this component.
setBracketOrientation(int) - Method in class chemaxon.struc.graphics.MBracket
Sets the orientation of the bracket.
setBridgehead(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing bridgehead H
setBridgingRAllowed(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets whether different undefined R-atoms can match the same group of atoms.
setBuiltInColorMapperMethod(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Selection of built-in color palettes through their identifier.
setBuiltInColorMapperMethod(int, boolean) - Method in class chemaxon.marvin.space.SurfaceColoring
Selection of built-in color palettes through their identifier.
setByteOrder(ByteBuffer) - Method in class chemaxon.marvin.io.PositionedInputStream
 
setC(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane
Sets the state of a checkbox in a GridBagView table.
setCacheCapacity(int) - Method in class chemaxon.marvin.view.MDocStorage
Sets the maximum number of cached documents.
setCalcAlways(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
replaced by setModel(int)
setCalculateEnergy(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the calculation of dreiding energy.
setCalculateForLEConformer(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the condition for lowest energy conformer calculation before geometry calculations are processed.
setCalculateMMFF94Energy(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the calculation of MMFF94 energy.
setCalculateMoleculeProjections(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the calculation of molecule projections.
setCalculateVolume(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
setCanceled(boolean) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Sets whether the process is cancelled
setCarbonVisibility(String) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility style of the C labels on Carbon atoms.
setCationic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the cationic property of the PharmacophorePoint.
setCellDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicCell
Sets the drawing properties of all components of the cell.
setCellDrawProperty(int, String, String) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given draw property to the given cell.
setCellIndex(int) - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Sets the internal index of the cell.
setCellIndex(int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Sets the viewer cell index.
setCellProperty(String, String) - Method in class chemaxon.marvin.space.MSpaceEasy
Sets a draw property of MarvinSpace that will affect the active cell only.
setCellSize(int) - Method in class chemaxon.descriptors.MDParameters
Sets the size (number of bits) of the bins (cells).
setCellSize(Dimension) - Method in class chemaxon.marvin.view.swing.TableSupport
Sets the molecule cell size for GridBagView.
setCellwiseWeights(boolean) - Method in class chemaxon.descriptors.MDParameters
Sets boolean telling whether cell weights are to be generated for current parametrized metric.
setCenter(float[]) - Method in class chemaxon.marvin.space.monitor.Control
Sets the center of the transformation.
setCenterMolecule(boolean) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Center the molecule before MD calculation (It is not set by default.)
setCentralAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Sets the central atom of this sgroup.
setChangeSupport(PropertyChangeSupport) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Sets the changeSupport
setCharge(int) - Method in class chemaxon.struc.MolAtom
Sets the charge.
setCharge(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the charge of an ion.
setChargeAngle(double) - Method in class chemaxon.struc.MolAtom
To be called when user changes charge position.
setCharged(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing charged H
setChargeFont(Font) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
in Marvin 15.5.18
setChargeLocation(int) - Method in class chemaxon.struc.Sgroup
Sets the charge location attribute of the S-group.
setChargeMatching(int) - Method in class chemaxon.sss.search.SearchOptions
Set charge matching behaviour.
setChargeWithCircle(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility of Charge with Circle
setCheck3DStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets the 3D stereo conformation checking of the structure.
setCheckerConfigFileName(String) - Method in class chemaxon.marvin.common.UserSettings
Deprecated, for removal: This API element is subject to removal in a future version.
Use UserSettings.setCheckerConfigURL(String) instead. Deprecated in 5.12 Sets the name of the configuration file for StructureChecker in marvin sketch
setCheckerConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the URL of the configuration for Checkers in marvin sketch.
setCheckSpHyb(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets whether the sp-hybridization state of the atoms should be considered.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Deprecated.
For internal use only.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Deprecated.
For internal use only.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Deprecated.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.logDPlugin
Deprecated.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Deprecated.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Deprecated.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Deprecated.
For internal use only.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.pKaPlugin
Deprecated.
For internal use only.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Deprecated.
For internal use only.
setChemicalTermsArgument(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated.
For internal use only.
setChemicalTermsParameters(Properties, String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated.
For internal use only.
setChemTermsFilter(String) - Method in class chemaxon.sss.search.SearchOptions
Sets the Chemical Terms filtering expression.
setChemTermsFilterConfig(File) - Method in class chemaxon.sss.search.SearchOptions
Sets the configuration file for Chemical Terms filter.
setChemTermsFilterConfig(String) - Method in class chemaxon.sss.search.SearchOptions
Sets the configuration string for Chemical Terms filter.
setChemTermsFilterOption(ChemTermsFilterOption) - Method in class chemaxon.sss.search.SearchOptions
FOR INTERNAL USE ONLY.
setChirality(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction
Sets the chirality value of absolute stereo action
setChirality(int, int) - Method in class chemaxon.struc.MoleculeGraph
Set chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
setChirality(Map<Integer, Integer>) - Method in class chemaxon.struc.MoleculeGraph
Sets the chiralities of atoms.
setChiralitySupport(int) - Method in class chemaxon.marvin.beans.MarvinPane
Sets chirality support to show or hide the R/S labels.
setChiralitySupport(int) - Method in class chemaxon.marvin.MolPrinter
Sets the chirality display mode.
setChiralitySupport(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the chirality support parameter.
setClassification(NMRCoefficient.ErrorClassification) - Method in class chemaxon.calculations.nmr.Shift
Sets the error classification of the stored chemical shift.
setClassName(String) - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
Sets the full class name of the service
setClassName(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Sets the name of the standardizer class
setClean(int, String) - Method in class chemaxon.formats.MolExporter
Sets molecule cleaning in exporter.
setClean(int, String, MolFilter) - Method in class chemaxon.formats.MolExporter
Sets molecule cleaning in exporter.
setClean2dOpts(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the 2D cleaning options.
setClean3dOpts(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the 3D cleaning options.
setCleanDim(int) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the space dimensions for cleaning.
setCleanHOption(boolean) - Method in class chemaxon.marvin.common.UserSettings
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.4, replaced by UserSettings.setCleanHOptionEnabled(boolean)
setCleanHOptionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets to add an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.
setCleanResultStructures(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets 2D cleaning of the result structures: if true then resonants returned by ResonancePlugin.getStructure(int) and ResonancePlugin.getStructures() methods are cleaned in 2D.
setCleanResultStructures(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
obsolete method
setCleanTemplates(Standardizer, Molecule[]) - Static method in class chemaxon.standardizer.StandardizerUtil
Sets the default clean templates.
setClearClipboardBeforeExport(boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Sets whether the subsystem should clear the clipboard before a copy operation.
setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the Cl- concentration (default: 0.1).
setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the Cl- concentration (default: 0.1).
setCloseEnabled(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Set the accessibility of the Close menu item in the File menu.
setColor(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the constant color of the component.
setColor(float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the constant color of the component.
setColor(float[]) - Method in class chemaxon.marvin.space.SurfaceComponent
Sets the constant color of the surface.
setColor(float, float, float) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the constant color of the component.
setColor(float, float, float) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the constant color of the component.
setColor(int, int, int) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the constant color of the component.
setColor(AlignmentProperties.ColoringScheme) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
sets which atomtypes to use.
setColor(Color) - Method in class chemaxon.marvin.space.ComponentElement
Assignes a color to the CompnentElement.
setColor(Color) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the constant color of the component.
setColor(Color) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
setColor(Color) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the constant color of the component.
setColor(Color) - Method in class chemaxon.marvin.space.SurfaceComponent
Sets the constant color of the surface.
setColor(Color) - Method in class chemaxon.struc.MObject
Sets the color of the object.
SETCOLOR_COLORLESS - Static variable in class chemaxon.struc.MDocument
The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.
SETCOLOR_DEFAULT - Static variable in class chemaxon.struc.MDocument
Default set colors are used for coloring the atom/bond set.
SETCOLOR_SPECIFIED - Static variable in class chemaxon.struc.MDocument
The user specified set colors are used for coloring the atom/bond set.
setColoring(int) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets hit coloring options.
setColoringScheme(AlignmentProperties.ColoringScheme) - Method in class chemaxon.marvin.alignment.Alignment
 
setColorScheme(String) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the color scheme.
setColorScheme(String) - Method in class chemaxon.marvin.MolPrinter
Sets the color scheme.
setColumnCount(int) - Method in class chemaxon.marvin.beans.MViewParams
Sets the nuber of columns.
setColumnWidth(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the default column width.
setColumnWidth(int, int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the default width of a specified column.
setComment(String) - Method in class chemaxon.struc.Molecule
Sets the comment.
setComment(String) - Method in class chemaxon.struc.RgMolecule
Sets the comment of the root molecule.
setCompleteHG(boolean) - Method in class chemaxon.sss.search.SearchOptions
Deprecated, for removal: This API element is subject to removal in a future version.
This option is no longer supported. This method does not change anything.
setComponent(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.Control
Sets the component to the transformation.
setComponent(GraphicComponent) - Method in class chemaxon.marvin.space.monitor.DihedralControl
Sets the affecting component of the DihedralControl which has to be a MoleculeComponent.
setComponentIndex(int) - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Warning: for internal use only.
setComponentProperty(Object, String, String) - Method in class chemaxon.marvin.space.MSpaceEasy
Sets a draw property of MarvinSpace that will affect only the given component.
setConfiguration(StandardizerConfiguration) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setConfiguration(StandardizerConfiguration) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets the configuration of the runner
setConfigurationReader(ConfigurationReader) - Method in interface chemaxon.checkers.runner.CheckerRunner
Sets a new configuration for the Runner.
setConfigurationReader(StandardizerConfigurationReader) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setConfigurationReader(StandardizerConfigurationReader) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets a new configuration for the runner.
setConfirmExit(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Sets to drop confirmation dialog about exit or not.
setConformerCount(int) - Method in class chemaxon.marvin.alignment.Alignment
The the dihedral angles of every flexible molecule should be randomized before alignment.
setConformerCount(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
setConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects connection count atom query properties or not.
setConnectivity(int) - Method in class chemaxon.struc.Sgroup
Sets S-group connectivity.
setConsiderHPLCEffect(boolean) - Method in class chemaxon.marvin.calculations.logDPlugin
 
setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets to consider tautomerization.
setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets to consider tautomerization in calculation.
setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets to consider tautomerization.
setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets to consider tautomerization.
setConstantAtomRadius(float) - Method in class chemaxon.marvin.space.SurfaceColoring
In case of {#RADIUS_CONSTANT} mode the constant radius can be set.
setConstantDistanceRadius(float) - Method in class chemaxon.marvin.space.SurfaceColoring
In case of distance weighted property values constant radius can be set.
setContext(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the context of this data sgroup.
setContext(CodeAssistDataProvider.Context) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the evaluation context
setContext(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the context of this data sgroup.
setContexts(int, int, int, int, int, GL2, GLU) - Method in class chemaxon.marvin.space.GraphicCell
Sets the indices of row and column of the scene in which this cell is in, and sets the GL2 related variables to be able to draw.
setControl(Control) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Sets the control of the monitor, and the center of the control to the center of the monitor.
setControl(DihedralControl) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Sets a DihedralControl to the monitor.
setConvergenceLimit(double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
setCoordDependent(long) - Method in class chemaxon.struc.MProp
Sets the property as coordinate dependent.
setCoordinateBondStyle(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the "coordinative" bond line style when both atoms are single.
setCoordinateBondStyle(String) - Method in class chemaxon.marvin.MolPrinter
Set the coordinate bond line style when both atoms are single.
setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the "coordinative" bond line style when one of the atoms is multicenter.
setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.MolPrinter
Set the coordinate bond line style.
setCoordinates(float[]) - Method in class chemaxon.marvin.space.ComponentElement
Sets the coordinates of the ComponentElement.
setCoordinates(Object, int) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
setCopolymerMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Adjusts copolymer matching mode.
setCopyAsFormat(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the selected format in the Copy As dialog.
setCorners(double, double, double, double) - Method in class chemaxon.struc.MolAtom
Used internally by MolPainter.
setCorners(MPoint, MPoint) - Method in class chemaxon.struc.graphics.MRectangle
Sets the corners.
setCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
setCorrectionData(PKaTrainingResult) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets correction data for calculation
setCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets the correction library.
setCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the correction library.
setCorrectionLibraryPath(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets the correction library file directly.
setCorrectionLibraryPath(String) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the correction library file directly.
setCount(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setCount(int) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
setCount(int) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setCoupled(boolean) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Coupled/decoupled spectrum.
setCouplingConstants(double[][]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets coupling constants.
setCouplingNeeded(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets whether spin-spin couplings are taken into account.
setCreateStatistics(boolean) - Method in class chemaxon.descriptors.MDGenerator
Toggles the create statistics flag.
setCreateStatistics(boolean) - Method in class chemaxon.descriptors.MDParameters
Toggles the create statistics flag of the MDGenerator object.
setCrossingBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Change the crossing bond of an attachment point.
setCTCrossedBond(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Convert wiggly type double bonds to crossed.
setCTWigglyBond(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Convert crossed double bonds to wiggly type.
setCTWigglyBond(MoleculeGraph, int) - Static method in class chemaxon.marvin.util.CleanUtil
Convert crossed double bond to wiggly type.
setCurrentDefaultFontMetrics(FontMetrics) - Method in class chemaxon.struc.graphics.MTextBox
Sets the current height of the text..
setCurrentFont(MFont, int) - Method in class chemaxon.struc.graphics.MTextBox
Sets font for selected text or the next character to be typed.
setCurrentForeground(Color) - Method in class chemaxon.struc.graphics.MTextBox
Sets color for selected text or the next character to be typed.
setCurrentHeight(double) - Method in class chemaxon.struc.graphics.MTextBox
Sets the current height of the text..
setCurrentParametrizedMetric(int) - Method in class chemaxon.descriptors.MDParameters
Selects the specified parametrized metric to be the current.
setCurrentParametrizedMetric(int) - Method in class chemaxon.descriptors.PFParameters
Selects a metric to be used.
setCurrentTextAttributes(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextBox
Sets the attributes for the selected text or the next character to be typed.
setCurrentWidth(double) - Method in class chemaxon.struc.graphics.MTextBox
Sets the current height of the text..
setCursorPos(int, boolean) - Method in class chemaxon.struc.graphics.MTextBox
Sets the cursor position.
setCursorRow(int) - Method in class chemaxon.struc.graphics.MTextBox
Sets the cursor row number.
setCustomHtmlToXmlConverter(XmlToHtmlConverter) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Provide a custom converter from XML to HTML, to be used instead of the default one.
setCustomName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the customName
setD2SOptions(String) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Sets the options string to use for document annotation.
setData(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the data value to be set.
setDataCollectionConsent(Consent) - Method in class chemaxon.marvin.common.UserSettings
 
setDataDetached(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets whether the data should be displayed close to the objects or separately (detached).
setDataLine(int, String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets a line of data.
setDebug(int) - Method in class chemaxon.marvin.beans.MarvinPane
Switches on the debug messages.
setDefaultFont(MFont) - Method in class chemaxon.struc.graphics.MTextDocument
Sets the default font.
setDefaultFont(JEditorPane) - Static method in class chemaxon.marvin.util.SwingUtil
Sets the SWING default font in the JEditorPane.
setDefaultNodeWeightBehavior(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.marvin.alignment.Alignment
 
setDefaultSaveFormat(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default molecule format in the "Save As" dialog.
setDehidrogenize(boolean) - Method in class chemaxon.marvin.alignment.MinMaxDistance
Deprecated, for removal: This API element is subject to removal in a future version.
setDehidrogenize(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
The explicit Hydrogens are not removed from the original input structure. No need to use.
setDehydrogenize(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set dehydrogenize parameter
setDependentRgroupDefinition(int, int) - Method in class chemaxon.struc.RgMolecule
Sets the dependent R-group definition (rgroupIndexThen) for the referenced R-group definition (rgroupIndexIf).
setDescription(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setDescription(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setDescription(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setDescription(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the description of the concerning checker
setDescription(String) - Method in class chemaxon.fixers.AbstractStructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
setDescription(String) - Method in interface chemaxon.fixers.StructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
setDescription(String) - Method in class chemaxon.fixers.StructureFixerDescriptor
Sets the description of the concerning fixer
setDescription(String) - Method in class chemaxon.marvin.space.ComponentElement
Sets a brief description to the ComponentElement that will be returned by {#getDescription()}.
setDescription(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the description of the action
setDescriptor(T) - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
Updates the editor to represent the specified descriptor NOTE: ServiceDescriptorEditor.getDescriptor() may NOT return same instance
setDescriptorURI(String) - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
Sets the URI of the JSON RPC descriptor file
setDesiredBufferSize(int) - Method in class chemaxon.marvin.io.PositionedInputStream
Sets desired buffer size.
setDetachable(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Sets the detachable property.
setDetectCumulatedDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker
Sets the detectCumulatedDoubleBonds property
setDetectTransDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker
Sets the detectTransDoubleBonds
setDetectTripleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker
Sets the detectTripleBonds property
setDiameter(int) - Method in class chemaxon.descriptors.ECFPParameters
Sets the diameter parameter.
setDiaStereoIsomerMixtureAllowedState(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
setDim(int) - Method in class chemaxon.struc.Molecule
Sets the dimension.
setDim(int) - Method in class chemaxon.struc.MoleculeGraph
Sets the dimension.
setDim(int) - Method in class chemaxon.struc.RgMolecule
Sets the dimension of the root structure and the R-groups.
setDim(int) - Method in class chemaxon.struc.RxnMolecule
Sets the dimension for all the structures.
setDirectory(File) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the working directory, if the Load/Save is in Last Opened Mode.
setDirty(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets or clears the dirty flag.
setDisabledGroupTypes(List<String>) - Method in class chemaxon.marvin.beans.MSketchPane
 
setDisplayChargeWithCircle(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setDisplayedChars(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the number of characters to be displayed (1...999 or 0 for no restriction)
setDisplayedLines(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the number of lines to be displayed (0: show all)
setDisplayLonePairsAsLine(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setDisplayQuality(int) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 6.4 only high quality exists
setDispopts(int) - Method in class chemaxon.marvin.beans.MarvinPane
Sets display options.
setDispopts(int) - Method in class chemaxon.marvin.MolPrinter
Modifies the display options in the advanced way of handling display options.
setDispopts(int, int) - Method in class chemaxon.marvin.MolPrinter
Modifies the display options as in MolPrinter.setDispopts(int), but affects only limited display options using a mask.
setDispoptsExt(int) - Method in class chemaxon.marvin.MolPrinter
Modifies the extended display options in the advanced way of handling display options.
setDispoptsExt(int, int) - Method in class chemaxon.marvin.MolPrinter
Modifies the extended display options as in MolPrinter.setDispoptsExt(int), but affects only limited display options using a mask.
setDistanceRadiusExtension(float) - Method in class chemaxon.marvin.space.SurfaceColoring
In case of distance weighted property values radius extension can be set.
setDistanceRadiusMode(int) - Method in class chemaxon.marvin.space.SurfaceColoring
In case of distance weighted property values the distance computation can be set differently from the property radius but in the same way.
setDistinctFirstAtomMatching(boolean) - Method in class chemaxon.sss.search.MolSearchOptions
Option ensuring that upon the findNext() call the first atom must be stepped as well.
setDiversity(double) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the diversity limit for the calculation.
setDoc(MDocument) - Method in class chemaxon.marvin.MolPrinter
Sets the current document and calculates its bounds.
setDocSource(MDocSource, int, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets the document source.
setDocument(int, MDocument) - Method in class chemaxon.marvin.beans.MViewPane
Sets the document
setDocument(int, MDocument) - Method in class chemaxon.marvin.view.swing.TableSupport
Sets the k-th record directly.
setDocument(MTextDocument) - Method in class chemaxon.struc.graphics.MTextBox
 
setDocument(MDocument) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the document.
setDocumentStyleName(String) - Method in class chemaxon.marvin.common.UserSettings
 
setDocumentStyleName(String, boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setDomainMax(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets the upper end of the spectrum.
setDomainMin(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets the lower end of the spectrum.
setDominantTautomerDistributionCalculation(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets dominant tautomer distribution calculation: if true then dominant tautomer distribution is calculated.
setDonor(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the donor property of the PharmacophorePoint.
setDontRemoveLastComponent(boolean) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
setDotDirName(String) - Static method in class chemaxon.util.DotfileUtil
Sets the subdirectory name for the configuration files.
setDoubleBond(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction
Sets the double bond value of absolute stereo action
setDoubleBondStereoMatchingMode(int) - Method in class chemaxon.sss.search.SearchOptions
Sets how double bond cis/trans stereo information should match during the search.
setDoublePrecision(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the double -> string conversion precision (maximal number of fraction digits) with zero-padding (12.56 -> 12.5600 if precision=4).
setDoublePrecision(int, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the double -> string conversion precision (maximal number of fraction digits).
setDoublePrecision(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the precision in the decimal format.
setDownWedge(String) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the wedge bond display convention.
setDownWedge(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the convention to use for displaying a down wedge.
setDownWedge(String) - Method in class chemaxon.marvin.MolPrinter
Set the down wedge orientation.
setDraggable(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Allows or denies mouse dragged events in cells.
setDraggedObject(MObject) - Method in class chemaxon.struc.MDocument
Sets the dragged object.
setDrawing(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
 
setDrawingPrimitiveType(int) - Method in class chemaxon.marvin.space.SurfaceComponent
Sets the type of drawn primitives.
setDrawingPrimitiveType(int, int) - Method in class chemaxon.marvin.space.SurfaceComponent
Sets the type of drawn primitives.
setDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent
Forces the component to set all drawing property stored in drawProperties, and loose every old setting.
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicCell
Sets the drawing properties of all components of the cell.
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicComponent
This is the gate of draw properties from outside to the component.
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicScene
Sets the draw property for all cells.
setDrawProperty(String, String) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
This is the gate of draw properties from outside to the component.
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.MoleculeComponent
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.monitor.Label
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets drawing properties specific to PharmacophoreSphere.
setDrawProperty(String, String) - Method in class chemaxon.marvin.space.SurfaceComponent
This is the gate of draw properties from outside to the component.
setDrawProperty(String, String, int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the draw property either to the entire scene or to the active cell.
setDrawProperty(String, String, MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the given draw property to the given visualizer.
setDrawProperty(Properties) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given draw properties to the entire scene.
setDrawSphere(boolean) - Method in class chemaxon.marvin.space.GraphicCell
Enables/disables drawing of the rotation sphere.
setDrawType(String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets current drawing type.
setDrawType(String) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets current drawing type.
setDrawType(String) - Method in class chemaxon.marvin.space.SurfaceComponent
Sets the drawing type of the surface.
setDropTarget(DropTargetListener) - Method in class chemaxon.marvin.space.GraphicScene
Sets the DropTarget of the graphic canvas.
setEditable(boolean) - Method in class chemaxon.standardizer.advancedactions.TransformAction
Sets if this action is editable.
setEditable(int) - Method in class chemaxon.marvin.beans.MViewEditor
Sets the mode that determines if the structure is editable.
setEditable(int) - Method in class chemaxon.marvin.beans.MViewPane
Sets the mode that determines if the structure is editable.
setEditorClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the editorClassName
setEditorClassName(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the editorClassName
setEditorClassName(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Sets the name of the editor of the standardizer class
setElectronIndex(String, int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
setElectronProp(int) - Method in class chemaxon.struc.MolAtom
Sets the number of lone pairs.
setElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
 
setEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Enables or disables this component, depending on the value of the parameter b.
setEnabled(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Enables or disables this component, depending on the value of the parameter b.
setEnabledT(int, int, boolean) - Method in class chemaxon.marvin.view.MDocStorage
Set the enabled state of a text field in a record.
setEnableStandardization(boolean) - Method in class chemaxon.descriptors.RFParameters
Sets if standardization is applied.
setEnableTranslateAndRotate(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
setEncoding(Encoding) - Method in class chemaxon.marvin.io.PositionedInputStream
Sets the encoding.
setEncoding(String) - Method in class chemaxon.marvin.io.PositionedInputStream
Sets the encoding.
setEncoding(String, String) - Method in class chemaxon.marvin.io.MolExportModule
Sets the output encoding using the export options.
setEncodings(String) - Method in class chemaxon.formats.MolConverter.Builder
Sets the input and/or output encoding.
setEncodings(String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
setEndgroupMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Adjusts polymer end group matching.
setEndPosition(long) - Method in class chemaxon.struc.MDocument
Sets the end position of this document in the input file.
setEndPosition(long) - Method in class chemaxon.struc.Molecule
Sets the end position of this molecule in the input file.
setEnforceAbsStereo(boolean) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
setEnrtyRadiusMode(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Atom properties will effect surface vertices being closer than a certain radius.
setEnumCodeNeeded(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Indicates whether unique Markush enumeration code should be generated.
setEnumerateHomology(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets if homology groups should be enumerated or not.
setErrorProcessor(ErrorProcessor) - Method in class chemaxon.formats.MolExporter
Sets the error handler interface for concurrent mode.
setEuler(double, double, double) - Method in class chemaxon.struc.CTransform3D
Sets the rotational component using the Euler angles provided.
setExact(boolean) - Method in class chemaxon.standardizer.advancedactions.TransformAction
Sets the exact value of the action
setExactBondMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Specifies whether bond types should match exactly - looking for query bonds target.
setExactQueryAtomMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets whether exact query atom matching should be used or not.
setExactSpecialAtomMatching(String) - Method in class chemaxon.sss.search.SearchOptions
Sets the identifiers of those special atoms that should match exactly during structure comparison.
setExcludeAntiAromaticCompounds(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets whether antiaromatic compounds should be generated.
setExcluded(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the excluded property of the PharmacophorePoint.
setExcluded(AtomLabels) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Sets the abbreviations to be excluded
setExcluded(AtomLabels) - Method in class chemaxon.checkers.PseudoAtomChecker
 
setExcluded(DataExclusionList) - Method in class chemaxon.checkers.AttachedDataChecker
 
setExcludeHalogens(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets if halogens should be excluded from hydrogen bond acceptors.
setExcludePhosphorus(boolean) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Sets to exclude phosphorus from PSA calculation.
Default: true, phosphorus i excluded.
setExcludeString(String) - Method in class chemaxon.standardizer.actions.ContractSgroupsAction
 
setExcludeString(String) - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction
 
setExcludeString(String) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
setExcludeSulfur(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets if sulfur atom should be excluded from hydrogen bond acceptors.
setExcludeSulfur(boolean) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Sets to exclude sulfur from PSA calculation.
Default: true, sulfur i excluded.
setExclusionRegexp(boolean) - Method in class chemaxon.checkers.AttachedDataChecker
Sets if the descriptor of the excluded-data (AtomLabels) should be treated as a regular expression (see also: AttachedDataChecker.isExclusionRegexp()
setExclusiveColor(byte[]) - Method in class chemaxon.marvin.space.SurfaceComponent
Vertices having the given color will not be drawn and also their neighbouring vertices belonging to the same primitive.
setExclusiveDrawing(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Enables/disables exclusive drawing, see SurfaceComponent.setExclusiveColor(byte[]).
setExclusiveDrawing(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
Enables/disables exclusive drawing, see SurfaceComponent.setExclusiveColor(byte[]).
setExhaustiveModeLimit(int) - Method in class chemaxon.sss.search.SearchOptions
Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
setExperimentalEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Enable or disable experimental features.
setExpertMode(boolean) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the expert mode
setExplicitConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects explicit connection count atom query properties or not.
setExplicitH(boolean) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.
setExplicitHVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.
setExpression(String) - Method in class chemaxon.marvin.services.DynamicArgument
Sets the expression
setExternalCheckerConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the URL of the configuration file containing the list of external Checkers in marvin sketch.
setExtraLabel(String) - Method in class chemaxon.struc.MolAtom
Sets the extra atom label (also called atom value): "label" or "label1|label2".
setExtraLabelColor(int, int) - Method in class chemaxon.struc.MolAtom
Sets the extra label colors: lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
setExtraLabelColor(long) - Method in class chemaxon.struc.MolAtom
Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
setExtraLabelColorsForDocument(Molecule) - Method in class chemaxon.struc.MDocument
Sets the coloring mode sets and colors of extra labels
setExtraLabelSetColorMode(int, int) - Method in class chemaxon.struc.MDocument
 
setExtraLabelSetRGBs(int, int) - Method in class chemaxon.struc.MDocument
 
setExtraLabelSetRGBs(int, int, int) - Method in class chemaxon.struc.MDocument
 
setExtraLabelSetSeq(int) - Method in class chemaxon.struc.MolAtom
 
setEZLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility state of absolute double bond stereo configuration labels.
setEzVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the E/Z display option.
setEzVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.2, replaced by MolPrinter.setEZLabelsVisible(boolean)
setEZVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
Show or hide E/Z labels
setField(int, Molecule, String, MProp) - Method in class chemaxon.marvin.io.MFieldAccessor
Sets a property.
setFieldAccessor(MFieldAccessor) - Method in class chemaxon.marvin.view.MDocStorage
Sets the field accessor.
setFieldFont(String, Font) - Method in class chemaxon.marvin.beans.MViewPane
Sets the font for a named field in a table.
setFieldFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the field font size.
setFieldName(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the data field name.
setFields(int, Molecule, String[], MProp[]) - Method in class chemaxon.marvin.io.MFieldAccessor
Sets properties.
setFields(String[]) - Method in class chemaxon.formats.MolConverter.Builder
Sets the included fields to be shown in a table.
setFields(String[]) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
setFieldsShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
Show or hide SDfile fields in the table
setFieldType(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the field type.
setFieldType(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the field type from string representation.
setFile(File) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the current molecule file but does not load it.
setFilter(MolFilter) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets the molecule filter.
setFilter(MolFilter) - Method in class chemaxon.marvin.util.MolFragLoader
Sets the fragment filter.
setFinalClean() - Method in class chemaxon.standardizer.Standardizer
Deprecated, for removal: This API element is subject to removal in a future version.
setFinalClean(int) - Method in class chemaxon.standardizer.Standardizer
Deprecated, for removal: This API element is subject to removal in a future version.
setFinalClean(int, boolean) - Method in class chemaxon.standardizer.Standardizer
Deprecated, for removal: This API element is subject to removal in a future version.
setFinalClean(StandardizerConfiguration) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility
Deprecated, for removal: This API element is subject to removal in a future version.
It's not required anymore.
setFinalClean(StandardizerConfiguration, int) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility
Deprecated, for removal: This API element is subject to removal in a future version.
It's not required anymore.
setFinalClean(StandardizerConfiguration, int, boolean) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility
Deprecated, for removal: This API element is subject to removal in a future version.
It's not required anymore.
setFinalStereoFix(boolean) - Method in class chemaxon.standardizer.Standardizer
Sets to perform final stereo fixes.
setFingerprint(int[]) - Method in class chemaxon.jep.context.MolContext
Sets the fingerprint of the input molecule.
setFingerprintGenerator(FingerprintGenerator) - Method in class chemaxon.jep.Evaluator
Sets the fingerprint generator object (needed for query strings).
setFiveLongRings(List<List<MolAtom>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
This method sets the fiveLongRings property.
setFixed(int) - Method in class chemaxon.marvin.view.MDocStorage
Sets a document as fixed.
setFixerClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the fixerClassName
setFixMode(FixMode) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the fixMode
setFlags(int) - Method in class chemaxon.struc.graphics.MPolyline
Sets the flags.
setFlags(int) - Method in class chemaxon.struc.MolAtom
Sets the flags.
setFlags(int) - Method in class chemaxon.struc.MolBond
Sets bond type (4 bit), stereo (2+2+1 bit), topology (2 bit) bond set (5 bit) and reacting center (7 bits) information.
setFlags(int) - Method in class chemaxon.struc.MoleculeGraph
Sets the flags of the molecule.
setFlags(int) - Method in class chemaxon.struc.RgMolecule
Sets the dimension and chiral flags.
setFlags(int, int) - Method in class chemaxon.struc.MolAtom
Sets the flags.
setFlags(int, int) - Method in class chemaxon.struc.MolBond
Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit) information.
setFlags(int, int) - Method in class chemaxon.struc.MoleculeGraph
Sets specified bits in the flags.
setFlags(int, int) - Method in class chemaxon.struc.RgMolecule
Sets specified bits in the flags.
setFlexible(boolean) - Method in class chemaxon.descriptors.ShapeParameters
 
setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
 
setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
 
setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setFlipped(boolean) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the flip property of this sgroup.
setFocus(MObject) - Method in class chemaxon.struc.MDocument
Focus to the specified object.
setFogFactor(int) - Method in class chemaxon.marvin.common.UserSettings
Sets the fog factor.
setFontScale(double) - Method in class chemaxon.struc.graphics.MTextBox
Sets the font scaling factor.
setForcedFlexible(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
setForceField(String) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the force field type.
setForegroundColor(Color) - Method in class chemaxon.marvin.space.monitor.Label
Sets the color of the characters on the label.
setFormat(String) - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
Sets the dipole export format.
setFormat(String) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Sets the spectrum export format.
setFormat(String) - Method in class chemaxon.formats.MolInputStream
Sets the molecule file format.
setFormat(String) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the default molecule file format.
setFormat(String) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
setFormulaRecognition(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Recognizes the molecular formulas in pseudo labels.
setForSpecIsotopeSymbol(String) - Method in class chemaxon.struc.MolAtom
Deprecated.
setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Sets NMR measurement frequency.
setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets the NMR measurement frequency.
setFromSgroupCopy(SgroupAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
Make a copy of this S-group superatom.
setFuzzinessFactor(float) - Method in class chemaxon.descriptors.PFParameters
Sets the value of the fuzziness factor, used in fuzzy bipolar pharmacophore autocorrelogram (FBPA) based convolution product in non-parametrized (generic) FBPA metric.
setFuzzyCutOff(float) - Method in class chemaxon.descriptors.PFParameters
 
setFuzzyLowerBound(int) - Method in class chemaxon.descriptors.PFParameters
 
setFuzzySmoothingFactor(float) - Method in class chemaxon.descriptors.PFParameters
Sets the value of the fuzzy smoothing factor used in the generation of fuzzy fingerprints.
setGenerateCASNumber(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Sets CAS number name generation.
setGenerateDistanceRanges(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Generate intermolecular atomic distance ranges by tweaking conformation.
setGeneratePreferredIUPACName(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Sets preferred IUPAC name generation.
setGenerateTraditionalIUPACName(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Sets traditional IUPAC name generation.
setGenNameFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the IUPAC name font size.
setGenNameShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
Set visibility of IUPAC names.
setGeom3D(boolean) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Sets 3D geometry consideration.
setGL(GL2, GLU) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the GL2 rendering environment.
setGL(GL2, GLU) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
setGL(GL2, GLU) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets GL2 in all of its visualizers.
setGL(GL2, GLU) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
setGL(GL2, GLU) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets drawing related variable.
setGlobalChecker(TaggedCalculatorInputChecker) - Static method in interface chemaxon.calculator.TaggedCalculator
Sets the global input checker that will be used by all calculators implementing this interface.
setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.beans.MarvinPane
 
setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.io.MolExportModule
Pass and set the global GUI properties container.
setGrabbingEnabled(boolean) - Method in class chemaxon.formats.MolImporter
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.2. It has no effect on the code.
setGraphInvariantVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the graph invariant visibility
setGridVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setGrinv(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.5, use setGrinvVisible(boolean) instead
setGrinvCC(long) - Method in class chemaxon.struc.MoleculeGraph
Sets the graph invariant change count.
setGrinvOptions(int) - Method in class chemaxon.struc.MoleculeGraph
Sets graph invariant calculation options passed to the module.
setGrinvVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Shows or hides the graph invariants.
setGroupIndices(List<Integer>) - Method in class chemaxon.checkers.result.DataSgroupCheckerResult
 
setGroups(Map<String, Molecule>) - Method in class chemaxon.standardizer.actions.AliasToGroupAction
Sets the abbreviated groups of the action
setGUIContracted(boolean) - Method in class chemaxon.struc.Molecule
Deprecated.
setGUIContracted(boolean, int) - Method in class chemaxon.struc.Molecule
Deprecated.
setGUIMode(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used.
setGUIPropertyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument
Sets the property container storing MarvinPane settings
setGUIProperyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument
Deprecated, for removal: This API element is subject to removal in a future version.
setGUIStateRecursively(boolean) - Method in class chemaxon.struc.Sgroup
Deprecated.
as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality
setGUIStateRecursively(boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated.
setGUIStateRecursively(boolean, int) - Method in class chemaxon.struc.Sgroup
Deprecated.
as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality
setHalfWidth(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets NMR half-width.
setHconnected(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing H connected H
setHCountMatching(int) - Method in class chemaxon.sss.search.SearchOptions
Sets the H count matching mode.
setHeadCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the head crossing bonds.
setHeaderCellSize(int, int) - Method in class chemaxon.marvin.beans.MViewParams
Sets a logical cell extent by interpreting rows and columns as part of a sub-table.
setHelpText(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setHelpText(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setHelpText(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setHelpText(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the help text of the concerning checker
setHelpText(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the help text displayed on empty component
setHelpText(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the help text of the action
setHighlighted(boolean) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
setHighlighted(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
This functionality is currently unavailable.
setHighlighted(boolean) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the component to be highlighted.
setHighlighted(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the highlighted state of the pharmacophore point.
setHitIndexType(int) - Method in class chemaxon.sss.search.MolSearchOptions
Set the representation to use for hit indexes in case of Markush search.
setHitOrdering(int) - Method in class chemaxon.sss.search.SearchOptions
Sets the hit ordering type.
setHomogeneousPaletteColors(byte[][]) - Method in class chemaxon.marvin.space.SurfaceColoring
This is an easy way to create a homogenous palette and use it as a color mapper.
setHomologyBroadTranslation(HomologyTranslationOption) - Method in class chemaxon.sss.search.SearchOptions
Adjusts for which query atoms broad translation on target homology groups is allowed.
setHomologyNarrowTranslation(HomologyTranslationOption) - Method in class chemaxon.sss.search.SearchOptions
Adjusts for which query homology atoms narrow translation on target specific atoms is allowed.
setHorizontalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox
Sets the horizontal alignment.
setHybridizationState(int) - Method in class chemaxon.struc.MolAtom
Sets the hybridization state.
setHybridizationState(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the hybridization state of an atom.
setHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects hydrogen count atom query properties or not.
SetHydrogenIsotopeSymbolAction - Class in chemaxon.standardizer.actions
Set hydrogen isotope symbol standardizer action
SetHydrogenIsotopeSymbolAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
Initializes the action
SetHydrogenIsotopeSymbolAction.Type - Enum Class in chemaxon.standardizer.actions
Hydrogen isotope representation type
setHydrogenize(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set hydrogenize parameter
setHydrophobic(boolean) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets or clears the hydrophobic property of the PharmacophorePoint.
setHyperfine(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the hyperfine option for calculation.
setIcon(Icon) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setIcon(Icon) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setIcon(Icon) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setIconImage(JFrame) - Static method in class chemaxon.marvin.space.MSpaceEasy
Sets the MarvinSpace icon to the frame.
setIconPath(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the icon path
setIconPath(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the path of icon associated to the action
setId(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the id of the action
setId(String) - Method in class chemaxon.struc.Molecule
 
setId(String) - Method in class chemaxon.struc.Sgroup
 
setID(String) - Method in class chemaxon.standardizer.AbstractStandardizerAction
Sets the identifier string of the standardizer action
setID(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Sets the id of the standardizer class
setIDBackgroundRGBA(int, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets the background color's RGBA value in a record.
setIdentifier(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the checker identifier
setIdentifier(String) - Method in class chemaxon.fixers.StructureFixerDescriptor
Sets the fixer identifier
setIdentity() - Method in class chemaxon.struc.CTransform3D
Makes identity transformation.
setIDForegroundRGBA(int, int) - Method in class chemaxon.marvin.view.MDocStorage
Sets the foreground color's RGBA value in a record.
setIgnoreAxialStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets ignoring axial stereo information during serching.
setIgnoreConfigurationErrors(boolean) - Method in interface chemaxon.checkers.runner.CheckerRunner
Sets whether configuration errors should be ignored on execution.
setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setIgnoreConfigurationErrors(boolean) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets whether configuration errors should be ignored
setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.standardizer.Standardizer
Sets whether the configuration errors should be ignored by the standardization process.
When configuration errors are ignored, invalid standardizer actions in the configuration are not executed, however all valid actions are to be executed.
When configuration errors are not ignored, IllegalArgumentException thrown when Standardizer.standardize(Molecule) method is called on an invalid configuration.
setIgnoreCumuleneOrRingCisTransStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets ignoring cumulene cis-trans stereo information during serching.
setIgnoreDoubleBondStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets ignoring double bond stereo information during serching.
setIgnoreError(boolean) - Method in class chemaxon.formats.MolConverter
Sets the 'ignoreError' option.
setIgnoreRotatableBonds(boolean) - Method in class chemaxon.descriptors.PFParameters
 
setIgnoreSynAntiStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets ignoring syn-anti stereo information during serching.
setIgnoreTetrahedralStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets ignoring tetrahedral stereo information during serching.
setImageImportServiceURL(String) - Method in class chemaxon.marvin.common.UserSettings
 
setImplicitH(String) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the display method of implicit hydrogens.
setImplicitH(String) - Method in class chemaxon.marvin.MolPrinter
Sets the display method of implicit hydrogens.
setImplicitHBasedOnValence(Valence) - Method in class chemaxon.struc.MolAtom
Deprecated.
as of Marvin 6.0.1, exists only for internal usage
Usage:
Internal usage only.
setImplicitHcount(int) - Method in class chemaxon.struc.MolAtom
Sets the number of implicit hydrogens.
setImplicitHcount(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the number of implicit Hydrogens.
setImplicitHMatching(int) - Method in class chemaxon.sss.search.SearchOptions
Set option for matching implicit and explicit hydrogens.
setImplicitHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects implicit hydrogen count atom query properties or not.
setImplicitHydrogenMode(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets implicit hydrogen mode.
setImplicitMul(boolean) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
This option will be removed without replacement.
setImporter(MolImporter) - Method in class chemaxon.marvin.util.MolFragLoader
Sets the fragment iterator from the specified importer.
setIn3D(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets to display the molecule in 3D.
setInactive() - Method in class chemaxon.marvin.space.GraphicCell
Deactivates this cell, so it is no longer the active cell of the scene.
setInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil
Sets the tasks with the provided ID inactive.
setIndex(int) - Method in class chemaxon.marvin.space.GraphicCell
Sets the internal index of the cell.
setIndex(int) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
Sets the index of the actual action of the configuration
setIndexOfOriginalLigand(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData
 
setIndices(int, int) - Method in class chemaxon.marvin.space.GraphicCell
Sets which row and column of the scene is this cell in.
setInitialTemperature(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the initial temperature.
setInput(Object) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Sets the input molecule.
setInput(Object) - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Sets the plugin object and the input molecule.
setInputFormat(String) - Method in class chemaxon.struc.MDocument
Sets the input file format.
setInputFormat(String) - Method in class chemaxon.struc.Molecule
Sets the input file format.
setInputFormat(String) - Method in class chemaxon.struc.RgMolecule
Sets the input file format.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ChargePlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set input molecule to process
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the input molecule.
setInputMoleculeModified(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Not used.
setInputMoleculeModified(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Not used.
setIntegrator(String) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the integrator used for calculations.
setInvisibleSets(long) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the visibility of the specified atom sets.
setIsotopeMatching(int) - Method in class chemaxon.sss.search.SearchOptions
Set the isotope matching mode.
setIsotopic(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing isotopic H
setIsValenceCheckNeeded(boolean) - Method in class chemaxon.struc.MolAtom
Sets the boolean value if MolAtom.isValenceCheckNeeded.
setIterator(MoleculeIterator) - Method in class chemaxon.marvin.util.MolFragLoader
Sets the fragment iterator.
setJar(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Sets the path of the jar containing the standardizer class
setKeepCounts(boolean) - Method in class chemaxon.descriptors.ECFPParameters
Sets the counts (multiplicity) parameter.
setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets if result molecule keeps explicit hydrogens or not
setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets if result molecule keeps explicit hydrogens or not
setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets if result molecule keeps explicit hydrogens or not
setKeepHydrogens(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
setKeepMapping(boolean) - Method in class chemaxon.standardizer.actions.MapAction
Sets keep mapping for the underlying mapper.
setKeepMapping(boolean) - Method in class chemaxon.standardizer.actions.MapReactionAction
Sets keep mapping for the underlying mapper.
setKeepMapping(boolean) - Method in class com.chemaxon.mapper.AutoMapper.Options
Default value true
setKeepMapping(boolean) - Method in class com.chemaxon.mapper.AutoMapper
 
setKeepMapping(boolean) - Method in interface com.chemaxon.mapper.Mapper
Sets if the initial mapping of the given object should be kept or not.
setKeepQueryOrder(boolean) - Method in class chemaxon.sss.search.SearchOptions
Set option for rearranging query atoms to increase search performance.
setKeepSingleAtom(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set behavior on acyclic input
setL(int, int, String) - Method in class chemaxon.marvin.view.MDocStorage
Sets a text label in a record.
setL(int, String) - Method in class chemaxon.marvin.beans.MViewPane
Sets a label in a GridBagView table.
setLabel(Label) - Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
Sets the Label of the monitor that is to display the measurement.
setLabel2DDrawing(boolean) - Method in class chemaxon.marvin.space.monitor.Label
Sets the drawing mode of the label that can be drawing in plane or in exact depth.
setLabelCenter(int) - Method in class chemaxon.struc.sgroup.SgroupAtom
Sets the index of the character in the label the bonds should point to.
setLabelProperty(int, boolean, boolean) - Method in class chemaxon.marvin.beans.MViewParams
Defines properties for cells containing label components.
setLabels(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
use setAtomSymbolsVisible(v) instead
setLabelSize(String) - Method in class chemaxon.marvin.space.monitor.Label
Sets the size of the label font.
setLastLicense(LastLicense) - Method in class chemaxon.marvin.common.UserSettings
 
setLastSketchFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings
 
setLastViewFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings
 
setLayout(int, int) - Method in class chemaxon.marvin.space.MSpaceEasy
Sets the number of rows and columns of cells the viewport is sepearted to.
setLeftName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom
Set the string that will be shown at the left side of the molecule.
setLength(int) - Method in class chemaxon.descriptors.CDParameters
 
setLength(int) - Method in class chemaxon.descriptors.CFParameters
 
setLength(int) - Method in class chemaxon.descriptors.ECFPParameters
 
setLength(int) - Method in class chemaxon.descriptors.MDParameters
Sets the length (number of cells) of the descriptor.
setLength(int) - Method in class chemaxon.descriptors.RFParameters
Sets the length (number of bits) of the reaction fingerprint.
setLength(int) - Method in class chemaxon.descriptors.SDParameters
 
setLfin(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set handling option for multi fragment (disconnected) inputs
setLfout(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set handling option for multi fragment (disconnected) results.
setLicense(String) - Static method in class chemaxon.license.LicenseManager
Sets a pre-read license file to the license manager to read and validate licenses from.
setLicenseEnvironment(String) - Method in class chemaxon.calculations.Ring
This method is for internal use only.
setLicenseEnvironment(String) - Method in class chemaxon.calculations.TopologyAnalyser
 
setLicenseEnvironment(String) - Method in class chemaxon.checkers.AbstractStructureChecker
 
setLicenseEnvironment(String) - Method in class chemaxon.descriptors.BCUT
Sets the license environment.
setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ECFP
Sets the license environment.
setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ECFPGenerator
Sets the license environment.
setLicenseEnvironment(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Sets the license environment.
setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ShapeDescriptor
 
setLicenseEnvironment(String) - Method in class chemaxon.jep.Evaluator
For internal usage only.
setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setLicenseEnvironment(String) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
 
setLicenseEnvironment(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets license environment to be stored.
setLicenseEnvironment(String) - Method in class chemaxon.sss.search.MolSearch
 
setLicenseEnvironment(String) - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
setLicenseEnvironment(String) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
setLicenseEnvironment(String) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setLicenseEnvironment(String) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets the license environment of the runner
setLicenseEnvironment(String) - Method in class chemaxon.standardizer.Standardizer
Sets the license environment.
setLicenseEnvironment(String) - Method in interface chemaxon.standardizer.StandardizerAction
Sets the license environment of the action
setLicenseEnvironment(String) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
 
setLicenseEnvironment(String) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the license environment.
setLicenseFile(String) - Static method in class chemaxon.license.LicenseManager
Sets the license file location to the license manager to read and validate licenses from.
setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
Show or hide ligand errors
setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the bond's ligand error visibility
setLigandOrder(int, MolAtom) - Method in class chemaxon.struc.MolAtom
Sets the order of a specified ligand.
setLigandOrderVisibility(String) - Method in class chemaxon.marvin.MolPrinter
Sets the ligand order visibility.
setLineColor(Color) - Method in class chemaxon.struc.MObject
Sets the color of the object.
setLineNumberInFile(int) - Method in exception chemaxon.formats.MolFormatException
Sets the line number relative to the first line of the file.
setLineNumberInRecord(int) - Method in exception chemaxon.formats.MolFormatException
Sets the line number relative to the first line of the record.
setLinkNodeDefaultOuters() - Method in class chemaxon.struc.MolAtom
Sets link node outer atoms to default values, if they are not set yet.
setLinkNodeDefaultOuters(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Sets link node outer atoms to default values, if they are not set yet; making sure that the resulting link node configuration is valid.
setLinkNodeOuterAtom(int, int) - Method in class chemaxon.struc.MolAtom
Sets one of the link node's outer neighbor atoms.
setList(int[]) - Method in class chemaxon.struc.MolAtom
Sets the list elements.
setList(int[], int) - Method in class chemaxon.struc.MolAtom
Sets the list elements.
setListener(DocumentAnnotator.Listener) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
setListeners(MDocStorage.Listener[]) - Method in class chemaxon.marvin.view.MDocStorage
 
setListFont(Font) - Method in class chemaxon.marvin.view.swing.TableOptions
 
setLoadSaveLocation(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the load/save filechooser working directory selection method names, based on the preferences dialog.
setLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the filechooser's default working directory, if the filechooser working directory selection method is saveCustomLocation.
setLocalAromaticChecking(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
 
setLocalAromatiChecking(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
Deprecated, for removal: This API element is subject to removal in a future version.
setLocalMenuName(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setLocalMenuName(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setLocalMenuName(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setLocalMenuName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the local menu name of the concerning checker
setLocalParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
In case of 2D molecule change the bonds flag (UP/DOWN), in case of 0D molecule set the atom flags to achieve the specified parity array.
setLocalParity(int[], int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
Set given local parity for the given atomic indexes.
setLocation(DPoint3) - Method in class chemaxon.struc.MolAtom
Sets the coordinates.
setLocation(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Set the origin of the molecule.
setLocation(DPoint3) - Method in class chemaxon.struc.RgMolecule
Set the origin of the molecule.
setLocation(DPoint3) - Method in class chemaxon.struc.RxnMolecule
Set the origin of the molecule.
setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Sets the atom coordinates.
setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Sets the atom coordinates.
setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
Sets the location
setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint
Sets the coordinates.
setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
Sets the point's location.
setLogger(CalculatorLogger) - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
setLogger(CalculatorLogger) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
 
setLogger(StructureCheckerLogger) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
Sets the logger.
setlogPMethod(int) - Method in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
Use {@link #setlogPMethod(LogPMethod))} instead.
setlogPMethod(int) - Method in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
setlogPMethod(LogPMethod) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the logP calculation method.
setlogPMethod(LogPMethod) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the logP calculation method.
setLogPTraining(InputStream) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the user defined logP training from a stream of parameters.
setLogPTrainingId(String) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the user defined logP training.
setLonely(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing lonely H
setLonePairAsLine(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility of Lone Pairs
setLonePairAutoCalc(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets the state of the automatic lone pair calculation.
setLonePairsAutoCalculated(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the state of the automatic calculation of lone pairs.
setLonePairsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Shows or hides (implicit) lone pairs.
setLonePairsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility state of lone pairs.
setLowerCutoffValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
Cutoff values can be set to the built-in two pole palettes.
setLowestEnergyConformerCalculation(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Switchs the lowest energy conformer calculation on/off.
setM(int, Molecule...) - Method in class chemaxon.marvin.beans.MViewPane
Sets the nth animation or structure.
setM(int, File, String) - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by using MolImporter, then set the cell synchronously using MViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.
setM(int, String) - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by using MolImporter, then set the cell synchronously using MViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.
setM(int, String, String) - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by using MolImporter, then set the cell synchronously using MViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.
setMacroMoleculeComponent(MacroMoleculeComponent) - Method in class chemaxon.marvin.space.MoleculeComponent
A MacroMoleculeComponent can be set and in this case this will be a visualizer of a ligand in the macromolecule.
setMag(double) - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 2.8.1, replaced by setScale()
setMainMoleculeGraph(MoleculeGraph) - Method in class chemaxon.struc.MDocument
Sets the main molecule graph.
setMapped(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing mapped H
setMappingStyle(Mapper.MappingStyle) - Method in class chemaxon.standardizer.actions.MapAction
Sets Mapping Style for the underlying mapper.
setMappingStyle(Mapper.MappingStyle) - Method in class chemaxon.standardizer.actions.MapReactionAction
Sets Mapping Style for the underlying mapper.
setMappingStyle(Mapper.MappingStyle) - Method in class com.chemaxon.mapper.AutoMapper.Options
setMappingStyle(Mapper.MappingStyle) - Method in class com.chemaxon.mapper.AutoMapper
Sets the mapping style
setMappingStyle(Mapper.MappingStyle) - Method in interface com.chemaxon.mapper.Mapper
Sets the mapping style
setMarginInPt(double) - Method in class chemaxon.marvin.MolPrinter
Sets the Margin of the painted molecule.
setMarginSize(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the documents margin size.
setMarginSize(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the documents margin size.
setMarkBonds(boolean) - Method in class chemaxon.standardizer.actions.MapAction
Sets mark bonds for the underlying mapper.
setMarkBonds(boolean) - Method in class chemaxon.standardizer.actions.MapReactionAction
Sets mark bonds for the underlying mapper.
setMarkBonds(boolean) - Method in class com.chemaxon.mapper.AutoMapper.Options
Default value false
setMarkBonds(boolean) - Method in class com.chemaxon.mapper.AutoMapper
 
setMarkBonds(boolean) - Method in interface com.chemaxon.mapper.Mapper
Sets if the changing bonds should be marked or not.
setMarkushAromHandling(MarkushAromaticityHandlingOption) - Method in class chemaxon.sss.search.SearchOptions
Set handling of Markush aromatization information (ambiguous aromatic rings) during Markush search
setMarkushEnabled(boolean) - Method in class chemaxon.sss.search.MolSearchOptions
Sets whether targets containing Markush features should be treated as Markush libraries
setMarvinCompMode(boolean) - Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Marvin compatibility mode.
setMassno(int) - Method in class chemaxon.struc.MolAtom
Sets the mass number.
setMassno(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the mass number.
setMax(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the maximum coordinates of the box.
setMaxCols(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Set maximum value of columns in the table
setMaximum(int) - Method in interface chemaxon.common.util.MProgressMonitor
Gets the maximum value.
setMaximum(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
 
setMaximumTautomerizationPathLength(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the maximum allowed length of the tautomerization path in chemical bonds.
setMaximumValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
Sets the greatest property value of the surface vertices considered.
setMaxIons(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
In case of pKaPlugin.MODEL_SMALL model, it sets the maximum number of ionizable atoms to be considered and uses simple calculation method to compute pKa values.
setMaxNumberOfConformers(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the maximum number of conformers to be calculated.
setMaxNumberOfStereoisomers(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets the maxinum number of stereoisomers to be generated.
setMaxRepetitions(int) - Method in class chemaxon.struc.MolAtom
Sets the maximum number of repetitions for a link atom.
setMaxRows(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Set maximum value of rows in the table
setMaxSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Set the maximum number of molecules displayed in the table.
setMaxStereoisomerCount(int) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Sets the maxinum number of stereoisomers to be generated.
setMaxStructureCount(int) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets the maximum number of structures to be generated.
setMaxStructureCount(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the maximum number of structures to be generated.
setMaxStructureCount(long) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets the maximum number of structures to be generated.
setMaxThreadCount(int) - Method in class com.chemaxon.mapper.AutoMapper.Options
Default value Integer.MAX_VALUE
The number of threads used for mapping will be the minimum of maxThreadCount and the number of available processors.
setMaxX(float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the maximum x coordinate of the box.
setMaxY(float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the maximum y coordinate of the box.
setMaxZ(float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the maximum z coordinate of the box.
setMeasure(RemoveFragmentAction.Measurement) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
Sets the measurement of the action
setMergedst(double) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the merge distance.
setMessage(String) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
 
setMetalAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
This method sets the metalAtoms property
setMetalconnected(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing metal connected H
setMethod(RemoveFragmentAction.Method) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
Sets the method of the action
setMethod(TautomerizeAction.TautomerForm) - Method in class chemaxon.standardizer.actions.TautomerizeAction
 
setMethylsRotatable(boolean) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
This is a speedup heuristics.
setMicropKaCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets micro pKa calculation.
setMin(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the minimum coordinates of the box.
setMinDistTryCount(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setMinimum(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
 
setMinimumCommonSize(int) - Method in class chemaxon.marvin.alignment.Alignment
Deprecated, for removal: This API element is subject to removal in a future version.
setMinimumCommonSize(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
Deprecated, for removal: This API element is subject to removal in a future version.
setMinimumCommonSize(int) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
setMinimumHeight(double) - Method in class chemaxon.struc.graphics.MTextBox
Sets the minimum height of the text..
setMinimumHeightSet(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Turns on/off minimum height calculation.
setMinimumValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
Sets the lowest property value of the surface vertices considered.
setMinRepetitions(int) - Method in class chemaxon.struc.MolAtom
Sets the minimum number of repetitions for a link node.
setMinX(float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the minimum x coordinate of the box.
setMinY(float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the minimum y coordinate of the box.
setMinZ(float) - Method in class chemaxon.marvin.space.BoundingBox
Sets the minimum z coordinate of the box.
setMixSgroupMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Set options for mixed S-group matching.
setMMFF94(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the forcefield to MMFF94.
setMMFF94Optimization(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets MMFF94 optimization.
setMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.Alignment
 
setMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setModel(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the calculation model.
setModified(boolean) - Method in class chemaxon.standardizer.Changes
Sets whether any modifications were applied on the molecule.
setMol(Molecule) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the molecule.
setMol(Molecule) - Method in class chemaxon.marvin.MolPrinter
Sets the current molecule and calculate its bounds.
setMol(Molecule, boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
use MSketchPane.setMol(Molecule) instead of this method.
setMol(File, String) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the molecule.
setMol(String) - Method in class chemaxon.marvin.beans.MSketchPane
Starts loading a molecule into the sketcher.
setMol(String) - Method in class chemaxon.marvin.MolPrinter
Sets the current molecule and calculate its bounds.
setMol(String, String) - Method in class chemaxon.marvin.beans.MSketchPane
Starts loading a molecule into the sketcher.
setMolbg(Color) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the molecule background color.
setMolBytes(byte[]) - Method in class chemaxon.marvin.io.MRecord
Sets the molecule bytes.
setMolCenter(int, String, DPoint3) - Method in class chemaxon.marvin.view.MDocStorage
Sets a molecule center.
setMolconvert(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
 
setMolecule(int, Molecule) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
Sets the molecule of the group at the provided index
setMolecule(int, Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Sets the molecule of the solvent at the provided index
setMolecule(int, Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Sets the molecule of the salt at the provided index
setMolecule(Molecule) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
setMolecule(Molecule) - Method in interface chemaxon.checkers.result.StructureCheckerResult
This method sets the molecule
setMolecule(Molecule) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
setMolecule(Molecule) - Method in interface chemaxon.checkers.runner.CheckerRunner
Sets the molecule to be checked by the checkers
setMolecule(Molecule) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
 
setMolecule(Molecule) - Method in class chemaxon.jep.context.MolContext
Sets the input molecule.
setMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setMolecule(Molecule) - Method in interface chemaxon.marvin.calculations.HlbPlugin
Sets the input molecule.
setMolecule(Molecule) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Sets the Molecule which will be represented by the MTransferable.
setMolecule(Molecule) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
Sets the Molecule which will be represented by the transferable.
setMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the input molecule after standardization.
setMolecule(Molecule) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the Molecule of the MoleculeComponent to mol, sets proper atomIterators, and computes the bounding box.
setMolecule(Molecule) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setMolecule(Molecule) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets the molecule to be standardized by the standardizer actions
setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.ElementalAnalyser
Specifies a molecule to calculate with.
setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.Ring
Specifies a molecule to calculate with.
setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.stereo.Stereochemistry
Specifies a molecule to calculate with.
setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.TopologyAnalyser
Specifies a molecule to calculate with.
setMolecule(MoleculeGraph, int) - Method in class chemaxon.calculations.Ring
Specifies a molecule to calculate with.
setMolecule(MoleculeGraph, int) - Method in class chemaxon.calculations.TopologyAnalyser
Specifies a molecule to calculate with.
setMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the input molecule after an optional standardization.
setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.calculations.ChargePlugin
 
setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
 
setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the input molecule after an optional standardization and/or modification.
setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
 
setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
setMolecule(Smolecule) - Method in class chemaxon.calculations.ElementalAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
setMolecule(Object) - Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
 
setMolecule(Object) - Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
setMolecule(String) - Method in class chemaxon.calculations.ElementalAnalyser
Specifies a molecule to calculate with.
setMolecule(String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Specifies a molecule to calculate with.
setMoleculeCellSize(int, int) - Method in class chemaxon.marvin.beans.MViewParams
Sets the preferred size of the cells containing molecules.
setMoleculeIterator(MoleculeIterator) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Sets the molecule iterator.
setMoleculeMovie(MMoleculeMovie) - Method in class chemaxon.struc.MDocument
Sets the molecule movie.
setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.marvin.alignment.Alignment
 
setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
setMolecules(Molecule, Molecule) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the two molecular structures to be matched.
setMolecules(ArrayList) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
The surface will be the molecular surface of the given molecules.
setMoleculeToAlign(Molecule, boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Sets the molecule to align to the reference.
setMolID(int) - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
setMolIndex(int) - Method in exception chemaxon.marvin.io.MolExportException
Sets the molecule index.
setMolNameFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the molecule name font size.
setMolNameShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets visibility of molecule names.
setMolPainter(int, String, MolPainter) - Method in class chemaxon.marvin.view.MDocStorage
Sets a molecule painter.
setMolString(String) - Method in class chemaxon.marvin.io.MRecord
 
setMolTemplate(Molecule) - Method in class chemaxon.marvin.MolPrinter
 
setMonomerTransform(boolean) - Method in class chemaxon.sss.search.SearchOptions
Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.
setMoreErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setMoreErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setMoreErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setMoreErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the more error message of the concerning checker
setMotionMode(int) - Method in class chemaxon.marvin.space.GraphicCell
Notifies every component of moving and standing modes.
setMotionMode(int) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the motion state of the component.
setMotionMode(int) - Method in class chemaxon.marvin.space.GraphicScene
Notifies every cell of moving and standing modes.
setMPLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility state of M/P labels.
setMPVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the M/P display option.
setMPVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setMrvWithSettings(String) - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets microspecies calculation.
setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets calculation of microspecies distributions.
setMSLogic(Map<MRArrow, RxnMolecule>) - Method in class chemaxon.struc.RxnMolecule
Deprecated, for removal: This API element is subject to removal in a future version.
Multi-step reactions not supported. Method performs no operations.
setMultiplets(Multiplet[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets Multiplet array of the spectrum.
setMultiplier(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Sets the multiplier.
setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the Na+, K+ concentration (default: 0.1).
setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the Na+, K+ concentration (default: 0.1).
setName(String) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets the name of the NMR spectrum
setName(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setName(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setName(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the checker name
setName(String) - Method in class chemaxon.fixers.AbstractStructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
setName(String) - Method in interface chemaxon.fixers.StructureFixer
Deprecated, for removal: This API element is subject to removal in a future version.
setName(String) - Method in class chemaxon.fixers.StructureFixerDescriptor
Sets the fixer name
setName(String) - Method in class chemaxon.marvin.services.ServiceArgument
Sets the name of the argument
setName(String) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the name of the component.
setName(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the name of the action
setName(String) - Method in class chemaxon.struc.Molecule
Sets the molecule name/title.
setName(String) - Method in class chemaxon.struc.RgMolecule
Sets the name of the root molecule.
setNameIOServiceURL(String) - Method in class chemaxon.marvin.common.UserSettings
 
setNameSpace(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Sets the namespace
setNavmode(String) - Method in class chemaxon.marvin.beans.MViewPane
Sets the mouse drag action.
setNearEdgeTolerance(int) - Method in class chemaxon.marvin.space.GraphicCell
Sets the tolerance we consider to be near the edge of the cell.
setNearEdgeTolerance(int) - Method in class chemaxon.marvin.space.GraphicScene
Sets a border near the boundary of the cells in which mouse handling can work other way.
setNegativeCriterium(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the lowest negative value colored.
setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
setNoErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setNoErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setNoErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setNoErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the no error message of the concerning checker
setNonQueryImplicitHcount(int) - Method in class chemaxon.struc.MolAtom
Sets the number of non-query implicit hydrogens attached.
setNormalized(boolean) - Method in class chemaxon.descriptors.MDParameters
Toggles the normalized flag of the current parametrized metric.
setNormalTautomerGenerationMode(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Generates only normal tautomers.
setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
setNucleus(NMRSpectrum.Nucleus) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Sets the NMR active nucleus.
setNumberOfAtomsAcceptToRotate(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
If only a given number of atoms (or less) can be found at one of the side of the dihedral skip this.
setNumberOfNMRActiveNuclei(int) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets number of the NMR active nuclei.
setObject(MObject, int) - Method in class chemaxon.struc.MDocument
Sets an object
setObject(MObject, int) - Method in class chemaxon.struc.MSelectionDocument
Sets an object
setObject(String, Object) - Method in class chemaxon.struc.MPropertyContainer
Sets a property object.
setObjectContainingSelection(MObject) - Method in class chemaxon.struc.MDocument
Sets the object that contains the selection.
setOeqcheck(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set oeqcheck parameter
SetOfSmallestRingsOption - Enum Class in chemaxon.sss.search.options
Option type describing the supported smallest set of rings used for property calculations.
setOKActionListener(ActionListener) - Method in class com.chemaxon.calculations.gui.PluginFactory
Sets the "OK" button pressed action listener.
setOneErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setOneErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker
Deprecated, for removal: This API element is subject to removal in a future version.
setOneErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker
Deprecated, for removal: This API element is subject to removal in a future version.
This method isn't needed anymore and will be removed in 6.0
setOneErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the one error message of the concerning checker
setOnlyExpanded(boolean) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
setOptimization(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the optimization criteria for the calculation.
setOptimization(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the optimization criteria for lowest energy conformer calculation.
setOptimizeProjection(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
setOption(String, String) - Method in class chemaxon.sss.search.SearchOptions
Sets search options.
setOptions(DocumentAnnotatorOptions) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Sets the options used for document annotation.
setOptions(String) - Method in class chemaxon.marvin.io.formats.mdl.MolImport
Sets the import options.
setOptions(String) - Method in class chemaxon.marvin.io.MolImportModule
Sets the import options.
setOptions(String) - Method in class chemaxon.marvin.io.MRecordImporter
Sets the options for the import module.
setOptions(String) - Method in class chemaxon.sss.search.SearchOptions
Sets search options.
setOrderSensitiveSearch(boolean) - Method in class chemaxon.sss.search.SearchOptions
Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
setOrientationType(AlignmentProperties.OrientationType) - Method in class chemaxon.marvin.alignment.Alignment
 
setOrigin(int, int) - Method in class chemaxon.marvin.space.GraphicCell
Sets the leftmost and bottomost coordinate of the cell.
setOriginal(Molecule) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
Sets the original molecule of the group.
setOrigTargetMayBeMarkush(boolean) - Method in class chemaxon.sss.search.MolSearch
Only for internal use!
Used for indicating that any bonds appeared after generating the generic tautomer of the target.
setOutput(File, String) - Method in class chemaxon.formats.MolConverter.Builder
Sets the output file.
setOutput(File, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
setOutput(OutputStream, String) - Method in class chemaxon.formats.MolConverter.Builder
Sets the output stream.
setOutput(OutputStream, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
setOutput(String, String) - Method in class chemaxon.formats.MolConverter.Builder
Sets the output file.
setOutput(String, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
setOutputFlags(int) - Method in class chemaxon.formats.MolConverter.Builder
Sets output flags.
setOutputFlags(int) - Method in class chemaxon.formats.MolConverter.Options
Deprecated, for removal: This API element is subject to removal in a future version.
setOutputIn3d(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
3D structures are generated (invalid 3D structure are filtered)
setOutputParameters(Object[]) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Prepares the output based on the result type string.
setOutputPrecision(int) - Method in class chemaxon.descriptors.MDParameters
Specifies the output precision for floating point values.
setOutputStream(OutputStream) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Sets the output stream.
setPageFormat(PageFormat, String) - Method in class chemaxon.marvin.common.UserSettings
 
setPageSettings(PageSettings) - Method in class chemaxon.struc.MDocument
Sets the page settings of multipage molecular document.
setPalette(byte[][]) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets colors to be used by the color palette.
setPalette(int) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets a built-in palette used during coloring the molecular surface.
setPaletteMaximum(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the largest positive value colored.
setPaletteMinimum(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the largest negative value colored.
setParameter(String, String) - Method in class chemaxon.descriptors.DescriptorGenerator
Sets a parameter of the current descriptor configuration.
setParameters() - Method in class chemaxon.sss.search.MolSearch
 
setParameters(CDParameters) - Method in class chemaxon.descriptors.CustomDescriptor
Sets parameters, allocates internal storage if needed and clears the descriptor.
setParameters(MDParameters) - Method in class chemaxon.descriptors.BCUT
Sets the parameters of an already created BCUT object.
setParameters(MDParameters) - Method in class chemaxon.descriptors.ChemicalFingerprint
Sets parameters, allocates internal storage if needed and cleans the descriptor.
setParameters(MDParameters) - Method in class chemaxon.descriptors.ECFP
Sets the parameters of an already created ECFP object.
setParameters(MDParameters) - Method in class chemaxon.descriptors.MolecularDescriptor
Sets the parameters for an already created MolecularDescriptor.
setParameters(MDParameters) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Sets parameters, allocates internal storage if needed and cleans the descriptor.
setParameters(MDParameters) - Method in class chemaxon.descriptors.ReactionFingerprint
Sets parameters, allocates internal storage if needed and cleans the descriptor.
setParameters(MDParameters) - Method in class chemaxon.descriptors.ScalarDescriptor
Sets parameters, allocates internal storage if needed and cleans the descriptor.
setParameters(File) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML file representation overwriting all previous settings with the new ones.
setParameters(File) - Method in class chemaxon.descriptors.PFParameters
Sets parameters from an XML file representation overwriting all previous settings with the new ones.
setParameters(String) - Method in class chemaxon.descriptors.BCUT
Sets the parameters of an already created BCUT object.
setParameters(String) - Method in class chemaxon.descriptors.ChemicalFingerprint
Sets the parameters of an already created ChemicalFingerprint object.
setParameters(String) - Method in class chemaxon.descriptors.CustomDescriptor
Sets the parameters of an already created CustomDescriptor object.
setParameters(String) - Method in class chemaxon.descriptors.ECFP
Sets the parameters of an already created ECFP object.
setParameters(String) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.
setParameters(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Sets the parameters for an already created MolecularDescriptor.
setParameters(String) - Method in class chemaxon.descriptors.PFParameters
Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.
setParameters(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Sets the parameters of an already created PharmacophoreFingerprint object.
setParameters(String) - Method in class chemaxon.descriptors.ReactionFingerprint
Sets the parameters of an already created ReactionFingerprint object.
setParameters(String) - Method in class chemaxon.descriptors.ScalarDescriptor
Sets the parameters of an already created ScalarDescriptor object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.HAcc
Sets the parameters of an already created HAcc object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.HDon
Sets the parameters of an already created HDon object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.Heavy
Sets the parameters of an already created HeavyAtomCount object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.LogD
Sets the parameters of an already created LogD object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.LogP
Sets the parameters of an already created LogP object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.Mass
Sets the parameters of an already created Mass object.
setParameters(String) - Method in class chemaxon.descriptors.scalars.TPSA
Sets the parameters of an already created TPSA object.
setParameters(String) - Method in class chemaxon.descriptors.ShapeDescriptor
Sets the parameters of an already created ShapeDescriptor object.
setParameters(String) - Method in interface chemaxon.jep.MolCondition
Deprecated.
Sets condition parameters.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.ChargePlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
setParameters(Properties) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.MSAPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Sets the input parameters for the plugin Accepted parameters: type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem| largestring|keep] Framework calculation type bmf: Bemis-Murcko framework bmfl: Bemis-Murcko loose framework mcs: Pairwise Maximum Common Substructure sssr: SSSR cssr: CSSR allringsystems: all fused ring systems largestringsystem: largest fused ring system largestring: largest ring keep: no framework reduction; useful for testing pre/post process keepsingleatom: [true|false] If set true then a single atom will be assigned to acyclic fragments.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets the input parameters for the plugin.
setParameters(Properties) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Sets the parameter table.
setParameters(Properties) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Sets parameters.
setParams(String) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the parameter string.
setParent(Component) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Sets the parent component.
setParentComponent(Component) - Method in class com.chemaxon.calculations.gui.PluginFactory
Sets the parent component - this is used to set options panes positions.
setParentMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
Sets the parent molecule.
setParity(int[]) - Method in class chemaxon.struc.MoleculeGraph
Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.
setParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph
Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.
setParity(int, int) - Method in class chemaxon.struc.MoleculeGraph
Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity.
setPath(String) - Method in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
 
setPath(String) - Method in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader
Sets the base path of the configuration.
setPath(String) - Method in class chemaxon.standardizer.configuration.reader.StandardizerXMLReader
 
setPatternMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MolAligner
Sets pattern molecule and calculates its dimension
setPeptideDisplay(String) - Method in class chemaxon.marvin.MolPrinter
Sets the Peptide display settings.
setPeptideDisplayType(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the peptide displaying tpye.
setpH(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets a single pH value for the calculation of charge distribution.
setpH(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets a single pH value for the logD calculation.
setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.
setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.
setpH(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the pH value for the calculation of microspecies distributions.
setpH(double) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.0 pH effect is not considered
setpH(double) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the pH to be considered in dominant tautomer generation.
setPhaseShiftedMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Adjusts if the phase shifted polymer should match on the original.
setpHLower(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets pH lower limit for the calculation of microspecies distributions.
setpHLower(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets pH lower limit for the calculation of charge distribution (default: 0.0).
setpHLower(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets pH lower limit (default: 0.0).
setpHLower(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets pH lower limit for the calculation of microspecies distributions.
setpHStep(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets pH step for the calculation of microspecies distributions.
setpHStep(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets pH step for the calculation of charge distribution.
setpHStep(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets pH step to be taken between the pH lower and upper limits (default: 1.0).
setpHStep(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets pH step for the calculation of microspecies distributions.
setpHUpper(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Sets pH upper limit for the calculation of microspecies distributions.
setpHUpper(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets pH upper limit for the calculation of charge distribution (default: 14.0).
setpHUpper(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets pH upper limit (default: 14.0).
setpHUpper(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets pH upper limit for the calculation of microspecies distributions.
setPickMatrix() - Method in class chemaxon.marvin.space.GraphicCell
 
setPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the molecule piece.
setpKaCorrectionLibrary(InputStream) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the pKa correction library from a stream.
setpKaCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.logDPlugin
Sets the pKa correction library.
setpKaPrefixType(int) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets pKa prefix type (default: pKaPlugin.STATICpKaPREFIX) STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state
setPlainText(String) - Method in class chemaxon.struc.graphics.MTextDocument
Sets the document as plain text.
setPlugin(CalculatorPlugin) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Sets the plugin object.
setPlugin(CalculatorPlugin) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Deprecated, for removal: This API element is subject to removal in a future version.
setPlugin(CalculatorPlugin) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Deprecated, for removal: This API element is subject to removal in a future version.
setPluginChecked(P) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Sets the calculator plugin object.
setPluginChecked(P) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Sets the plugin.
setPMAPTagName(String) - Method in class chemaxon.descriptors.PFGenerator
Sets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.
setPMAPTagName(String) - Method in class chemaxon.descriptors.PFParameters
Sets the name of the pharmacophore map tag to be considered in the input SDfile.
setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MPolyline
Sets the points.
setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MTextBox
Sets the points.
setPolymerendgroup(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing polymer end group H
setPolymerMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Adjust polymer matching.
setPopupMenusEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Allows popup menus.
setPortName(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Sets the port name
setPos(int) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the data display DASP position (0...9).
setPosition(double, double, double) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the position of the PharmacophoreArrow.
setPosition(double, double, double) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the position of the PharmacophorePoint.
setPosition(float[]) - Method in class chemaxon.marvin.space.monitor.Label
Sets the monitor's position defined by 3 coordinates.
setPosition(float[]) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Sets the monitor's position
setPosition(float, float) - Method in class chemaxon.marvin.space.monitor.Label
Sets the monitor's position defined by 2 coordinates.
setPosition(float, float, float) - Method in class chemaxon.marvin.space.monitor.Label
Sets the monitor's position defined by 3 coordinates.
setPosition(float, float, float) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Sets the monitor's position
setPositiveCriterium(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the lowest positive value colored.
setPreferredSize(Dimension) - Method in class chemaxon.marvin.beans.MViewPane
Sets the preferred size of the component.
setPrefix(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the code assist invoke prefix
setPrehydrogenize(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Turns the prehydrogenization on/off.
setPreprocessor(ConcurrentStandardizerProcessor.MolTransformer) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Sets the preprocessor.
setPrintEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Set the accessibility of the Print menu item in the File menu.
setPriority(int) - Method in class chemaxon.fixers.StructureFixerDescriptor
Sets the fixer priority.
setProbeRadius(double) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets thwe probe radius that is the radius of a water molecule used in computing surfaces.
setProductAtomsByMap(MolAtom[]) - Method in class chemaxon.jep.context.ReactionContext
Deprecated.
use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> product atom array.
setProducts(Molecule[]) - Method in class chemaxon.jep.context.ReactionContext
Deprecated.
Use ReactionContext.setReaction(RxnMolecule) instead. Sets the products.
setProgress(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
 
setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setProgressBar(JMSpaceProgressBar) - Method in class chemaxon.marvin.space.GraphicScene
Deprecated, for removal: This API element is subject to removal in a future version.
setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.GraphicComponent
 
setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
 
setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
setProgressBar(ProgressBarInterface) - Method in class chemaxon.marvin.space.SurfaceColoring
 
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
Sets a progress observer to be used in AlignmentPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets a progress observer to be used in ConformerPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Sets a progress observer to be used to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Sets a progress observer to be used in IsoelectricPointPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets a progress observer to be used in MolecularDynamicsPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets a progress observer to be used in pKaPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets a progress observer to be used in ResonancePlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets a progress monitor to be used in StereoisomerPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets a progress observer to be used in TautomerizationPlugin.run() to display progress status.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Sets the progress monitor.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.io.MRecordImporter
Sets the progress monitor.
setProgressMonitor(MProgressMonitor) - Method in interface chemaxon.marvin.io.MRecordReader
Sets the progress monitor.
setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Sets a progress observer to be used in CalculatorPlugin.run() to display progress status.
setProgressValue(int) - Method in interface chemaxon.common.util.MProgressMonitor
Set progress.
setProperties(Properties) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Sets display properties of the Molecule.
setProperties(Properties) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
Sets display properties of the Molecule.
setProperty(AlignmentProperties) - Method in class chemaxon.marvin.alignment.Alignment
 
setProperty(AlignmentProperties) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setProperty(String, String) - Method in class chemaxon.marvin.common.UserSettings
Sets a property for the given key with the given value.
setProperty(String, String) - Method in class chemaxon.marvin.space.MSpaceEasy
Sets a draw property of MarvinSpace.
setProperty(String, String) - Method in class chemaxon.struc.Molecule
Sets an RDfile/SDfile property.
setProperty(String, String, boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets a property for the given key with the given value.
setPropertyColorMapperMethod(Method) - Method in class chemaxon.marvin.space.SurfaceColoring
Colors will be got by this method.
setPropertyColorMapperRange(double, double) - Method in class chemaxon.marvin.space.SurfaceColoring
Sets the range of the built-in palette.
setPropertyColorObject(Object) - Method in class chemaxon.marvin.space.SurfaceColoring
Colors will be got from this object.
setPropertyMethod(Method) - Method in class chemaxon.marvin.space.SurfaceColoring
Atom properties will be got by this method.
setPropertyObject(Object, int) - Method in class chemaxon.marvin.space.SurfaceColoring
Atom properties will be get from this object.
setPropertyObject(String, Object) - Method in class chemaxon.struc.Molecule
Sets an RDfile/SDfile property object.
setPropertyValueDecreasement(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Atom property values can decrease when getting farhter from the atom center.
setProtectAllTetrahedralStereoCenters(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the protection of all tetrahedral stereo centers: if true then all tetrahedral stereo information is preserved by the tautomer generator.
setProtectAromaticity(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets aromaticity protection: if true then aromatic bonds are not modified by the tautomer generator.
setProtectCharge(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets charge protection: if true then the charge of charged atoms are not modified by the tautomer generator.
setProtectDoubleBondStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets double bond stereo protection: if true then the stereo configuration of double bonds with preset stereo information will not be changed.
setProtectDoubleBondStereo(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets double bond stereo protection: if true then double bonds stereo information is preserved by the tautomer generator.
setProtectDoubleBondStereo(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Sets double bond stereo protection.
setProtectEsterGroups(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the protection of ester groups: if true then ester groups are excluded from the tautomerization.
setProtectLabeledTetrahedralStereoCenters(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets the protection of labeled tetrahedral stereo centers: if true then labeled tetrahedral stereo centers are protected by the tautomer generator.
setProtectTetrahedralStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets the protection of tetrahedral stereo centers: if true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed.
setProtectTetrahedralStereo(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Sets the protection of tetrahedral stereo centers.
setProximity(AlignmentProperties.ProximityPotentialType) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setPruneIn(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set prunein parameter
setPruneOut(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set pruneout parameter
setQProp(String, int) - Method in class chemaxon.struc.MolAtom
Sets a query property as an integer.
setQProp(String, Object) - Method in class chemaxon.struc.MolAtom
Sets a query property.
setQuery(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setQuery(AlignmentMolecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
setQuery(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setQuery(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setQuery(Molecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
setQuery(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setQuery(Molecule) - Method in class chemaxon.sss.search.MolComparator
Loads the query molecule into this comparator.
setQuery(Molecule) - Method in class chemaxon.sss.search.MolSearch
 
setQuery(Molecule) - Method in class chemaxon.sss.search.Search
Specifies the query structure to search for.
setQuery(Molecule) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the query structure.
setQuery(Molecule) - Method in interface com.chemaxon.search.SimpleSearcher
Sets the query structure of the searcher.
setQuery(Molecule, int[]) - Method in class chemaxon.sss.search.MolSearch
 
setQuery(Molecule, int[]) - Method in class chemaxon.sss.search.Search
Specifies the query structure to search for.
setQuery(Molecule, int[]) - Method in interface com.chemaxon.search.SimpleSearcher
Sets the query structure of the searcher with excluded atoms.
setQuery(String) - Method in class chemaxon.sss.search.MolSearch
Specifies the query structure to search for in String format.
setQueryAbsoluteStereo(boolean) - Method in class chemaxon.sss.search.MolSearchOptions
Sets whether the chiral flag should be ignored or not for the query molecule.
setQueryAromaticity(int) - Method in class chemaxon.struc.MolAtom
Sets the aromatic/aliphatic query property.
setQueryAtom(MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Sets the atom to be searched for by the action (the query atom)
setQueryCode(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the program code for the query option.
setQueryFingerprint(T) - Method in class chemaxon.descriptors.SimilarityCalculator
Sets the query fingerprint
setQueryMode(boolean) - Method in class chemaxon.formats.MolImporter
Sets query mode.
setQueryMode(boolean) - Method in class chemaxon.marvin.io.MRecordImporter
Sets the query mode.
setQueryOp(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the data query operator.
setQueryRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setQueryRigidForced(boolean) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
setQueryRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setQuerySearchData(ReadOnlySearchData) - Method in class chemaxon.sss.search.MolComparator
 
setQuerystr(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Assigns the query properties string to this atom while setting all necessary atom and query properties.
setQuerystr(MolAtom, String, int) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Assigns the query properties string to this atom while setting all necessary atom and query properties.
setQuerystr(String) - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
setQuerystr(String) - Method in class chemaxon.struc.QueryBond
Sets the query string.
setQuerystr(String, int) - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
setQueryString(String) - Method in class chemaxon.struc.MolAtom
Assigns the query string to this atom.
setRadical(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing radical H
setRadical(int) - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.2. Use MolAtom.setRadicalValue(AtomProperty.Radical) instead.
setRadical(int, int) - Method in interface chemaxon.struc.WSmolecule
Deprecated, for removal: This API element is subject to removal in a future version.
setRadicalMatching(int) - Method in class chemaxon.sss.search.SearchOptions
Set the radical matching mode.
setRadicalValue(int, AtomProperty.Radical) - Method in interface chemaxon.struc.WSmolecule
Sets the radical value of an atom.
setRadicalValue(AtomProperty.Radical) - Method in class chemaxon.struc.MolAtom
Sets the radical value.
setRadius(double) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the radius of the arrow.
setRadius(float) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the radius of the PharmaCophorePoint.
setRandomEnumeration() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets random enumeration.
setRandomSeed(long) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets the random seed to be used in case of random enumeration.
setRandomSeed(long) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the random seed value.
setRange(IntRange) - Method in class chemaxon.marvin.util.MolFragLoader
Sets the (1-based) fragment index range to be loaded.
setRationalTautomerGenerationMode(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
setReactantAtomsByMap(MolAtom[]) - Method in class chemaxon.jep.context.ReactionContext
Deprecated.
use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> reactant atom array.
setReactants(Molecule[]) - Method in class chemaxon.jep.context.ReactionContext
Deprecated.
Use ReactionContext.setReaction(RxnMolecule) instead. Sets the reactants.
setReaction(RxnMolecule) - Method in class chemaxon.jep.context.ReactionContext
Sets the reaction.
setReactionArrow(DPoint3...) - Method in class chemaxon.struc.RxnMolecule
Sets the endpoint coordinates of the reaction arrow.
setReactionArrow(DPoint3[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Sets the reaction arrow.
setReactionArrow(MRArrow) - Method in class chemaxon.struc.RxnMolecule
Sets the reaction arrow.
setReactionArrow0(DPoint3...) - Method in class chemaxon.struc.RxnMolecule
Sets the reaction arrow.
setReactionArrowEndPoints(DPoint3[]) - Method in class chemaxon.struc.RxnMolecule
Sets the endpoints of the reaction arrow in this reaction.
setReactionArrowType(int) - Method in class chemaxon.struc.RxnMolecule
Sets the reaction arrow type.
setReactionArrowType(String) - Method in class chemaxon.struc.RxnMolecule
Sets the reaction arrow type from type name.
setReactionSmarts(String) - Method in class chemaxon.checkers.SubstructureChecker
Sets the reactionSmarts
setReactionStereo(int) - Method in class chemaxon.struc.MolAtom
Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
setReactionSupport(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Allows or disallows reaction drawing.
setReactionUnpairedMapMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Set option for matching unpaired(orphan or widow) atom maps to any atom.
setReciprocalConstant(double) - Method in class chemaxon.marvin.space.SurfaceColoring
Atom property values will decrease by (1.0/(4*PI*c)) * (v/(d*d)).
setRecordIDBackground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane
Highlights a record by setting the background of its identifier field.
setRecordIDForeground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane
Highlights a record by setting the foreground of its identifier field.
setReference(double[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
sets the coordinates of the reference molecule directly If this used the AlignRigidEasy.getReferenceAndRotatedFused() cannot be applied
setReference(Molecule) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
sets the reference molecule which remains intact
setReferenceMolecule(Molecule, boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Sets the reference molecule to align to.
setRelativeXCoordinate(float) - Method in class chemaxon.marvin.space.monitor.Label
Sets the coordinate considered as the x coordinate of the origin in window coordinates.
setRelativeYCoordinate(float) - Method in class chemaxon.marvin.space.monitor.Label
Sets the coordinate considered as the y coordinate of the origin in window coordinates.
setRendering(String) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the rendering style.
setRendering(String) - Method in class chemaxon.marvin.MolPrinter
Sets the rendering style of atoms and bonds.
setRenderingQuality(int) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the rendering quality.
setRenderingQuality(int) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the rendering quality, see RENDERING_* constants.
setRenderingQuality(int) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the rendering quality, see GraphicComponent.RENDERING_QUALITY_HIGH constants.
setRenderingQuality(String) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the rendering quality and calls PharmacophoreArrow.setRenderingQuality(int).
setRenderingQuality(String) - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the rendering quality and calls PharmacophorePoint.setRenderingQuality(int).
setRepeatingUnitAtom(MolAtom, boolean) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Adds or removes an atom to/from the list of paradigmatic repeating unit atoms.
setReplaceAtom(MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
Sets the atom to replaced with by the action
setRequestMethod(JsonServiceDescriptor.Method) - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
Sets the HTTP method of the request.
setResidueAtomId(int) - Method in class chemaxon.struc.MolAtom
Sets the residue atom identifier.
setResidueSeq(int) - Method in class chemaxon.struc.MolAtom
Sets the residue sequence number.
setResidueType(int) - Method in class chemaxon.struc.MolAtom
Sets the residue type.
setResourceDirectory(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
Set the directory where resources will be stored.
setRestH(int) - Method in class chemaxon.struc.RgMolecule
Sets the restH condition on an R-group definition.
setReturnTypes(Class<?>[]) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Sets the array of return types
setRgroup(int) - Method in class chemaxon.struc.MolAtom
Sets the R-group ID.
setRgroupAttachmentPointOrder(int) - Method in class chemaxon.struc.MolAtom
Sets the attachment point order of an R-group attachment point.
setRgroupId(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the R-group identifier of an atom.
setRgroupsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Shows or hides R-group definitions.
setRgroupsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets whether the R-group definitions are visible.
setRHLB(boolean) - Method in interface chemaxon.marvin.calculations.HlbPlugin
User can inquire the so called rHLB value.
setRightName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom
Set the string that will be shown at the right side of the molecule.
setRingBondCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects ring bond count atom query properties or not.
setRingChainTautomerizationAllowed(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets if ring tautomers are allowed or not.
Default true
setRingCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects ring count atom query properties or not.
setRingFlexibility(int, int) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
If BOTH the two parameters is true for the ring then the ring is treated flexible.
setRLigandEqualityCheck(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets whether undefined R-atoms with the same R-group ID should match the same structure.
setRlogic(int, int) - Method in class chemaxon.struc.RgMolecule
Sets R-logic flags.
setRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
Sets R-logic occurrence range.
setRLogicVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Set R-logic visibility.
setRLogicVisible(String) - Method in class chemaxon.marvin.common.UserSettings
Sets R-logic visibility
setRoot(Molecule) - Method in class chemaxon.struc.RgMolecule
Sets the root structure.
setRotatable(double[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
sets the coordinates of the rotatable molecule directly If this used the AlignRigidEasy.getReferenceAndRotatedFused() and AlignRigidEasy.getRotatedMolecule() cannot be applied
setRotatable(Molecule) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
sets the molecule to translate and rotate during the alignment
setRotateMatrix(float[]) - Method in class chemaxon.marvin.space.GraphicCell
Sets the matrix of rotation explicitly.
setRotateMatrix(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the rotation matrix in order to get the proper mapping of a vector to the viewing plane.
setRotateMatrix(float[]) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
setRotation(double, double, double, double) - Method in class chemaxon.struc.CTransform3D
Sets the rotation components.
setRotationCenter(DPoint3) - Method in class chemaxon.struc.CTransform3D
Sets the rotation center.
setRowAndColumn0(int) - Method in class chemaxon.struc.graphics.MTextBox
 
setRowCount(int) - Method in class chemaxon.marvin.beans.MViewParams
Sets the total nuber of rows.
setRowHeight(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the row height.
setSaltID(int, String) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Sets the name of the salt at the provided index
setSamplingAccuracy(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Set sampling accuracy.
setSamplingAccuracy(AtropIsomerDetector.Accuracy) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Set sampling accuracy.
setSamplingInterval(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Number of trajectory frames to be stored from the sampling start time to the end of calculation.
setSamplingStart(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the beginning of trajectory sampling.
setSaveBOM(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setSaveGUIPropertiesInMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets whether the GUI properties should be saved when saving as a Marvin file
setSaveIniEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Enables or disables automatic preference saving.
setSaveLoadZoomFactorToMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings
Tells wether to save the zoom factor information to mrv files or not.
setScale(double) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the scale factor and changes magnification of the canvas.
setScale(double) - Method in class chemaxon.marvin.MolPrinter
Sets the scale factor in units of regular bond length.
setScale(double) - Method in class chemaxon.struc.CTransform3D
Sets the scale factor.
setScaleFactor(float) - Method in class chemaxon.descriptors.MDParameters
Sets scaleFactor used with the current parametrized metrics.
setScalingHypothesis(MolecularDescriptor) - Method in class chemaxon.descriptors.MDParameters
Sets (stores) the specified scaling hypothesis.
setSceneSize(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the number of rows and columns.
setScreeningConfiguration(String) - Method in class chemaxon.descriptors.MolecularDescriptor
Sets the screening configuration.
setSDFColoring(String, Properties) - Method in class chemaxon.marvin.view.swing.TableSupport
Sets SDF coloring.
setSearchAll(boolean) - Method in class chemaxon.checkers.RatomChecker
Sets the option determining if the checker detects all R-atoms or not.
setSearchBridgehead(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for bridgehead explicit hydrogens
setSearchCharged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for charged explicit hydrogens
setSearchContracted(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Sets the checker should search for contracted abbreviated groups or not
setSearchDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker
Sets checker to detect valence properties with the default valence of the current atom type.
setSearchDisconnected(boolean) - Method in class chemaxon.checkers.RatomChecker
Sets the option determining if the checker detects R-atoms not connected to any other atoms or not.
setSearchExpanded(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
Sets the checker should search for expanded abbreviated groups or not
setSearchGeneric(boolean) - Method in class chemaxon.checkers.RatomChecker
Sets the option determining if the checker detects R-atoms without identifier numbers or not.
setSearchHConnected(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for H connected explicit hydrogens
setSearchIsotopic(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for isotopic explicit hydrogens
setSearchLinker(boolean) - Method in class chemaxon.checkers.RatomChecker
Sets the option determining if the checker detects R-atoms with more than one connection or not.
setSearchLonely(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for lonely explicit hydrogens
setSearchMapped(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for mapped explicit hydrogens
setSearchMode(SearchMode) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the search mode that controls the running time and the accuracy of the algorithm.
setSearchNested(boolean) - Method in class chemaxon.checkers.RatomChecker
Sets the option determining if the checker detects R-atoms within R-groups or not.
setSearchNonDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker
Sets checker to detect valence properties with non-default valence of the current atom type.
setSearchOptions(MolSearchOptions) - Method in class chemaxon.sss.search.MolComparator
 
setSearchOptions(MolSearchOptions) - Method in class chemaxon.sss.search.MolSearch
Sets search options.
setSearchOptions(SearchOptions) - Method in class chemaxon.sss.search.Search
Sets search options.
setSearchOptions(String) - Method in class chemaxon.standardizer.advancedactions.TransformAction
Sets the search options of the action
setSearchPolymerEndGroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for polymer end group explicit hydrogens
setSearchRadical(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for radical explicit hydrogens
setSearchSgroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for S-group explicit hydrogens
setSearchSgroupEnd(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for S-group end explicit hydrogens
setSearchValenceError(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for valence errored explicit hydrogens
setSearchWedged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Sets whether the checker search for wedged explicit hydrogens
setSelectable(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Enables the user to select a cell by clicking on it or using the cursor movement keys.
setSelected(boolean) - Method in class chemaxon.struc.graphics.MChemicalStruct
Selects or unselects the object.
setSelected(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Selects or unselects the text box.
setSelected(boolean) - Method in class chemaxon.struc.MObject
Selects or unselects the object.
setSelected(boolean) - Method in class chemaxon.struc.MolAtom
Selects or unselects this atom.
setSelected(boolean) - Method in class chemaxon.struc.NoStructure
Sets whether this NoStructure is selected.
setSelected(MoleculeGraph, boolean) - Static method in class chemaxon.struc.graphics.MChemicalStruct
Selects or unselects atoms in a molecule graph.
setSelectedAtoms(int, String, int[]) - Method in class chemaxon.marvin.view.MDocStorage
Sets the selected atom indices.
setSelectedAtoms(int, String, String) - Method in class chemaxon.marvin.view.MDocStorage
Sets the selected atom indices.
setSelectedFields(String[]) - Method in class chemaxon.marvin.view.swing.TableOptions
Set selected fields array in Table Options dialog box
setSelectedIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
Selects a molecule.
setSeparator(String) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Sets the separator string.
SETSEQ_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum atom set sequence number is currently 63.
SETSEQ_MAX - Static variable in class chemaxon.struc.MolBond
Maximum bond set sequence number.
SETSEQ_OFF - Static variable in class chemaxon.struc.MolBond
Bond set sequence number offset in flags.
setServicesConfigurationPath(String) - Method in class chemaxon.jep.Evaluator
Sets the custom services configuration path.
setServicesConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the URL of the configuration for Services in marvin
setSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3, replaced by setAtomSetColor
setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Enable or disable atom/bond set coloring.
setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.MolPrinter
Colors atoms and bonds according to the color of the pre-defined set they belong to.
setSetSeq(int) - Method in class chemaxon.struc.MolAtom
Sets the atom set sequence number.
setSetSeq(int) - Method in class chemaxon.struc.MolBond
Sets the bond set.
setSetSeq(int, int, int) - Method in class chemaxon.marvin.beans.MViewPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3, replaced by setAtomSetSeq
setSeverity(CheckerSeverity) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Sets the severity of the concerning checker
setSgroup(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing s-group H
setSgroupDataFormatted(boolean) - Method in class chemaxon.marvin.beans.MarvinPane
Sets if the Sgroup data to be formatted.
setSgroupDataFormatted(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets if the Sgroup data to be formatted.
setSgroupend(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing s-group end H
setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.Sgroup
Sets the molecule graph.
setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Sets the molecule graph.
setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.Molecule
Sets or unsets an S-group as a parent of an atom.
setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule
Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.
setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule
Sets or unsets an S-group as a parent of an atom in reactants, products or agents.
setShapeData(ShapeData) - Method in class chemaxon.descriptors.ShapeDescriptor
 
setShift(double) - Method in class chemaxon.calculations.nmr.Shift
Sets the chemical shift.
setShiftError(double) - Method in class chemaxon.calculations.nmr.Shift
Sets the error (confidence interval radius) of the shift.
setShifts(Shift[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets chemical shifts.
setShowMultiMoleculeOnEditSource(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setSimpView(int) - Method in class chemaxon.marvin.beans.MSketchPane
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.5, replaced by MSketchPane.setBondDraggedAlong(boolean)
setSingleCellLabelShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
Tests whether label should be shown for a single cell.
setSingleUpOrDownBond(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction
Sets the single wedge value of absolute stereo action
setSize(int) - Method in class chemaxon.marvin.view.MDocStorage
Sets the total number of entries.
setSize(int, int) - Method in class chemaxon.marvin.space.GraphicCell
Sets the size of the viewport of this cell in pixels.
setSize(int, int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the physical size of the scene.
setSize(int, int) - Method in class chemaxon.marvin.space.MSpaceEasy
Sets the physical size of the graphic canvas.
setSketchAnyBond(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default any bond drawing style in the sketcher.
setSketchArrowHeadLength(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the arrow head length.
setSketchArrowHeadWidth(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the arrow head width.
setSketchArrowTailLength(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the arrow tail length.
setSketchArrowTailWidth(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the arrow tail width.
setSketchCarbonVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default carbon visibility style in the sketcher.
setSketchColorScheme(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the sketcher's default color scheme.
setSketchImplicitH(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the display method of implicit hydrogens for the sketcher.
setSketchLigandOrderVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default ligand order visibility style in the sketcher.
setSketchLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the load working directory for MarvinSketch load filechooser.
setSketchMode(int) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the sketching mode.
setSketchMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings
Sets the sketcher's default 2D molecule background color.
setSketchMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings
Sets the sketcher's default 3D molecule background color.
setSketchRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings
Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than UserSettings.MAX_RECENT_FILE_LIST_SIZE then the size will be the value of UserSettings.MAX_RECENT_FILE_LIST_SIZE
setSketchRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the rendering style for the 2D sketcher.
setSketchRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the rendering style for the 3D sketcher.
setSketchSaveWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
Not implemented yet, don't use it.
setSkip(int, double) - Method in class chemaxon.struc.graphics.MPolyline
Sets the distance of the (visible) head or tail from the corresponding line end point.
setSkipsToEndPoints() - Method in class chemaxon.struc.graphics.MEFlow
 
setSmallestRingSizeChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects smallest ring size atom query properties or not.
setSMARTS(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Sets SMARTS query string data.
setSMARTS(String) - Method in class chemaxon.struc.MolAtom
Deprecated, for removal: This API element is subject to removal in a future version.
setSmartsQueryChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects SMARTS query properties or not.
setSMILESFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the SMILES font size.
setSMILESShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
Set visibility of SMILES strings.
setSmoothBackgroud(boolean) - Method in class chemaxon.marvin.space.GraphicCell
Enables/disables shaded background coloring.
setSmoothBackground(boolean) - Method in class chemaxon.marvin.space.GraphicScene
Enables/disables shaded background.
setSmoothColoringToCutoffValues(boolean) - Method in class chemaxon.marvin.space.SurfaceColoring
See Palette.smoothColorToCutoffValues(boolean).
setSolventID(int, String) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Sets the name of the solvent at the provided index
setSolventRadius(double) - Method in class chemaxon.marvin.calculations.MSAPlugin
Sets solvent radius.
setSpecIsotopeSymbolPreferred(boolean) - Method in class chemaxon.struc.MolAtom
Sets special isotope symbol usage preference.
setSrgoups(List<Sgroup>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
This method sets the groups property
setSSRType(SetOfSmallestRingsOption) - Method in class chemaxon.sss.search.SearchOptions
Sets which type of set of smallest rings to use for property calculations
setStandardizer(Standardizer) - Method in class chemaxon.descriptors.DescriptorGenerator
Sets the standardizer object to be used during descriptor generation.
setStandardizer(Standardizer) - Method in class chemaxon.sss.search.MolSearch
Sets the standardizer to be used for query and target molecules and re-standardization of query tautomers in case of tautomer substructure search.
setStandardizer(Standardizer) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Sets the standardizer that will be used for performing standardizations.
setStartAt(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Set the index number of the molecule that is the first to be displayed.
setStartEnd(MolAtom, MPoint) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Sets the atoms.
setStartPosition(long) - Method in class chemaxon.struc.MDocument
Sets the starting position of this document in the input file.
setStartPosition(long) - Method in class chemaxon.struc.Molecule
Sets the starting position of this molecule in the input file.
setStartupSelectorShown(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
setStepLimit(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setStepNumber(int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the number of simulation steps.
setStepTime(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Sets the simulation timestep.
setStereo2Flags(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond
Sets double bond stereo information.
setStereoFontRatio(float) - Method in class chemaxon.marvin.MolPrinter
Sets the ratio of the font size of the stereo label compared to the normal atom label size.
setStereoGroupNumber(int) - Method in class chemaxon.struc.MolAtom
Sets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
setStereoGroupType(int) - Method in class chemaxon.struc.MolAtom
Sets the stereochemical group type for enhanced stereo representation.
setStereoisomerismType(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Sets which type of stereoiseomers should be generated.
setStereoisomerType(EnumSet<StereoisomerSettings.StereoisomerType>) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Sets which types of stereoisomers should be generated.
setStereoModel(int) - Method in class chemaxon.sss.search.SearchOptions
Set stereo model option.
setStereoSearchType(int) - Method in class chemaxon.sss.search.SearchOptions
Specifies the way stereo information is considered during searching.
setStickdst(double) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the sticking distance.
setStickThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the stick thickness.
setStickThickness(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the stick diameter for ball and stick mode.
setStickThickness(double) - Method in class chemaxon.marvin.MolPrinter
Sets the 3D stick's diameter.
setStoichiometry(String) - Method in class chemaxon.standardizer.actions.ExpandAction
Sets the stoichiometry value of the action
setStoreAppliedTaskData(boolean) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
setString(String, String) - Method in class chemaxon.struc.MPropertyContainer
Sets a property.
setStructure(String) - Method in class chemaxon.standardizer.advancedactions.TransformAction
Deprecated, for removal: This API element is subject to removal in a future version.
setStructureID(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Sets structure ID to be used in Markush code generation.
setSubscript(String) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Sets the subscript.
setSubscript(String) - Method in class chemaxon.struc.Sgroup
Sets the subscript for non-superatom S-groups.
setSubsetChangable(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets whether startAt and maxSize can be changed.
setSubstitutionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects substitution count atom query properties or not.
setSubType(int) - Method in class chemaxon.struc.Sgroup
Sets polymer S-group subtype.
setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Sets the given molecule as the supergraph of this graph.
setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Sets the given molecule as the supergraph of this graph and its components.
setSupplier(Supplier<Molecule>) - Method in class chemaxon.jep.context.MolContext
 
setSurface(SurfaceComponent) - Method in class chemaxon.marvin.space.SurfaceColoring
Sets the surface for coloring.
setSurfaceAreaType(int) - Method in class chemaxon.marvin.calculations.MSAPlugin
Sets surface area calculation type: MSAPlugin.VAN_DER_WAALS or MSAPlugin.SOLVENT.
setSurfacePrecision() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Resolution will be set automatically according to the number of atoms and the rendering quality.
setSurfacePrecision(float) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Explicitly sets the grid resolution from which the surface is computed.
setSurfacePrecision(String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the surface precision by setting a quality.
setSurfaceSimplificationEnabled(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
The number of surface polygons can be reduced by the following algorithm: Paul Bourke: Surface (polygonal) Simplification http://astronomy.swin.edu.au/~pbourke/modelling/surfsimp/ This method enables/disables simplification.
setSurfaceType(String) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the type of the surface and computes the surface with the necessary method.
setSwitchOffAllProtectsForTDF(boolean) - Method in class chemaxon.sss.search.MolSearchOptions
Deprecated, for removal: This API element is subject to removal in a future version.
Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.
setSymbolTable(SymbolTable) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
setSymmetricalFuzzy(boolean) - Method in class chemaxon.descriptors.PFParameters
 
setSymmetryFiltering(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.
setSymmetryFiltering(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.
setSynchronousMode(boolean) - Method in class chemaxon.marvin.space.GraphicScene
Sets handling of cells to synchronous/asynchronous.
setT(int, int, String) - Method in class chemaxon.marvin.view.MDocStorage
Sets a text field in a record.
setT(int, String) - Method in class chemaxon.marvin.beans.MViewPane
Sets a text field in a GridBagView table.
setTabScale(double) - Method in class chemaxon.marvin.beans.MViewPane
Sets the magnification in the molecule cells.
setTag(char) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the tag character for the footnote display.
setTags(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the tags of the action
setTailCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the tail crossing bonds.
setTakeCanonicalForm(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets whether canonical form should be taken.
setTakeCanonicalForm(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets whether canonical form should be generated.
setTakeDominantTautomers(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets whether dominant tautomers should be generated.
setTakeFullTautomerizationSpectrum(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets to consider the full tautomer distribution upon the macro pka calculation.
setTakeGenericTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets whether generic tautomer should be generated.
setTakeGenericTautomer(boolean, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
setTakeMajorContributors(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Sets whether major contributors should be taken.
setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Sets to use major tautomeric form in calculation.
setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
setTakeMajorTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets whether major tautomer should be generated.
setTakeMostStableTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
setTakePartialNeutralization(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets if partial neutralization prior to canonical tauotmer generation is allowed or not.
setTakeResonantStructures(boolean) - Method in class chemaxon.marvin.calculations.ChargePlugin
Sets calculation with resonant structures.
setTakeResonantStructures(boolean) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
Sets calculation with resonant structures.
setTakeStandardForm(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
For internal use only.
setTarget(Molecule) - Method in class chemaxon.sss.search.MolComparator
Loads the target molecule into this comparator.
setTarget(Molecule) - Method in class chemaxon.sss.search.MolSearch
 
setTarget(Molecule) - Method in class chemaxon.sss.search.Search
Specifies the target molecule.
setTarget(Molecule) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the target structure.
setTarget(Molecule) - Method in interface com.chemaxon.search.SimpleSearcher
Sets the target structure of the searcher.
setTarget(Molecule, int[]) - Method in class chemaxon.sss.search.MolSearch
 
setTarget(Molecule, int[]) - Method in class chemaxon.sss.search.Search
Specifies the target molecule with excluded atoms.
setTarget(Molecule, int[]) - Method in interface com.chemaxon.search.SimpleSearcher
Sets the target structure of the searcher with excluded atoms.
setTargetAbsoluteStereo(boolean) - Method in class chemaxon.sss.search.MolSearchOptions
Sets whether the chiral flag should be ignored or not for the target molecule.
setTargetGroup(String) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setTargetGroup(String) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets the target group of standardizer action of the runner
setTargetGroups(String...) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
setTargetGroups(String...) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Sets the target groups of standardizer action of the runner
setTargetHomologyMatchingMode(TargetHomologyMatchingMode) - Method in class chemaxon.sss.search.SearchOptions
Sets the target homology matching mode option.
setTargetMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MolAligner
Sets target molecule and calculates its dimension
setTargetRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
setTargetRigidForced(boolean) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
Set this molecule to be rigid in the input conformation even if it contains rotatable bonds
setTargetRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
setTargetSearchData(ReadOnlySearchData) - Method in class chemaxon.sss.search.MolComparator
 
setTautomerEqualityMode(TautomerEqualityMode) - Method in class chemaxon.sss.search.MolSearchOptions
Internal use only.
setTautomerSearch(int) - Method in class chemaxon.sss.search.SearchOptions
Sets if tautomers of the query should be enumerated for search.
setTCenter(int) - Method in class chemaxon.struc.graphics.MRectangle
Sets the transformed point.
setTemperature(double) - Method in class chemaxon.marvin.calculations.pKaPlugin
Sets the temperature (default: 298 Kelvin).
setTemplates(Molecule[]) - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
Sets the clean templates of the action
setTerminalBondDeletionStyle(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the bond deletion style.
setText(String) - Method in class chemaxon.marvin.space.monitor.Label
Sets an explicit text to the label, that has priority to the description of the selected component.
setText(String) - Method in class chemaxon.struc.graphics.MTextBox
Sets the text.
setThickness(double) - Method in class chemaxon.struc.graphics.MPolyline
Sets the line thickness.
setThreadCount(int) - Method in class chemaxon.formats.MolConverter
Sets the number of threads for concurrent processing.
setThreadCount(int) - Method in class chemaxon.formats.MolExporter
Sets the number of threads for concurrent processing.
setThreadCount(int) - Method in class chemaxon.formats.MolImporter
Sets the number of threads for concurrent processing.
setThreadCount(int) - Method in class chemaxon.marvin.io.MRecordImporter
Sets the number of threads for concurrent processing.
setThreshold(float) - Method in class chemaxon.descriptors.MDParameters
Sets the value of the threshold of the current parametrized metric.
setThrowable(Throwable) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Sets the throwable object.
setThrowExceptionOnTimeout(boolean) - Method in class chemaxon.sss.search.SearchOptions
Sets if search should throw exception upon timeout.
setTimelimit(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Sets the timelimit for the calculation.
setTimeLimit(double) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets an upper time limit for the canonical tautomer generation.
setTimeLimit(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
setTimeLimit(long) - Method in class com.chemaxon.mapper.AutoMapper
 
setTimeLimit(long) - Method in interface com.chemaxon.mapper.Mapper
Sets time limit for calculation.
setTimeLimit(long) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Sets the maximum allowed time for MCS search.
setTimeoutInSeconds(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Set time out.
setTimeoutLimitMilliseconds(int) - Method in class chemaxon.sss.search.SearchOptions
The search on a single target timeouts reaching this amount of time.
setTitle(String) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Sets the frame title.
setToolbarConfigPath(String) - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
Sets the toolbar configuration path
setTopLeftIndex(int) - Method in class chemaxon.marvin.beans.MViewPane
Scrolls to the specified cell.
setTopLevelContainer(Container) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the top level container (JFrame, JDialog, etc) of the pane.
setTopologyConstraint(int) - Method in class com.chemaxon.search.mcs.buildup.BuildupMcs
Sets the the maximum difference in topology the mapped part of the molecules can have.
setTOption(int) - Method in class chemaxon.struc.graphics.MRectangle
Sets the transformation options.
setTraditionalNitrogenAllowed(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
 
setTraining(String) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the user defined training.
setTrainingResults(InputStream) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets the user defined training from a stream.
setTransfer(Transferable) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Sets the Transferable which contains the Molecule that should be retrieved.
setTransfer(Transferable) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
Sets the Transferable for importing Molecule from that.
setTransform(RxnMolecule) - Method in class chemaxon.standardizer.advancedactions.TransformAction
Sets the transformation
setTransformationCenter(float[]) - Method in class chemaxon.marvin.space.GraphicScene
Sets the transformation center explicitly to the given value.
setTransformationCenter(float, float, float) - Method in class chemaxon.marvin.space.GraphicCell
Sets the transformation center and resets shifting values.
setTransformationCenter(UOID) - Method in class chemaxon.marvin.space.GraphicCell
Sets the transformation center to the center of the component with the given id and resets shifting values.
setTransformationCenter(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Sets the center of transformation of the active cell to the coordinates of the named component.
setTransformationCenterX(float) - Method in class chemaxon.marvin.space.GraphicCell
Sets the x coordinate of the transformation center.
setTransformationCenterY(float) - Method in class chemaxon.marvin.space.GraphicCell
Sets the y coordinate of the transformation center.
setTransformationCenterZ(float) - Method in class chemaxon.marvin.space.GraphicCell
Sets the z coordinate of the transformation center.
setTransformationEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
Enable/disable transformation
setTransformer(Transformer) - Method in class chemaxon.sss.search.MolSearch
Sets the Transformer to be used for query and target standardization.
setTranslation(double, double, double) - Method in class chemaxon.struc.CTransform3D
Sets the translation components (CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
setTranslation(DPoint3) - Method in class chemaxon.struc.CTransform3D
Sets the translation components (CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
setTransparent(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the transparency state of the painting.
setTransparentBackground(boolean) - Method in class chemaxon.marvin.space.GraphicScene
Enables/disables transparent background color.
setTraverse(boolean) - Method in class chemaxon.jep.ChemJEP
Deprecated, for removal: This API element is subject to removal in a future version.
Use Evaluator.setVerbose(boolean) instead before creating the ChemJEP.
setType(int) - Method in class chemaxon.checkers.AromaticityErrorChecker
 
setType(int) - Method in class chemaxon.struc.graphics.MBracket
Sets the bracket type.
setType(int) - Method in class chemaxon.struc.MolBond
Sets bond type and does valence checking for the endpoints.
setType(StructuralFrameworksPlugin.FrameworkTypes) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set framework type to calculate.
setType(AbsoluteStereoAction.Type) - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
Sets the type of absolute stereo action
setType(AromatizeAction.Type) - Method in class chemaxon.standardizer.actions.AromatizeAction
Sets the type of aromatization
setType(ConvertDoubleBondsAction.Type) - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
Sets the type of action
setType(SetHydrogenIsotopeSymbolAction.Type) - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
Sets the type of action
setType(Clean2DAction.Type) - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
Sets the type of action
setType(Class<T>) - Method in class chemaxon.marvin.services.ServiceArgument
Sets the class of the argument
setType(String) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Sets the type value of the action
setTypes(List<String>) - Method in class chemaxon.checkers.AtomTypeChecker
Sets the checked atom types
setUndefinedRAtom(int) - Method in class chemaxon.sss.search.SearchOptions
Sets the matching behaviour of an undefined R atom in the query.
setUndefinedRAtomUserDefined(boolean) - Method in class chemaxon.sss.search.SearchOptions
For internal use only!
setUndo(int) - Method in class chemaxon.marvin.beans.MSketchPane
Sets the maximum undo depth.
setUnit(DipoleResult.Unit) - Method in class chemaxon.calculations.dipole.DipoleResult
Sets the dipole moment unit, see DipoleResult.Unit.
setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
Sets NMR spectrum unit.
setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum
Sets the unit type.
setUnitDisplayed(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets whether the units string should be displayed.
setUnits(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the unit of this data field.
setUnsaturationChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
Sets the option determining if the checker detects unsaturation atom query properties or not.
setUpperCutoffValue(double) - Method in class chemaxon.marvin.space.SurfaceColoring
Cutoff values can be set to the built-in two pole palettes.
setUseAllAtoms(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
setUseDefaultSalts(boolean) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
Sets whether default salt dictionary should be used
setUseDefaultSolvents(boolean) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Sets whether default solvent dictionary should be used
setUseOriginal(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
Deprecated, for removal: This API element is subject to removal in a future version.
always false: Molecule is always converted before alignment, but coordinates are written back to the original one.
setUsePMAP(boolean) - Method in class chemaxon.descriptors.PFGenerator
Omit or use pharmacophore map data optionally available in molecular structure.
setUsePMAP(String) - Method in class chemaxon.descriptors.PFParameters
Pharmacophore map data in imported Molecule-s should be used.
setUserSettings(UserSettings) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the user settings object.
setUserTypes(String) - Method in class chemaxon.marvin.calculations.logPPlugin
Sets user types.
setVagueBondLevel(int) - Method in class chemaxon.sss.search.SearchOptions
Option for less strict evaluation of query bonds (e.g.
setValence(int, int) - Method in interface chemaxon.struc.WSmolecule
Sets the valence.
setValenceCheckEnabled(boolean) - Method in class chemaxon.struc.MoleculeGraph
Enables or disables valence check on this molecule graph, depending on the value of the parameter b.
setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.MoleculeGraph
Sets the options for valence checking.
setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.RgMolecule
 
setValenceCheckState(MoleculeGraph.ValenceCheckState) - Method in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and MoleculeGraph.setValenceCheckEnabled(boolean).
Usage:
             // Same as setValenceCheckState(ValenceCheckState.OFF):
             setValenceCheckEnabled(false);
             // Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED):
             setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             // Same as setValenceCheckState(ValenceCheckState.FULL):
             setValenceCheckOptions(ValenceCheckOptions.GLOBAL);
             
setValenceerror(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing valence error H
setValenceError(boolean) - Method in class chemaxon.struc.MolAtom
Sets or clears the valence error flag.
setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.beans.MSketchPane
Shows or hides valence errors
setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
Show or hide valence errors
setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the visibility state of valence errors.
setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.beans.MViewPane
Shows or hides valence errors
setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.common.UserSettings
Show or hide valence errors in MarvinView
setValenceMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions
Set valence check option.
setValenceProp(int) - Method in class chemaxon.struc.MolAtom
Sets the valence property.
setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets atom valence property visibility.
setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.MolPrinter
Sets the atom valence propertiy visibility
setValid(boolean) - Method in class chemaxon.standardizer.AbstractStandardizerAction
Sets the validity of the standardizer action.
setvalidateSgroupsAtCreation(boolean) - Method in class chemaxon.marvin.common.UserSettings
Set the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.
setValue(T) - Method in class chemaxon.marvin.services.ServiceArgument
Sets the service argument value
setVerbose(boolean) - Method in class chemaxon.jep.Evaluator
Sets verbose mode.
setVerbose(boolean) - Method in class chemaxon.marvin.space.GraphicCell
Sets the verbose level on/off.
setVerbose(boolean) - Method in class chemaxon.marvin.space.GraphicScene
Sets the verbose level on/off.
setVerbose(boolean) - Method in class chemaxon.marvin.space.MSpaceEasy
Sets whether writing technical details to console is enabled or not.
setVerbose(boolean) - Method in class chemaxon.sss.search.Search
For debugging purposes only.
setVerbose(boolean) - Method in class chemaxon.sss.search.SearchOptions
For debugging purposes only.
setVerbose(int) - Method in class chemaxon.marvin.space.GraphicCell
Sets the verbose level to the given level.
setVerbose(int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the verbose level to the given level.
setVerbosePrinter(StructuralFrameworksPlugin.VerbosePrinter) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Set or clear verbose printer Verbose messages will be sent to the verbose printer to ease debugging
setVerify3d(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Invalid 3D structures of generated stereoisomers are filtered.
setVerticalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox
Sets the vertical alignment.
setViewAnyBond(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default any bond drawing style in the viewer.
setViewAtomMarkEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings
Sets atom mark and highlight visibility in Marvin View.
setViewCarbonVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default carbon visibility style in the viewer.
setViewColorScheme(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the viewer's default color scheme.
setViewHandlerType(int) - Method in class chemaxon.marvin.view.swing.TableOptions
Sets the view handler type.
setViewImplicitH(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the display method of implicit hydrogens for the viewer.
setViewLayout(int) - Method in class chemaxon.marvin.common.UserSettings
Set the layout of MarvinView.
setViewLigandOrderVisibility(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the default ligand order visibility style in the viewer.
setViewLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the load working directory for MarvinView load filechooser.
setViewMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings
Sets the default molecule background color for the 2D viewer.
setViewMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings
Sets the default molecule background color for the 3D viewer.
setViewNavmode2d(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the navigation mode for the 2D viewer.
setViewNavmode3d(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the navigation mode for the 3D viewer.
setViewRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings
Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than 10 then the size will be 10.
setViewRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the rendering style for the 2D viewer.
setViewRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings
Sets the rendering style for the 3D viewer.
setViewSaveWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings
Not implemented, don't use it.
setVisible(boolean) - Method in class chemaxon.marvin.space.GraphicComponent
Indicates whether the component will appear on the graphic scene at the next draw or not.
setVisible(boolean) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
setVisible(boolean) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets all of the visualizers to visible/invisible.
setVisible(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Sets the surface to be visible/invisible.
setVisible(boolean) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the component to be visible/invisible.
setVisibleRows(int) - Method in class chemaxon.marvin.beans.MViewParams
Sets the nuber of visible rows.
setWebServiceName(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Sets the webservice name
setWedged(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
Sets the value of property for removing wedged H
setWeightMode(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Way of handling values when multiple atoms have effect on one surface vertex.
setWeightOfMethods(double, double, double, double) - Method in class chemaxon.marvin.calculations.logDPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
This function will not be available from May 2016. Use logDPlugin.setlogPMethod(LogPMethod) instead.
setWeightOfMethods(double, double, double, double) - Method in class chemaxon.marvin.calculations.logPPlugin
Deprecated, for removal: This API element is subject to removal in a future version.
This function will not be available from May 2016. Use logPPlugin.setlogPMethod(LogPMethod) instead.
setWeights(double[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Sets the atom weights for location calculation.
setWeights(float[]) - Method in class chemaxon.descriptors.MDParameters
Sets the cell-wise weight factors for the current parametrized metric.
setWeights(float[], float[]) - Method in class chemaxon.descriptors.PFParameters
Sets the cell-wise weight factors for the current parametrized metric.
setWigglyBondVisibility(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Sets how wiggly bonds connected to double bonds are displayed.
For internal use only.
setWinScale(double) - Method in class chemaxon.marvin.beans.MViewPane
Sets the magnification in the zoom windows.
setWireThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane
Sets the line thickness for wireframe mode.
setWireThickness(double) - Method in class chemaxon.marvin.common.UserSettings
Sets the bond thickness in wireframe mode.
setWireThickness(double) - Method in class chemaxon.marvin.MolPrinter
Sets the line thickness for wireframe mode.
setWithCondition(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
This is the best way of passing coordinates to the box.
setWithCondition(BoundingBox) - Method in class chemaxon.marvin.space.BoundingBox
Extends the box with the given box, say gives the bounding box of the two boxes.
setWord(ByteBuffer, int, int) - Method in class chemaxon.marvin.io.PositionedInputStream
 
setWorkerThreadCount(int) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Sets the number of worker threads.
setWorkOnBackground(boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Starts or stops the background worker thread and ensures the required state for the type of work.
setWsdlURI(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Sets the WSDL URI
setX(double) - Method in class chemaxon.struc.MolAtom
Sets the X coordinate.
setX(double) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the X coordinate.
setXMLTokens(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
Sets the XML tokens of the action
setXState(int) - Method in class chemaxon.struc.Sgroup
Sets the expanded/contracted state.
setXState(int, int) - Method in class chemaxon.struc.Sgroup
Deprecated.
as of Marvin 6.2, use Sgroup.setXState(int) instead
setXState0(int) - Method in class chemaxon.struc.Sgroup
 
setXY(double, double) - Method in class chemaxon.struc.MolAtom
Sets the x and y coordinates.
setXYZ(double, double, double) - Method in class chemaxon.struc.MolAtom
Sets the coordinates.
setY(double) - Method in class chemaxon.struc.MolAtom
Sets the Y coordinate.
setY(double) - Method in class chemaxon.struc.sgroup.DataSgroup
Sets the Y coordinate.
setZ(double) - Method in class chemaxon.struc.MolAtom
Sets the Z coordinate.
setZero() - Method in class chemaxon.struc.CTransform3D
Sets all components to zero.
setZoomToScaffoldOnLoad(boolean) - Method in class chemaxon.marvin.common.UserSettings
 
severity() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the severity of the checker
SEVERITY - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
severity of checker
Sg - Static variable in class chemaxon.core.ChemConst
 
Sgroup - Class in chemaxon.struc
Structural group representation in the molecule.
Sgroup(Molecule, int) - Constructor for class chemaxon.struc.Sgroup
Deprecated.
As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType).
Sgroup(Molecule, int, int) - Constructor for class chemaxon.struc.Sgroup
Deprecated.
As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType) and Sgroup.setXState(int).
Sgroup(Molecule, SgroupType) - Constructor for class chemaxon.struc.Sgroup
 
Sgroup(Molecule, SgroupType, int) - Constructor for class chemaxon.struc.Sgroup
 
Sgroup(Sgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.Sgroup
Copy constructor.
Sgroup(Sgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.Sgroup
Copy constructor.
SGROUP - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of an Sgroup.
SGROUP_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom which is the only atom in an Sgroup.
SGROUP_SGROUP_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
This String represents the key of cloned sgroup, original sgroup map
SGROUP_TYPE_COUNT - Static variable in class chemaxon.struc.Sgroup
Number of S-group types.
SGROUP_TYPENAMES - Static variable in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Array of S-group type names.
SgroupAtom - Class in chemaxon.struc.sgroup
S-group superatom.
SgroupAtom(SuperatomSgroup) - Constructor for class chemaxon.struc.sgroup.SgroupAtom
Constructs a superatom for a superatom type S-group.
SgroupCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.
SgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.SgroupCheckerResult
Constructor which initialize all the properties.
SGROUPEND_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom which have a neighbor that is in a SuperatomSgroup.
sgroupGraph - Variable in class chemaxon.struc.Sgroup
The S-group's internal structure.
SgroupIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.SgroupIterator
Constructs an s-group iterator for the specified molecule of the factory.
sgroupList - Variable in class chemaxon.marvin.io.formats.mdl.MolImport
 
sgroupType - Variable in class chemaxon.struc.Sgroup
The S-group type.
SgroupType - Enum Class in chemaxon.struc
Enum of possible sgroup types.
ShapeDescriptor - Class in chemaxon.descriptors
Shape descriptor implements a 3D alignment based similarity calculation.
ShapeDescriptor() - Constructor for class chemaxon.descriptors.ShapeDescriptor
 
ShapeDescriptor(ShapeDescriptor) - Constructor for class chemaxon.descriptors.ShapeDescriptor
Copy constructor.
ShapeDescriptor(ShapeParameters) - Constructor for class chemaxon.descriptors.ShapeDescriptor
Creates a new instance of ShapeDescriptor according to the parameters given.
ShapeDescriptor(String) - Constructor for class chemaxon.descriptors.ShapeDescriptor
Creates a new instance of ShapeDescriptor according to the parameters given.s
ShapeGenerator - Class in chemaxon.descriptors
 
ShapeGenerator(AlignmentProperties.ColoringScheme) - Constructor for class chemaxon.descriptors.ShapeGenerator
 
ShapeParameters - Class in chemaxon.descriptors
 
ShapeParameters() - Constructor for class chemaxon.descriptors.ShapeParameters
 
ShapeParameters(File) - Constructor for class chemaxon.descriptors.ShapeParameters
 
ShapeParameters(String) - Constructor for class chemaxon.descriptors.ShapeParameters
Creates a new object based on a given configuration string.
shift(double, double) - Method in class chemaxon.marvin.space.GraphicCell
 
shift(double, double) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given shift factor in the active cell or in every cells in case of synchronous mode.
shift(int, int) - Method in class chemaxon.marvin.space.monitor.Label
A label can be shifted in x,y direction.
Shift - Class in chemaxon.calculations.nmr
NMR chemical shift class.
Shift(int, double) - Constructor for class chemaxon.calculations.nmr.Shift
Constructor.
shiftAnimated(double, double, int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given shift factor dividing by n parts.
shiftx - Variable in class chemaxon.marvin.space.monitor.Label
Relative position of the label of the component with respect to the reference point of the labeled component.
shifty - Variable in class chemaxon.marvin.space.monitor.Label
Relative position of the label of the component with respect to the reference point of the labeled component.
shininess - Static variable in class chemaxon.marvin.space.monitor.Control
 
SHORTCUTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "shortcuts".
shortestPath(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the shortest topological path (number of bonds) between two atoms.
shortName() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
 
shortName() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
 
shortName() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
Returns the name of category.
SHOW_SETS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "showSets".
showAllComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all components to visible.
showAllComponents() - Method in class chemaxon.marvin.space.GraphicScene
Sets all invisible component of the active cell to visible.
showAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicCell
Sets all components of the given class to visible.
showAllComponents(Class) - Method in class chemaxon.marvin.space.GraphicScene
Sets all components of the given class in the active cell to be visible.
showAllMonitors() - Method in class chemaxon.marvin.space.GraphicCell
Sets all monitor type components (labels as well) to visible.
showAllMonitors() - Method in class chemaxon.marvin.space.GraphicScene
Sets all monitor component of the active cell to visible.
showDialog() - Method in class chemaxon.marvin.view.swing.TableOptions
Bring up Table Options dialog box
showErrorDialog(String, Throwable) - Method in class chemaxon.marvin.beans.MarvinPane
Show error dialog.
showFaded() - Method in class chemaxon.marvin.space.GraphicCell
Sets all faded components to visible.
showFaded() - Method in class chemaxon.marvin.space.GraphicComponent
A descendant should overwrite this method to have its faded part become visible.
showFaded() - Method in class chemaxon.marvin.space.GraphicScene
Sets the drawing mode of all faded elements back to the original drawing mode.
showFaded() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
showFaded() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The faded visualizers will be fully visible again.
showFaded() - Method in class chemaxon.marvin.space.MoleculeComponent
Faded atoms will be fully visible again.
showFileDialog(String, Molecule) - Method in class chemaxon.marvin.beans.MarvinPane
Shows an Open or Save file dialog.
showFileOpenDialog() - Method in class chemaxon.marvin.beans.MarvinPane
Shows file open dialog.
showInsertFunctionDialog() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Shows the modal insert function dialog
showManageFavoritesDialog() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Shows the modal favourite manager dialog
showManageMacrosDialog() - Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Shows the modal macro manager dialog
showSelectedNodes() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
showStartupSelector() - Method in class chemaxon.marvin.beans.MSketchPane
This method is used in startup time to throw up a skin selector dialog.
showVolume(boolean) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
For Gaussian Cube surfaces it can be enabled to visualize the volumetric data from which the surface is generated.
Si - Static variable in class chemaxon.core.ChemConst
 
similarity(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
similarity(AlignmentMolecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
similarity(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
similarity(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
similarity(Molecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
Calculates the 3D similarity between the previously set query and the target.
similarity(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
SIMILARITY - Static variable in interface chemaxon.sss.SearchConstants
Similarity search.
SimilarityCalculator<T> - Class in chemaxon.descriptors
Descriptor similarity calculation can be performed using SimilarityCalculator.
SimilarityCalculator() - Constructor for class chemaxon.descriptors.SimilarityCalculator
 
SimilarityCalculatorFactory - Class in chemaxon.descriptors
This factory creates a similarity calculator object according to the user defined parameters.
SimilarityCalculatorFactory.Representation - Enum Class in chemaxon.descriptors
 
similarityNode - Variable in class chemaxon.descriptors.MDParameters
node holding the similarity calculations related parameters
SIMPLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
 
SIMPLE_VIEW - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "simpView".
SimpleSearcher - Interface in com.chemaxon.search
Search interface for different Molecule-Molecule search types.
SimpleSearcherFactory - Class in com.chemaxon.search
Factory for creating SimpleSearcher instances.
SimpleSearcherFactory() - Constructor for class com.chemaxon.search.SimpleSearcherFactory
 
simplifyIncompleteReactionToMolecule() - Method in class chemaxon.struc.RxnMolecule
Simplify a reaction to a molecule if possible.
simplifyMolecule() - Method in class chemaxon.struc.MDocument
Simplifies the main molecule object if possible.
simplifyToMolecule() - Method in class chemaxon.struc.RxnMolecule
Simplifies this RxnMolecule by moving the atoms and bonds from the reactants, products, and agents to a Molecule.
Single - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
Indicates, that the structure checker puts all structures to the output file.
SINGLE - Static variable in class chemaxon.struc.MolBond
Single bond type.
SINGLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond
Single or aromatic query bond type.
SINGLE_OR_DOUBLE - Static variable in class chemaxon.struc.MolBond
Single or double query bond type.
sinkIsAtom() - Method in class chemaxon.struc.graphics.MEFlow
Gets whether this arrow's sink is an atom.
sinkIsBond() - Method in class chemaxon.struc.graphics.MEFlow
Gets whether this arrow's sink is a bond.
sinkIsIncipBond() - Method in class chemaxon.struc.graphics.MEFlow
Gets whether this arrow's sink is an incipient bond.
size - Variable in class chemaxon.marvin.space.monitor.Control
 
size() - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Gets the total number of elements.
size() - Method in class chemaxon.struc.MPropertyContainer
Gets the total number of properties.
size() - Method in class chemaxon.struc.prop.MHashProp
Gets the table size.,
size() - Method in class chemaxon.struc.prop.MListProp
Gets the array size.
size(int) - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Gets the size of list at the specified level.
sizeToString(double) - Static method in class chemaxon.struc.graphics.MFont
Converts an integer or fractional size to a string.
sizeX - Variable in class chemaxon.marvin.space.monitor.Label
 
sizeY - Variable in class chemaxon.marvin.space.monitor.Label
 
SKC - Static variable in class chemaxon.formats.MFileFormat
SKC file format
SKETCH_ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "sketchAnyBond".
SKETCH_ARROW_HEAD_LENGTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "sketchArrowHeadLength".
SKETCH_ARROW_HEAD_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "sketchArrowHeadWidth".
SKETCH_ARROW_TAIL_LENGTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "sketchArrowTailLength".
SKETCH_ARROW_TAIL_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "sketchArrowTailWidth".
SKETCH_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "sketchCarbonVisibility".
SKETCH_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "sketchHelp".
SKETCH_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "sketchLigandOrderVisibility".
SKETCH_STARTUP_SHOWN - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
SKETCHABLE - Static variable in class chemaxon.marvin.beans.MViewPane
Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinSketch in a new window.
SketchCheckerRunner - Class in chemaxon.checkers.runner
Deprecated, for removal: This API element is subject to removal in a future version.
SketchCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
Initiate a SketchCheckerRunner instance which will can execute StructureChecker instances read from configurationReader
SKETCHPANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
SKETCHPANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
SketchParameterConstants - Class in chemaxon.marvin.sketch
Parameters of MarvinSketch Applet and Bean.
The parameters of the JMSketch applet can be set using the <param> HTML tag.
SKIN - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "skin".
skip(long) - Method in class chemaxon.marvin.io.PositionedInputStream
Skips over and discards n bytes of data.
SKIP - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
In case of standardization error the output does not contain the molecule
SKIP_COORDINATE_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
Exclude coordinate bonds from bond iteration.
SKIP_COVALENT_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory
Exclude covalent bonds from bond iteration.
SKIP_EXPLICIT_H - Static variable in class chemaxon.util.iterator.IteratorFactory
Exclude explicit hydrogens from atom iteration.
SKIP_LONE_PAIR - Static variable in class chemaxon.util.iterator.IteratorFactory
Exclude lone pairs from atom iteration.
SKIP_MULTICENTER - Static variable in class chemaxon.util.iterator.IteratorFactory
Exclude multicenters from atom iteration.
SKIP_PSEUDO_ATOM - Static variable in class chemaxon.util.iterator.IteratorFactory
Exclude pseudo atoms from atom iteration.
skipLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Skips the next line.
skipLine() - Method in class chemaxon.marvin.io.PositionedInputStream
Skips the next line.
skipRecord() - Method in class chemaxon.formats.MolImporter
Skips the next molecule or document instead of reading it into memory.
skipRecord() - Method in class chemaxon.marvin.io.ArrayMDocSource
Skips the next document.
skipRecord() - Method in class chemaxon.marvin.io.MDocSource
Skips the next document.
skipRecord() - Method in class chemaxon.marvin.io.MRecordImporter
Skips the next document.
skipRecord() - Method in interface chemaxon.marvin.io.MRecordReader
Skips the next record.
skipRecords(int, int, MProgressMonitor, int, Runnable) - Method in class chemaxon.marvin.io.MDocSource
 
Sm - Static variable in class chemaxon.core.ChemConst
 
SM_ATOM - Static variable in class chemaxon.marvin.beans.MSketchPane
Atom mode.
SM_BOND - Static variable in class chemaxon.marvin.beans.MSketchPane
Bond mode.
SM_DELETE - Static variable in class chemaxon.marvin.beans.MSketchPane
Delete mode.
SM_FLAGS_OFF - Static variable in class chemaxon.marvin.beans.MSketchPane
Offset of flags in sketch mode.
SM_MASK - Static variable in class chemaxon.marvin.beans.MSketchPane
Sketch mode mask.
SM_SELECT - Static variable in class chemaxon.marvin.beans.MSketchPane
Select mode.
SM_SELECT_LASSO - Static variable in class chemaxon.marvin.beans.MSketchPane
Lasso select mode.
SMALL_FONT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Label
 
SMALL_RING - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that small ring error had found in the molecule
smallestRing() - Method in class chemaxon.calculations.Ring
Identifies the smallest ring (number of atoms) in the molecule.
smallestRing() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.smallestRing()
smallestRingSize() - Method in class chemaxon.calculations.Ring
Calculates the size of the smallest ring in the molecule.
smallestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.smallestRingSize()
smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.Ring
Calculates the size of the smallest ring an atom is a member of.
smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.smallestRingSizeOfAtom(int)
smallestRingSystem() - Method in class chemaxon.calculations.Ring
Identifies the smallest ring system (number of rings) in the molecule.
smallestRingSystem() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.smallestRingSystem()
smallestRingSystemSize() - Method in class chemaxon.calculations.Ring
Calculates the size of the smallest ring system (number of rings) in the molecule.
smallestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Ring.smallestRingSystemSize()
SMARTS - Static variable in class chemaxon.formats.MFileFormat
SMARTS.
SMARTS_H_DAYLIGHT_COMP_MODE - Static variable in class chemaxon.struc.MolAtom
Option flag to express daylight-type smarts atom parsing of H.
SMARTS_H_MARVIN_COMP_MODE - Static variable in class chemaxon.struc.MolAtom
Option flag to express marvin-pre-3.5-type smarts atom parsing of H.
SmartsAtomQuerifier - Class in chemaxon.marvin.io.formats.smiles
Class for partial interpretation of smarts atoms.
SmartsAtomQuerifier() - Constructor for class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
Creates a new SmartsAtomQuerifier object.
SMILES - Static variable in class chemaxon.formats.MFileFormat
SMILES.
SMILESRecognizer - Class in chemaxon.formats.recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
SMILESRecognizer() - Constructor for class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated.
 
smol() - Method in class chemaxon.struc.MoleculeGraph
Gets a Smolecule representation of this molecule.
Smolecule - Interface in chemaxon.struc
Array-based abstract molecule class.
SmoleculeAtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
SMOOTH_STICKS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
smoothStickColoring - Variable in class chemaxon.marvin.space.MoleculeComponent
 
Sn - Static variable in class chemaxon.core.ChemConst
 
SoapServiceDescriptor - Class in chemaxon.marvin.services.soap
Service descriptor of SOAP type requests.
SoapServiceDescriptor() - Constructor for class chemaxon.marvin.services.soap.SoapServiceDescriptor
 
SolubilityCalculator - Class in com.chemaxon.calculations.solubility
Solubility calculator.
API usage example:
SolubilityCalculator() - Constructor for class com.chemaxon.calculations.solubility.SolubilityCalculator
 
SolubilityCalculator(FragmentBasedSolubilityParameters) - Constructor for class com.chemaxon.calculations.solubility.SolubilityCalculator
Constructor.
SolubilityCategories - Class in com.chemaxon.calculations.solubility
Array of solubility categories.
SolubilityCategories(SolubilityCategory[], SolubilityUnit) - Constructor for class com.chemaxon.calculations.solubility.SolubilityCategories
Constructor.
SolubilityCategories.UndefinedSolubilityCategory - Class in com.chemaxon.calculations.solubility
Undefined category.
SolubilityCategory - Interface in com.chemaxon.calculations.solubility
Interface for solubility categories.
SolubilityResult - Interface in com.chemaxon.calculations.solubility
Solubility prediction result.
SolubilityUnit - Enum Class in com.chemaxon.calculations.solubility
Solubility unit.
SOLVENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that solvent had found in the molecule
SOLVENT - Static variable in class chemaxon.marvin.calculations.MSAPlugin
Surface area type: 3D solvent accessible surface area.
SOLVENT_AMBIGOUS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that more than one type of solvents had found in the molecule
SOLVENT_ID_PROPERTY - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Property key for solvent ID
SOLVENT_LIST_KEY - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Property key for solvent list modification
SolventChecker - Class in chemaxon.checkers
SolventChecker detects common solvents in multicomponent structures.
SolventChecker() - Constructor for class chemaxon.checkers.SolventChecker
Default constructor
sort(Sgroup[], int) - Static method in class chemaxon.struc.Sgroup
Sorts S-groups in parent-child or child-parent order.
SORT_CHILD_PARENT - Static variable in class chemaxon.struc.Sgroup
Parent-child sort order.
SORT_PARENT_CHILD - Static variable in class chemaxon.struc.Sgroup
Parent-child sort order.
sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
Sorts bonds in the same order as they appear in another chemical graph.
sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RgMolecule
Sort edges in the same order as they appear in the specified array.
sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RxnMolecule
Sort edges in the same order as they appear in the specified array.
sortSgroupXBonds() - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.12, no replacement.
Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
sortXBonds() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 5.12, no replacement.
Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
SOURCE_TEXT - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the source text, as it appears in the original document.
sourceIsAtom() - Method in class chemaxon.struc.graphics.MEFlow
Gets whether this arrow's source is an atom.
sourceIsBond() - Method in class chemaxon.struc.graphics.MEFlow
Gets whether this arrow's source is a bond.
spacefillPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
specular - Static variable in class chemaxon.marvin.space.monitor.Control
 
SPHERIC - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
 
SPIN - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "spin".
SPLASH_SCREEN_IMAGE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "splashScreenImage".
splitAllDisconnectedComponents() - Method in class chemaxon.struc.RxnMolecule
Replaces all disconnected reaction components by its connected fragments in the structure array.
splitComponentParts(MoleculeGraph, int) - Method in class chemaxon.struc.RxnMolecule
Finds those component parts that are contained in the molecule graph m and creates separate components from the fragments contained in m, splitting them from the previous merges.
splitDisconnectedComponent(int, int) - Method in class chemaxon.struc.RxnMolecule
Replaces a disconnected reaction component by its connected fragments in the structure array.
splitDisconnectedComponent(long) - Method in class chemaxon.struc.RxnMolecule
Replaces a disconnected reaction component by its connected fragments in the structure array.
splitFileAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil
Parses "file{options}" strings used in molecule file import.
splitFormatAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil
Parses "format:options" strings used in molecule file import and export.
Spreadsheet - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView
 
Sr - Static variable in class chemaxon.core.ChemConst
 
sringsize() - Method in class chemaxon.struc.MolAtom
Calculate the size of smallest ring containing this atom.
SRU - Enum constant in enum class chemaxon.struc.SgroupType
 
sssr - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
SSSR - Enum constant in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
Smallest set of smallest rings.
SST_ALTERNATING - Static variable in class chemaxon.struc.Sgroup
Alternating polymer S-group subtype.
SST_BLOCK - Static variable in class chemaxon.struc.Sgroup
Block polymer S-group subtype.
SST_RANDOM - Static variable in class chemaxon.struc.Sgroup
Random polymer S-group subtype.
ST_AMINOACID - Static variable in class chemaxon.struc.Sgroup
Amino acid s-group type.
ST_ANY - Static variable in class chemaxon.struc.Sgroup
Any polymer S-group type.
ST_COMPONENT - Static variable in class chemaxon.struc.Sgroup
Component S-group type.
ST_COPOLYMER - Static variable in class chemaxon.struc.Sgroup
Copolymer S-group type.
ST_CROSSLINK - Static variable in class chemaxon.struc.Sgroup
Crosslink S-group type.
ST_DATA - Static variable in class chemaxon.struc.Sgroup
Data S-group type.
ST_FORMULATION - Static variable in class chemaxon.struc.Sgroup
Formulation S-group type.
ST_GENERIC - Static variable in class chemaxon.struc.Sgroup
Generic S-group type.
ST_GRAFT - Static variable in class chemaxon.struc.Sgroup
Graft S-group type.
ST_MER - Static variable in class chemaxon.struc.Sgroup
Mer S-group type.
ST_MIXTURE - Static variable in class chemaxon.struc.Sgroup
Mixture S-group type.
ST_MODIFICATION - Static variable in class chemaxon.struc.Sgroup
Modification S-group type.
ST_MONOMER - Static variable in class chemaxon.struc.Sgroup
Monomer S-group type.
ST_MULTICENTER - Static variable in class chemaxon.struc.Sgroup
Multicenter S-group type.
ST_MULTIPLE - Static variable in class chemaxon.struc.Sgroup
Multiple group S-group type.
ST_SRU - Static variable in class chemaxon.struc.Sgroup
SRU (Structural Repeating Unit: polymers and repeating units with repetition ranges) S-group type.
ST_SUPERATOM - Static variable in class chemaxon.struc.Sgroup
Superatom S-group type.
standardize() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Performs the standardization of the next input molecule, and returns the standardized molecule.
standardize() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
standardize() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Invoke a background thread which will run all standardizer actions on the given molecule
standardize(MolImporter, MolExporter, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Reads the molecules from the importer, standardizes them, and writes to the exporter.
standardize(Molecule) - Method in class chemaxon.descriptors.MDParameters
Standardizes the Molecule and returns the standardized form.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.AlignmentPlugin
 
standardize(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Expands sgroups.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Prevents default standardization: does nothing.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Expands sgroups.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Expands sgroups.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Clears enhanced stereo information.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Standardize input molecule
Standardization currently ungroups SGroups
standardize(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Expands sgroups.
standardize(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).
standardize(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction
Calls AbstractStandardizerAction.standardize1(Molecule)
If molecule has more components AbstractStandardizerAction.standardize1(Molecule) is invoked on all components instead of the molecule itself.
If AbstractStandardizerAction.standardize1(Molecule) doesn't return a not null Change object for the molecule or for any of the components the value of the returned changes object's Changes.isModified() property is set based on whether molecule's MoleculeGraph.getGrinvCC() property value has changed during the standardization action.
standardize(Molecule) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
standardize(Molecule) - Method in class chemaxon.standardizer.Standardizer
Standardization for one input molecule: performs the standardization actions according to the XML configuration.
standardize(Molecule) - Method in interface chemaxon.standardizer.StandardizerAction
Standardizes the provided molecule.
Logs of standardization should be generated to a Logger, that can be collected by using StandardizerLogger.getLogger() method.
standardize1(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction
This method contains the current standardization mechanism.
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AddExplicitHydrogensAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AliasToAtomAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AliasToGroupAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AromatizeAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ClearIsotopesAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ClearStereoAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ContractSgroupsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertPiMetalBondsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.DearomatizeAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.DisconnectMetalAtomsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ExpandAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MapAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MapReactionAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MesomerizeAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.NeutralizeAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RearrangeReactionAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAbsoluteStereoAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAtomValuesAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAttachedDataAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveRGroupDefinitionsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveStereoCareBoxAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.SetAbsoluteStereoAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.TautomerizeAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.UnmapAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.actions.WedgeCleanAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.Clean3DAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.TransformAction
 
standardizeAndWait() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
standardizeAndWait() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Executes all standardizer actions contained by the pre-set configuration on the given molecule and returns the list of applied changes.
StandardizedMolSearch - Class in chemaxon.sss.search
MolSearch subclass that standardizes (e.g.
StandardizedMolSearch() - Constructor for class chemaxon.sss.search.StandardizedMolSearch
Constructs a StandardizedMolSearch object.
standardizeIonicGroups(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Default standardization: nitro groups: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1] sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
standardizeNeutralGroups(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Neutral -> ionic standardization: [O:1]=[N:2] >> [O-:1][N+:2], [H:3][O:2][N:1] >> [NH1+:1][O-:2] sulphynil group transformation: [#6][S:1]([#6])=[O:2] >> [#6][S+:1]([#6])[#8-:2]
standardizer - Variable in class chemaxon.descriptors.MDParameters
transform molecules into standard form before descriptor generation
Standardizer - Class in chemaxon.standardizer
Performs the standardization determined by the XML configuration file, or simple action string configuration.
See the documentation for details: User's Guide Configuration Developer's Guide
Standardizer(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.Standardizer
Initializes a new standardizer with XML configuration
Standardizer(Standardizer) - Constructor for class chemaxon.standardizer.Standardizer
Initializes a new standardizer based on an existing standardizer
Standardizer(File) - Constructor for class chemaxon.standardizer.Standardizer
Initializes a new standardizer with XML configuration
Standardizer(InputStream) - Constructor for class chemaxon.standardizer.Standardizer
Initializes a new standardizer with XML configuration
Standardizer(String) - Constructor for class chemaxon.standardizer.Standardizer
Initializes a new standardizer with auto-recognized XML or action string configuration
Standardizer(String, String) - Constructor for class chemaxon.standardizer.Standardizer
Initializes a new standardizer with auto-recognized XML or action string configuration
STANDARDIZER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Standardizer
StandardizerAction - Interface in chemaxon.standardizer
Interface of standardizer actions.
StandardizerActionDescriptor - Class in chemaxon.standardizer
Descriptor of StandardizerAction objects.
Contains all needed interface informations.
StandardizerActionDescriptor(Class<? extends StandardizerAction>) - Constructor for class chemaxon.standardizer.StandardizerActionDescriptor
Constructs a descriptor based on standardizer action class.
StandardizerActionFactory - Class in chemaxon.standardizer
Factory of StandardizerAction objects
Initializes the list of available standardizer action based on the provided factory configuration XML files, defining the factory: Internal list: the factory configuration XML containing the definitions of internal (Chemaxon defined) standardizer actions, that should be available using the factory External list: the factory configuration XML containing the definitions of external (user defined) standardizer actions, that should be available using the factory The schema of the definition XML is defined by the StandardizerActionFactory.DEFAULT_CONFIGURATION_SCHEMA:
StandardizerActionFactory() - Constructor for class chemaxon.standardizer.StandardizerActionFactory
Default constructor.
StandardizerActionFactory(String, String) - Constructor for class chemaxon.standardizer.StandardizerActionFactory
With this constructor inner and external configuration location can be defined.
StandardizerActionFactory.Builder - Class in chemaxon.standardizer
Builder class for StandardizerActionFactory.
StandardizerActionFactory.StandardizerClassDescriptor - Class in chemaxon.standardizer
Descriptor of a standardizer class
StandardizerActionInfo - Annotation Interface in chemaxon.standardizer
Standardizer action info annotation
This annotation is responsible for adding user interface related meta data for StandardizerAction implementations
StandardizerActionRunner - Interface in chemaxon.standardizer.runner
The descendant of StandardizerActionRunner interface has to provide the functionality to run StandardizerConfiguration instances automatically on the given molecule.
As standardizer configuration may contain actions in groups, using StandardizerActionRunner.setTargetGroup(String) and StandardizerActionRunner.setTargetGroups(String...) methods, the target groups, containing the actions to be executed can be defined.
By default, in case of the provided configuration containing error(s) the runner throws IllegalArgumentException.
StandardizerActionStringReader - Class in chemaxon.standardizer.configuration.reader
An implementation of StandardizerConfigurationReader for parsing action strings
If the configuration contains references to molecules/molecule files not contained by the configuration file, the base path of the configuration must be set by the method StandardizerActionStringReader.setPath(String) before gathering the configuration.
Syntax of action strings:
<actionString>::=<actionStringEntry>(..<actionStringEntry>) *
<actionStringEntry>::=<standardizerAction>|<groupDefinitions& gt;<standardizerAction>
<groupDefinitions>::=<groupDefinition>(,<groupDefinition>)*
<groupDefinition>::=(a-zA-Z0-9)+
<standardizerAction>::=<actionName>|<actionName>< parameters>
<actionName>::=(a-zA-Z0-9)+
<parameters>::=<parameter>(:<parameter>)*
<parameter>::=<key>| '<extendedKey>'|<key>=<value>|<key>='<extendedValu e & g t ; '
<key>::=(a-zA-Z0-9)+
<value>::=(anything\{.':,"})*
<extendedKey>::=(anything\{'" })*
<extendedValue>::=(anything\{'"})*
StandardizerActionStringReader(String) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Default constructor of the reader.
StandardizerActionStringReader(String, StandardizerActionFactory) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
Constructor with custom standardizer action factory
StandardizerClassDescriptor() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Initializes an empty standardizer class descriptor
StandardizerClassDescriptor(String, String, String, String) - Constructor for class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
Initializes a standardizer class descriptor
STANDARDIZERCONFIG_XML - Static variable in class chemaxon.standardizer.StandardizerActionFactory
Chemaxon's default standardizer action configuration file name
StandardizerConfiguration - Class in chemaxon.standardizer.configuration
Standardizer configuration class.
Contains a list of StandardizerAction instances.
StandardizerConfiguration() - Constructor for class chemaxon.standardizer.configuration.StandardizerConfiguration
 
standardizerConfigurationNode - Variable in class chemaxon.descriptors.MDParameters
node defining the Standardizer configuration
StandardizerConfigurationReader - Interface in chemaxon.standardizer.configuration.reader
This interface is provided for classes which can read the configuration of StandardizerActionRunner
Configuration error
There are 2 kinds of configuration errors for execution configuration.
StandardizerResult - Class in chemaxon.standardizer.concurrent
Result of a standardization process for a molecule
StandardizerResult(Molecule, Molecule, List<Changes>, List<StandardizerAction>) - Constructor for class chemaxon.standardizer.concurrent.StandardizerResult
Initializes a standardizer result for a successful execution
StandardizerResult(Molecule, Molecule, List<StandardizerAction>) - Constructor for class chemaxon.standardizer.concurrent.StandardizerResult
Initializes a standardizer result for a successful execution
StandardizerResult(Molecule, Exception) - Constructor for class chemaxon.standardizer.concurrent.StandardizerResult
Initializes a standardizer result for an error
StandardizerRunner - Class in chemaxon.standardizer.concurrent
Concurrent executor of the standardizer
StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration) - Constructor for class chemaxon.standardizer.concurrent.StandardizerRunner
Deprecated.
Won't be public in the future
StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration, int) - Constructor for class chemaxon.standardizer.concurrent.StandardizerRunner
Deprecated.
Won't be public in the future
StandardizerRunner(Iterator<Molecule>, StandardizerConfiguration, int, String) - Constructor for class chemaxon.standardizer.concurrent.StandardizerRunner
Deprecated.
Won't be public in the future
StandardizerRunner.ErrorHandlingPolicy - Enum Class in chemaxon.standardizer.concurrent
Policy for error handling
StandardizerUtil - Class in chemaxon.standardizer
Utility class for standardizer
Functionalities of old standardizer can be simulated using this class.
StandardizerUtil() - Constructor for class chemaxon.standardizer.StandardizerUtil
 
StandardizerXMLReader - Class in chemaxon.standardizer.configuration.reader
XML Configuration reader for standardizer configurations.
StandardizerXMLReader(InputStream) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerXMLReader
Initiate an StandardizerXMLReader instance with the given inputSteam with the configuration
StandardizerXMLReader(InputStream, StandardizerActionFactory) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerXMLReader
Initiate an StandardizerXMLReader instance with the given inputSteam with the configuration
StandardUpperBoundCalculator - Class in com.chemaxon.search.mcs.upperbound
This class implements a max-weight matching-based upper bound calculator for the MCS problem.
StandardUpperBoundCalculator() - Constructor for class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator
 
STAR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that star atom had found in the molecule
STAR - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the star atom.
StarAtomChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting so called star atoms having "*" as atomic symbol.
StarAtomChecker() - Constructor for class chemaxon.checkers.StarAtomChecker
Default constructor
start() - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
 
start(MDocSource, String) - Method in class chemaxon.marvin.view.swing.TableSupport
Starts loading molecules.
startEMFGenerator() - Static method in class chemaxon.util.ImageExportUtil
Starts the initialization of the .NET based EMF generator on a background thread.
startGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream
Starts grabbing lines.
startNow(MDocSource, String) - Method in class chemaxon.marvin.view.swing.TableSupport
Starts loading molecules immediately.
startPermanentResources() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Starts all the permanent native resources that have to be started to do fast and reliable copy in Marvin.
STATICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin
pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)
STATUS_BAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "statusBar".
STEP_DEFAULT - Static variable in class chemaxon.marvin.calculations.AlignmentPlugin
 
stepWedge() - Method in class chemaxon.struc.MolBond
Set the bond from 0 to MolBond.UP or UP to MolBond.DOWN.
stereo(int) - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates absolute stereo configuration of the given atom.
stereo(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.stereo(int)
stereo(int, int) - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates absolute stereo configuration of the given double bond.
stereo(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.stereo(int, int)
STEREO_CARE_BOX - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing stereo search markers in the molecule
STEREO_DIASTEREOMER - Static variable in interface chemaxon.sss.SearchConstants
The diastereomers targets of a given query structure are also matched.
STEREO_ENANTIOMER - Static variable in interface chemaxon.sss.SearchConstants
The enantiomer targets of a given query structure are also matched.
STEREO_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Equality is needed in stereochemistry.
STEREO_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Stereo information is not considered during searching.
STEREO_INVERSION_RETENTION_MARK - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing stereo inversion/retention marks in the molecule/reaction
STEREO_MASK - Static variable in class chemaxon.struc.MolBond
Single and double bond stereo mask.
STEREO_MODEL_COMPREHENSIVE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to use comprehensive stereo model, which combines the advantages of local and global stereo models.
STEREO_MODEL_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
For markush search in all cases and for non-markush duplicate search in query tables SearchConstants.STEREO_MODEL_LOCAL, for non-markush duplicate search (with the exception of query tables) SearchConstants.STEREO_MODEL_GLOBAL.
STEREO_MODEL_GLOBAL - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to use global stereo information (global parity, global double bond stereo configuration, etc).
STEREO_MODEL_LOCAL - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to use local stereo information only (local parity, local double bond stereo configuration, etc).
STEREO_SPECIFIC - Static variable in interface chemaxon.sss.SearchConstants
Stereo information is considered during searching.
STEREO1_MASK - Static variable in class chemaxon.struc.MolBond
Single bond stereo mask.
STEREO2_CARE - Static variable in class chemaxon.struc.MolBond
Cis/trans info of this bond is taken care of during the SSS process if this flag is set - used only for query bonds.
StereoActivePart - Class in chemaxon.struc
Stereo active molecule part with stereo active atom index and its ligands which takes part in the stereo description.
StereoActivePart(int, int[]) - Constructor for class chemaxon.struc.StereoActivePart
Creates a new stereo active part.
StereoAnalysis - Class in com.chemaxon.calculations.stereoanal
The stereo analysis module is able to calculate stereochemical descriptors for a molecule, giving an analysis in terms of the stereochemical properties.
API usage example:
StereoAnalysis(Molecule) - Constructor for class com.chemaxon.calculations.stereoanal.StereoAnalysis
Creates an analysis.
StereoAnalysis(Molecule, String) - Constructor for class com.chemaxon.calculations.stereoanal.StereoAnalysis
Creates an analysis.
StereoCareBoxChecker - Class in chemaxon.checkers
Checker to find molecules containing Stereo Care Boxes.
StereoCareBoxChecker() - Constructor for class chemaxon.checkers.StereoCareBoxChecker
Creates a stereo care box checker.
StereoCenter - Interface in com.chemaxon.calculations.stereoanal.stereocenters
Interface for stereo centers.
StereoCenterVisitor - Interface in com.chemaxon.calculations.stereoanal.filters
Visitor interface for stereo centers.
StereoCheckUtility - Class in chemaxon.checkers
Deprecated, for removal: This API element is subject to removal in a future version.
Will be removed from the public API.
StereoCheckUtility() - Constructor for class chemaxon.checkers.StereoCheckUtility
Deprecated.
 
Stereochemistry - Class in chemaxon.calculations.stereo
Central class for accessing functions analyzing the topology of a molecule.
Stereochemistry() - Constructor for class chemaxon.calculations.stereo.Stereochemistry
 
stereoClean() - Method in class chemaxon.struc.MoleculeGraph
Reset the wedges of the molecule, based on the actual parity information in 2D, remove wedges in 3D.
stereoClean() - Method in class chemaxon.struc.RgMolecule
Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.
stereoClean() - Method in class chemaxon.struc.RxnMolecule
Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.
StereoConstants - Interface in chemaxon.struc
Constants for atom parity and double bond stereo.
StereoConstants - Interface in com.chemaxon.calculations.stereoanal
Wrapper interface for stereo constants.
StereoConstants.EnhancedStereoType - Enum Class in com.chemaxon.calculations.stereoanal
Enhanced stereo flags.
StereoConstants.StereoValue - Interface in com.chemaxon.calculations.stereoanal
Deprecated, for removal: This API element is subject to removal in a future version.
Check the implementing enums for details.
StereoConstants.StereoValue.AtropStereo - Enum Class in com.chemaxon.calculations.stereoanal
Deprecated, for removal: This API element is subject to removal in a future version.
StereoConstants.StereoValue.AxialStereo - Enum Class in com.chemaxon.calculations.stereoanal
Deprecated, for removal: This API element is subject to removal in a future version.
StereoConstants.StereoValue.CisTransStereo - Enum Class in com.chemaxon.calculations.stereoanal
Deprecated, for removal: This API element is subject to removal in a future version.
StereoConstants.StereoValue.TetrahedralStereo - Enum Class in com.chemaxon.calculations.stereoanal
Deprecated, for removal: This API element is subject to removal in a future version.
StereoConstants.Type - Enum Class in com.chemaxon.calculations.stereoanal
Stereo center type.
stereoDoubleBondCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of stereo double bonds.
stereoDoubleBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated, for removal: This API element is subject to removal in a future version.
as of release 5.5, replaced by Stereochemistry.stereoDoubleBondCount()
StereoInversionRetentionMarkChecker - Class in chemaxon.checkers
Detects reaction inversion/retention marks on atoms.
StereoInversionRetentionMarkChecker() - Constructor for class chemaxon.checkers.StereoInversionRetentionMarkChecker
Default constructor
STEREOISOMER_DOUBLEBOND - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
STEREOISOMER_TETRAHEDRAL - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
StereoisomerEnumeration - Class in com.chemaxon.calculations.stereoisomers
Enumerates stereoisomers of the specified molecule.
StereoisomerEnumeration(Molecule) - Constructor for class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
Constructs a StereoisomerEnumeration object with default settings.
StereoisomerEnumeration(Molecule, StereoisomerSettings) - Constructor for class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
Construct new StereoisomerEnumeration object.
StereoisomerEnumeration(Molecule, StereoisomerSettings, String) - Constructor for class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
Construct new StereoisomerEnumeration object.
StereoisomerPlugin - Class in chemaxon.marvin.calculations
Deprecated.
StereoisomerPlugin() - Constructor for class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
StereoisomerSettings - Class in com.chemaxon.calculations.stereoisomers
Settings class for StereoisomerEnumeration.
StereoisomerSettings.StereoisomerType - Enum Class in com.chemaxon.calculations.stereoisomers
Types of stereoisomers.
stereoisomerTypes() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Returns the type of generated stereoisomers.
stericEffectIndex(int) - Method in class chemaxon.calculations.TopologyAnalyser
Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.
STGRP_ABS - Static variable in interface chemaxon.struc.StereoConstants
Absolute stereo group type for enhanced stereo representation.
STGRP_AND - Static variable in interface chemaxon.struc.StereoConstants
AND stereo group type for enhanced stereo representation.
STGRP_NONE - Static variable in interface chemaxon.struc.StereoConstants
Empty stereo group type setting meaning no enhanced stereo label.
STGRP_OR - Static variable in interface chemaxon.struc.StereoConstants
OR stereo group type for enhanced stereo representation.
STICK_DISTANCE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "stickdst".
STICK_THICKNESS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "stickThickness".
stickRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
stickSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
Sticky(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky
Copy constructor.
Sticky(MPolyline, int) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky
Constructor.
Sticky(MRectangle, int) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky
Constructor.
Sticky(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky
Copy constructor.
STOICHIOMETRY_KEY - Static variable in class chemaxon.standardizer.actions.ExpandAction
Key of type for parsing and property changes
stop() - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
 
stop() - Method in class chemaxon.sss.search.MolSearch
 
stop() - Method in class chemaxon.sss.search.Search
Tries to stop the running search as fast as possible.
storageSizeChanged(MDocStorage, int, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
Storage size changed.
storageSizeFinalized(MDocStorage) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
Final storage size determined.
store() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Stores a new result item.
storeDoc(MDocument, int, String) - Method in class chemaxon.marvin.view.MDocStorage
Store new document and free the oldest accessed if the number of documents is too much to fit in memory.
storeDrawProperty(String, String) - Method in class chemaxon.marvin.space.GraphicComponent
Stores the given property.
storeInDocument(NoStructure, MDocument) - Static method in class chemaxon.struc.NoStructure
Puts the given NoStructe into the document.
storeMainDoc(MDocument, int) - Method in class chemaxon.marvin.view.MDocStorage
Store new document and free the oldest accessed if the number of documents is too much to fit in memory.
storeTemporaryObject(String, Object) - Method in class chemaxon.struc.MolAtom
Stores an object temporarily.
STRAIGHT_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents molecules containing "either" double bonds.
StraightDoubleBondChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting double bonds in molecule which can be either "E" or "Z".
StraightDoubleBondChecker() - Constructor for class chemaxon.checkers.StraightDoubleBondChecker
Constructs EitherDoubleBondChecker instance
stringBuffer - Variable in class chemaxon.marvin.io.MolExportModule
This buffer can contain the molecule file contents, in case of a text format.
stringFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Read the contents of a location into a String.
stringFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Read the contents of a location into a String.
stringFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Read the contents of a location when it is not null.
stringFromNullableLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Deprecated.
Read the contents of a location when it is not null.
stringToArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
 
stringToScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
 
stringValue() - Method in class chemaxon.struc.prop.MStringProp
Gets the string value.
StripSaltsAction - Class in chemaxon.standardizer.advancedactions
Strip salts standardizer action
StripSaltsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.StripSaltsAction
Initializes strip salts action
STRUCTURAL_FRAMEWORKS_PLUGIN - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Structural Frameworks Plugin
StructuralFrameworksPlugin - Class in chemaxon.marvin.calculations
Plugin class to calculate Bemis-Murcko and other structural scaffolds of input molecules.
StructuralFrameworksPlugin() - Constructor for class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
StructuralFrameworksPlugin.FrameworkTypes - Enum Class in chemaxon.marvin.calculations
FrameworkTypes represents the available calculations
StructuralFrameworksPlugin.VerbosePrinter - Interface in chemaxon.marvin.calculations
Verbose printer specification
STRUCTURE_CHECKER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Structure Checker
STRUCTURE_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction
Key of query molecule for parsing and property change
STRUCTURE_TO_NAME - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Structure to Name
StructureCheck - Class in chemaxon.checkers
This class contains the command line interface for running inner StructureChecker and StructureFixer instances.
StructureCheck() - Constructor for class chemaxon.checkers.StructureCheck
Creates a new structures checker console, sets the logging on null stream.
StructureChecker - Interface in chemaxon.checkers
General interface describing functions that are available for a chemical structure checker.
StructureCheckerDescriptor - Class in chemaxon.checkers
Descriptor for StructureChecker
StructureCheckerDescriptor(Class<? extends StructureChecker>) - Constructor for class chemaxon.checkers.StructureCheckerDescriptor
Constructs a descriptor based on checker class.
StructureCheckerErrorType - Enum Class in chemaxon.checkers
Enum containing possible error types for structure checkers.
StructureCheckerFactory - Class in chemaxon.checkers
Deprecated.
use CheckerFixerFactory instead
StructureCheckerFactory() - Constructor for class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Please consider using StructureCheckerFactory.getInstance() instead of calling this constructor directly.

Default constructor. Default configurations will be read.
StructureCheckerFactory(InputStream, InputStream) - Constructor for class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Please consider using StructureCheckerFactory.getInstance(String, String) instead of calling this constructor directly.

With this constructor inner and external configuration location can be defined.
StructureCheckerFactory(String, String) - Constructor for class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Please consider using StructureCheckerFactory.getInstance(String, String) instead of calling this constructor directly.

With this constructor inner and external configuration location can be defined.
StructureCheckerHelper - Class in chemaxon.checkers
This helper class contains utility functions used by StructureChecker instances providing constants and utility functions.
StructureCheckerHelper() - Constructor for class chemaxon.checkers.StructureCheckerHelper
 
StructureCheckerResult - Interface in chemaxon.checkers.result
An instance of StructureCheckerResult identifies a molecule problem
StructureCheckerUtility - Class in chemaxon.checkers
Utility to handle core features
StructureCheckerUtility() - Constructor for class chemaxon.checkers.StructureCheckerUtility
 
StructureCheckOptions - Class in chemaxon.checkers
Options descriptor for structure checker command line interface
StructureCheckOptions() - Constructor for class chemaxon.checkers.StructureCheckOptions
 
StructureCheckOptions.Mode - Enum Class in chemaxon.checkers
The mode of the structure check
StructureCheckOptions.ModeConverter - Class in chemaxon.checkers
Converter for Mode enumeration.
StructureCheckOptions.Type - Enum Class in chemaxon.checkers
The output type of the structure check
StructureCheckOptions.TypeConverter - Class in chemaxon.checkers
Converter for Type enumeration.
StructureFixer - Interface in chemaxon.fixers
A StructureFixer can fix a Molecule problem identified by a StructureCheckerResult
StructureFixerDescriptor - Class in chemaxon.fixers
Descriptor class for StructureFixer classes.
StructureFixerDescriptor(Class<? extends StructureFixer>) - Constructor for class chemaxon.fixers.StructureFixerDescriptor
Constructs a descriptor based on fixer class.
StructureFixerFactory - Class in chemaxon.fixers
Deprecated.
use CheckerFixerFactory instead
StructureFixerFactory() - Constructor for class chemaxon.fixers.StructureFixerFactory
Deprecated.
Default constructor.
StructureFixerFactory(InputStream, InputStream) - Constructor for class chemaxon.fixers.StructureFixerFactory
Deprecated.
Parameterized constructor.
StructureFixerFactory(String) - Constructor for class chemaxon.fixers.StructureFixerFactory
Deprecated.
Parameterized constructor.
StructureFixerFactory(String, String) - Constructor for class chemaxon.fixers.StructureFixerFactory
Deprecated.
Parameterized constructor.
structureFormat - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
The structure format used to represent hits converted from other sources than names (OSR, embedded structures, ...).
structureFormat(String) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
SubjectToRemoval - Annotation Interface in com.chemaxon.common.annotations
Denotes that an entity has been deprecated and is subject to removal in a release following the specified date.
SubProgressObserver - Interface in com.chemaxon.calculations.common
Deprecated, for removal: This API element is subject to removal in a future version.
Use ProgressObserver instead. Will be removed.
substring(int) - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets a substring.
substring(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a substring of the document.
substring(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets a substring.
substring(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a substring of the document.
SUBSTRUCTURE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that the needed substructure had found
SUBSTRUCTURE - Enum constant in enum class chemaxon.descriptors.MetricsType
 
SUBSTRUCTURE - Static variable in interface chemaxon.sss.SearchConstants
Substructure search that applies both screening and atom-by-atom search.
SUBSTRUCTURE_NOFIX - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that the needed substructure had found but no data will be available for the fix in the result
SubstructureChecker - Class in chemaxon.checkers
This descendant of AbstractStructureChecker is responsible for detecting substructures in a Molecule instance.
SubstructureChecker() - Constructor for class chemaxon.checkers.SubstructureChecker
Default constructor.
SubstructureChecker(String) - Constructor for class chemaxon.checkers.SubstructureChecker
Parameterized constructor.
SubstructureChecker(Map<String, String>) - Constructor for class chemaxon.checkers.SubstructureChecker
Parameterized constructor.
SubstructureCheckerResult - Class in chemaxon.checkers.result
 
SubstructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<int[]>, String) - Constructor for class chemaxon.checkers.result.SubstructureCheckerResult
Constructor which initialize all the properties.
SubstructureFixer - Class in chemaxon.fixers
Fixer to fix substructure issues.
SubstructureFixer() - Constructor for class chemaxon.fixers.SubstructureFixer
 
subTask(String, long) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
subtract(DPoint3) - Method in class chemaxon.struc.DPoint3
Subtract the given v2 vector from this one.
subtract(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Calculates the difference of the two vectors
SUM_OF_VALUES - Static variable in class chemaxon.marvin.space.SurfaceColoring
Will the sum of the affecting properties be mapped onto the surface.
sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.MoleculeGraph
For internal use only.
sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.RgMolecule
For internal use only.
sumDistanceSquare(MoleculeGraph, DPoint3) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the sum of the distance square for each atom from a point.
sumNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator
 
sumOfRadicals() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the sum of the radicals of all atoms of the molecule.
SUPERATOM - Enum constant in enum class chemaxon.struc.SgroupType
 
SuperatomSgroup - Class in chemaxon.struc.sgroup
Superatom S-group.
SuperatomSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
Constructs a superatom S-group in expanded state.
SuperatomSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
Constructs a superatom S-group.
SuperatomSgroup(SuperatomSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
Copy constructor.
superGraph - Variable in class chemaxon.struc.MoleculeGraph
Parent of all parents.
SUPERSTRUCTURE - Enum constant in enum class chemaxon.descriptors.MetricsType
 
SUPERSTRUCTURE - Static variable in interface chemaxon.sss.SearchConstants
Superstructure search (Value=6)
support - Variable in class chemaxon.standardizer.AbstractStandardizerAction
 
SURE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
SURE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
SURFACE_COLOR_GRID_MAPPING - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_ATOMTYPE - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_B_FACTOR - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_CHAIN - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_CONSTANT - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_EP - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_RAINBOW - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_COLOR_TYPE_SS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_SIMPLIFICATION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_SMOOTHNESS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_TYPE_BLOBBY - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_TYPE_CONNOLLY - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_TYPE_GAUSSIAN - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_TYPE_SAS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SURFACE_TYPE_VDW - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SurfaceColoring - Class in chemaxon.marvin.space
SurfaceColoring is an easy-to-use tool to map different properties as colors onto surfaces.
SurfaceColoring(SurfaceComponent) - Constructor for class chemaxon.marvin.space.SurfaceColoring
The given surface is to be colored after the parametrization.
SurfaceColoring(ArrayList, SurfaceComponent) - Constructor for class chemaxon.marvin.space.SurfaceColoring
The given surface of the given molecules is to be colored after the parametrization.
SurfaceColoring(ArrayList, SurfaceComponent, float) - Constructor for class chemaxon.marvin.space.SurfaceColoring
The given surface of the given molecules is to be colored after the parametrization.
surfaceColorType - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
SurfaceComponent - Class in chemaxon.marvin.space
Class that represents a surface defined by its vertices, normal vectors and polygons.
SurfaceComponent(int) - Constructor for class chemaxon.marvin.space.SurfaceComponent
Creates a new instance of SurfaceComponent, sets its draw type to FILLED_TYPE.
SurfaceComponent(int, int) - Constructor for class chemaxon.marvin.space.SurfaceComponent
Creates a new SurfaceComponent, sets its draw type to FILLED_TYPE.
SurfaceComponent(int, int, int, int) - Constructor for class chemaxon.marvin.space.SurfaceComponent
Creates a new SurfaceComponent, sets its draw type to FILLED_TYPE.
surfaceGridPrecision - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
surfaceOf(GraphicComponent) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Tells whether it is the molecular surface of the given component (molecule).
surfaceSimplification() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Runs the (might be time-consuming) algorithm thst reduces the number of triangles of the surface.
surfaceSimplificationEnabled - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
surfaceSimplificationTolerance - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
surfaceSmoothnessFactor - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
surfaceType - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
svFuzzyIncrements - Variable in class chemaxon.descriptors.PFParameters
Fuzzy smoothing values for smoothing with user defined smoothing vector.
SVG - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat
 
SVG - Static variable in class chemaxon.formats.MFileFormat
Scalable Vector Graphics.
swap() - Method in class chemaxon.struc.MolBond
Change orientation.
swapAtoms(int, int) - Method in class chemaxon.struc.SelectionMolecule
Swap two atoms.
swapHeadTail() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Swaps the head and tail bonds of this sru if both are set.
SwingUtil - Class in chemaxon.marvin.util
Swing utility functions.
SwingUtil() - Constructor for class chemaxon.marvin.util.SwingUtil
 
switchToDeterminate(long) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Notifies that the remaining amount of work units to complete this task is known.
SYBYLMOL - Static variable in class chemaxon.formats.MFileFormat
Tripos SYBYL molfiles.
SYM_CX - Static variable in class chemaxon.struc.MolAtom
Atom symbol string for CxSMILES export.
SYM_EXPLH - Static variable in class chemaxon.struc.MolAtom
Atom symbol string contains explicit H count if this flag is set.
SYM_IMPLH - Static variable in class chemaxon.struc.MolAtom
Atom symbol string contains implicit H count is shown flag is set.
SYM_MOLEX - Static variable in class chemaxon.struc.MolAtom
Atom symbol string for Molfile export.
SYM_NEUTRAL - Static variable in class chemaxon.struc.MolAtom
Atom symbol string does not contain the charge if this flag is set.
SYM_SMARTS - Static variable in class chemaxon.struc.MolAtom
Atom symbol string for SMILES export.
SYM_SQBRACKETS - Static variable in class chemaxon.struc.MolAtom
Atom symbol is shown in square brackets if this flag is set.
symbolOf(int) - Static method in class chemaxon.struc.MolAtom
Gets the element symbol for the specified atomic number.
symbolOf(int, int) - Static method in class chemaxon.struc.MolAtom
Gets the special element symbol for the specified atomic and mass numbers.
SYN - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, syn (relative configuration).
szegedIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Szeged index of the molecule.

T

T_BRACES - Static variable in class chemaxon.struc.graphics.MBracket
Braces.
T_CHEVRONS - Static variable in class chemaxon.struc.graphics.MBracket
Chevrons.
T_DOUBLE - Static variable in class chemaxon.struc.graphics.MBracket
The bracket has two sides.
T_NOROT - Static variable in class chemaxon.struc.graphics.MRectangle
Disable rotation.
T_ROUND - Static variable in class chemaxon.struc.graphics.MBracket
Round bracket type (parenthesis).
T_SINGLE - Static variable in class chemaxon.struc.graphics.MBracket
The bracket has one side.
T_SQUARE - Static variable in class chemaxon.struc.graphics.MBracket
Square bracket type.
Ta - Static variable in class chemaxon.core.ChemConst
 
TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "tabScale".
TableOptions - Class in chemaxon.marvin.view.swing
SDF table options for MarvinView.
TableSupport - Class in chemaxon.marvin.view.swing
Viewer table support class.
TaggedCalculator - Interface in chemaxon.calculator
Base interface for calculator objects that can report a set of optional tags, which are used primarily to identify the calculator in configuration files.
TaggedCalculatorInputChecker - Interface in chemaxon.calculator
Instances of this interface are used by calculators to check if they can process an input molecule.
tags() - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
tags() - Method in class chemaxon.calculations.nmr.NMRCalculator
 
tags() - Method in interface chemaxon.calculator.TaggedCalculator
Returns the set of tags reported by this calculator.
tags() - Method in class chemaxon.marvin.calculations.ConformerPlugin
 
tags() - Method in class chemaxon.marvin.calculations.GeometryPlugin
 
tags() - Method in class chemaxon.marvin.calculations.HBDAPlugin
 
tags() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
 
tags() - Method in class chemaxon.marvin.calculations.MSAPlugin
 
tags() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
 
tags() - Method in class chemaxon.marvin.calculations.ResonancePlugin
 
tags() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
tags() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
 
tags() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the tags of the action as a string, divided by comma characters
tags() - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
 
TAGS - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
tags of action
TAIL - Static variable in class chemaxon.struc.graphics.MPolyline
Arrow tail (feather).
tanimoto() - Method in class chemaxon.marvin.alignment.Alignment
Calculates the atomic colored volume Tanimoto similarity of two 3D molecules.
tanimoto(float[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates Tanimoto dissimilarity for floating point values.
tanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
Calculates Tanimoto dissimilarity for floating point values.
TANIMOTO - Enum constant in enum class chemaxon.descriptors.MetricsType
 
target - Variable in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
The target molecule.
target - Variable in class chemaxon.sss.search.MolComparator
 
TargetHomologyMatchingMode - Enum Class in chemaxon.sss.search.options
Option to control homology matching on target side.
targetMol - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Target molecule (it is neither cloned nor modified).
targetSearchData - Variable in class chemaxon.sss.search.MolComparator
 
TaskScheduler - Interface in chemaxon.marvin.view
Generic task scheduler interface.
TAUTOMER_SEARCH_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for indicating that tautomer duplicate search option is not explicitly set.
TAUTOMER_SEARCH_OFF - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for switching tautomer searching off.
TAUTOMER_SEARCH_ON - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for switching tautomer searching on.
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.
TAUTOMERIZATION_CANONICAL - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
TAUTOMERIZATION_DOMINANTS - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
TAUTOMERIZATION_GENERIC - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
TAUTOMERIZATION_MAJOR - Enum constant in enum class chemaxon.calculator.CalculatorTag
 
TautomerizationPlugin - Class in chemaxon.marvin.calculations
Plugin class for generating tautomer structures.
TautomerizationPlugin() - Constructor for class chemaxon.marvin.calculations.TautomerizationPlugin
Constructor.
TautomerizeAction - Class in chemaxon.standardizer.actions
Tautomerize standardizer action
TautomerizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.TautomerizeAction
Initializes the action
TautomerizeAction.TautomerForm - Enum Class in chemaxon.standardizer.actions
 
Tb - Static variable in class chemaxon.core.ChemConst
 
Tc - Static variable in class chemaxon.core.ChemConst
 
Te - Static variable in class chemaxon.core.ChemConst
 
tell() - Method in class chemaxon.formats.MolImporter
Returns the current file offset.
TEMPLATE_FILE_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction
Key of template file for parsing and property change
TEMPLATE_TOOLBAR_CUSTOMIZABLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "templateToolbarCustomizable".
TEMPLATEBASED - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Template based clean
TEMPLATES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "tmpls".
TEMPLATES_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction
Key for templates property change
temporaryObjects - Variable in class chemaxon.struc.MDocument
 
testEncoding(String) - Static method in class chemaxon.formats.MFileFormatUtil
Tests whether the given charset name is supported by this JVM
testLine(String) - Static method in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
testLine(String) - Static method in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
testRecord(String) - Static method in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated, for removal: This API element is subject to removal in a future version.
TETRAHEDRAL - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
 
TETRAHEDRAL - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
Tetrahedral stereo center.
TETRAHEDRAL - Enum constant in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType
Tetrahedral stereoisomers.
TETRAHEDRAL - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
TetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral
Filter for tetrahedral centers.
TetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter
 
TetrahedralStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Tetrahedral stereo center implementation.
TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Constructs a new instance of tetrahedral stereo center.
TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue, EnhancedStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Constructs a new instance of tetrahedral stereo center.
TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue, EnhancedStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Constructs a new instance of tetrahedral stereo center with attached data.
TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue, Optional<EnhancedStereo>, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Constructs a new instance of tetrahedral stereo center with attached data.
TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, EnhancedStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, EnhancedStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, Optional<EnhancedStereo>, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
Deprecated, for removal: This API element is subject to removal in a future version.
tetrahedralStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the tetrahedral stereogenic centers.
tetrahedralStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the tetrahedral stereogenic centers (with attached data).
TetrahedralStereoDescriptor - Class in chemaxon.struc
 
TetrahedralStereoDescriptor(CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue, StereoActivePart) - Constructor for class chemaxon.struc.TetrahedralStereoDescriptor
 
TetrahedralStereoDescriptor(CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue, StereoActivePart, int) - Constructor for class chemaxon.struc.TetrahedralStereoDescriptor
 
text - Variable in class chemaxon.marvin.space.monitor.Label
 
TEXT - Static variable in class chemaxon.formats.MolExporter
Use this flag to write text files with OS dependent line separators.
TEXT - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Property display type: display in text.
TEXTMODE - Static variable in class chemaxon.formats.MdlCompressor
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.1, there is no possibility to do that
textPositionX - Variable in class chemaxon.marvin.space.monitor.Label
 
textPositionY - Variable in class chemaxon.marvin.space.monitor.Label
 
textPosWindow - Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
 
Th - Static variable in class chemaxon.core.ChemConst
 
theAtoms - Variable in class chemaxon.struc.MoleculeGraph
The atoms (nodes).
theBonds - Variable in class chemaxon.struc.MolAtom
The bonds.
theBonds - Variable in class chemaxon.struc.MoleculeGraph
The bonds (edges).
THICKNESS_SET_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Thickness is set flag.
THREE_DIM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that 3d coordinates had found in the molecule
ThreeDimensionChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms having non-zero Z coordinates.
ThreeDimensionChecker() - Constructor for class chemaxon.checkers.ThreeDimensionChecker
Default constructor
thresholds - Variable in class chemaxon.descriptors.MDParameters
dissimilarity thresholds values
Ti - Static variable in class chemaxon.core.ChemConst
 
TIFF - Static variable in class chemaxon.formats.MFileFormat
Tagged Image File Format.
timeLimit - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Time limit in milliseconds (-1 means disabled).
timeoutCanceller(long) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Deprecated, for removal: This API element is subject to removal in a future version.
timeoutLimitMilliseconds - Variable in class chemaxon.sss.search.SearchOptions
The search on a single target timeouts reaching this number of milliseconds.
title - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The result frame title.
Tl - Static variable in class chemaxon.core.ChemConst
 
Tm - Static variable in class chemaxon.core.ChemConst
 
toBinaryString() - Method in class chemaxon.descriptors.ChemicalFingerprint
Converts the fingerprint into a 0,1 string.
toBinaryString() - Method in class chemaxon.descriptors.ECFP
Converts the fingerprint into a fixed-length 0,1 string.
toBinaryString() - Method in class chemaxon.descriptors.MolecularDescriptor
Creates the binary string representation of a MolecularDescriptor object.
toBinaryString() - Method in class chemaxon.descriptors.ReactionFingerprint
Converts the fingerprint into a 0,1 string.
toBinaryString() - Method in class chemaxon.descriptors.ShapeDescriptor
 
toBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Returns a binary representation of the given molecule.
toBinFormat(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
toBitSet() - Method in class chemaxon.descriptors.ECFP
Returns a bit vector storing the "folded" binary representation of the fingerprint.
toData() - Method in class chemaxon.descriptors.BCUT
Converts a BCUT object into a byte array.
toData() - Method in class chemaxon.descriptors.ChemicalFingerprint
Converts a chemical fingerprint object into a byte array.
toData() - Method in class chemaxon.descriptors.CustomDescriptor
Converts a CustomDescriptor object into a byte array.
toData() - Method in class chemaxon.descriptors.ECFP
Converts an ECFP object into a byte array.
toData() - Method in class chemaxon.descriptors.MolecularDescriptor
Converts the internal (memory) representation of a MolecularDescriptor instance into an external format that can be stored in a database.
toData() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Converts a PharmacophoreFingerprint object into a byte array.
toData() - Method in class chemaxon.descriptors.ReactionFingerprint
Converts a reaction fingerprint object into a byte array.
toData() - Method in class chemaxon.descriptors.ScalarDescriptor
Converts a ScalarDescriptor object into an array of bytes.
toData() - Method in class chemaxon.descriptors.ShapeDescriptor
 
toData() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
Deprecated.
use ShapeData.toData() instead.
toDecimalString() - Method in class chemaxon.descriptors.BCUT
Converts the BCUT descriptor into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.ChemicalFingerprint
Converts the fingerprint into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.CustomDescriptor
Converts the descriptor into a readable string of decimal numbers (float or integer, depending on descriptor type).
toDecimalString() - Method in class chemaxon.descriptors.ECFP
Converts the ECFP fingerprint into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.MolecularDescriptor
Creates the string representation of a MolecularDescriptor object.
toDecimalString() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Converts the fingerprint into a string of decial numbers.
toDecimalString() - Method in class chemaxon.descriptors.ReactionFingerprint
Converts the fingerprint into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.ScalarDescriptor
Converts the descriptor value into a readable string.
toDecimalString() - Method in class chemaxon.descriptors.ShapeDescriptor
 
toFeatureSet() - Method in class chemaxon.descriptors.ECFP
Deprecated, for removal: This API element is subject to removal in a future version.
As of JChem 5.4.1, replaced by ECFP.toIdentiferSet().
toFloatArray() - Method in class chemaxon.descriptors.BCUT
Creates the float array representation of a BCUT descriptor object.
toFloatArray() - Method in class chemaxon.descriptors.ChemicalFingerprint
Creates the float array representation of the fingerprint.
toFloatArray() - Method in class chemaxon.descriptors.CustomDescriptor
Creates the float array representation of a CustomDescriptor object.
toFloatArray() - Method in class chemaxon.descriptors.ECFP
Creates the float array representation of a ECFP fingerprint object.
toFloatArray() - Method in class chemaxon.descriptors.MolecularDescriptor
Creates the float array representation of a MolecularDescriptor object.
toFloatArray() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Creates the float array representation of a MolecularDescriptor object.
toFloatArray() - Method in class chemaxon.descriptors.ReactionFingerprint
Creates the float array representation of the fingerprint.
toFloatArray() - Method in class chemaxon.descriptors.ScalarDescriptor
Creates the float array representation of the descriptor.
toFloatArray() - Method in class chemaxon.descriptors.ShapeDescriptor
 
toFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Returns a string representation of the given molecule.
toFormat(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
toHistogramString(String, boolean) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Creates the string representation of the fingerprint.
toIdentiferSet() - Method in class chemaxon.descriptors.ECFP
Converts the fingerprint to a set of Integer identifiers.
toIntArray() - Method in class chemaxon.descriptors.ECFP
Converts the fingerprint to an array of int identifiers.
token - Variable in exception chemaxon.naming.NamePrefixException
 
toList() - Method in class chemaxon.sss.search.MolSearchOptions
Get all search option names.
toList() - Method in class chemaxon.sss.search.SearchOptions
Converts this options object to a list of a strings.
toMolecule() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult
Creates a single two-fragment molecule from the reference and aligned molecule.
toObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Returns a String, byte[] or Image representation of the given molecule.
toObject(String) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
toolbar - Variable in class chemaxon.marvin.space.MSpaceEasy
Deprecated, for removal: This API element is subject to removal in a future version.
TOOLBAR_FLOATABLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "toolbarFloatable".
TOOLBAR_TEMPLATES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "ttmpls".
topLevelContainer - Static variable in class chemaxon.marvin.beans.MarvinPane
The top level container of the pane
toPoint2D() - Method in class chemaxon.struc.DPoint3
 
TOPOLOGY_CHAIN - Static variable in class chemaxon.struc.MolBond
Bond is in a chain.
TOPOLOGY_MASK - Static variable in class chemaxon.struc.MolBond
Bond topology mask.
TOPOLOGY_RING - Static variable in class chemaxon.struc.MolBond
Bond is in a ring.
TopologyAnalyser - Class in chemaxon.calculations
Central class for accessing functions analysing the topology of a molecule.
TopologyAnalyser() - Constructor for class chemaxon.calculations.TopologyAnalyser
 
TopologyAnalyserPlugin - Class in chemaxon.marvin.calculations
Calculates topological data.
TopologyAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Constructor.
torsion(double, float[], float[], int[]) - Method in class chemaxon.marvin.space.MoleculeComponent
Changes torsion angle.
toString() - Method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
 
toString() - Method in class chemaxon.calculations.nmr.Shift
 
toString() - Method in class chemaxon.checkers.AbstractStructureChecker
 
toString() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
toString() - Method in enum class chemaxon.checkers.FixMode
 
toString() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
toString() - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
toString() - Method in class chemaxon.checkers.SubstructureChecker
 
toString() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
 
toString() - Method in class chemaxon.descriptors.BCUT
Converts the descriptor into a readable string.
toString() - Method in class chemaxon.descriptors.BCUTParameters
Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.ChemicalFingerprint
Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.CustomDescriptor
Converts the descriptor into a readable string.
toString() - Method in class chemaxon.descriptors.ECFP
Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.MDParameters
Returns the parameter values in string.
toString() - Method in class chemaxon.descriptors.MolecularDescriptor
Creates the string representation of a MolecularDescriptor object.
toString() - Method in class chemaxon.descriptors.PFParameters
Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.ReactionFingerprint
Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.ScalarDescriptor
Converts the descriptor value into a readable string.
toString() - Method in class chemaxon.descriptors.scalars.HBParameters
Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.scalars.LDParameters
Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.ShapeDescriptor
 
toString() - Method in class chemaxon.fixers.StructureFixerDescriptor
 
toString() - Method in class chemaxon.formats.MFileFormat
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.formats.recognizer.RecognizerList
Deprecated.
Gets the string representation of the list.
toString() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
toString() - Method in class chemaxon.marvin.alignment.atrop.BondInfo
 
toString() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanStep
 
toString() - Method in class chemaxon.marvin.alignment.Pharmacophore3D
 
toString() - Method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
 
toString() - Method in class chemaxon.marvin.io.MRecordReader.Position
 
toString() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
 
toString() - Method in class chemaxon.marvin.services.DynamicArgument
 
toString() - Method in class chemaxon.marvin.services.ServiceArgument
 
toString() - Method in class chemaxon.marvin.space.BoundingBox
Returns the minimum and maximum coordinates of the box.
toString() - Method in class chemaxon.marvin.space.CellOrComponentId
Deprecated.
Returns the internal cell and component indices.
toString() - Method in class chemaxon.marvin.space.ComponentElement
Returs the indices of the CompnentElement.
toString() - Method in class chemaxon.marvin.space.GraphicComponent
 
toString() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
toString() - Method in class chemaxon.marvin.space.PharmacophorePoint
 
toString() - Method in class chemaxon.marvin.util.OptionDescriptor
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.sss.search.MarkushFeature
Deprecated.
 
toString() - Method in enum class chemaxon.sss.search.options.HaltOnErrorOption
Returns the string representation.
toString() - Method in enum class chemaxon.sss.search.options.HomologyTranslationOption
 
toString() - Method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
 
toString() - Method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
 
toString() - Method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
toString() - Method in class chemaxon.sss.search.SearchHit
 
toString() - Method in class chemaxon.sss.search.SearchOptions
Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
toString() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
toString() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
 
toString() - Method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
 
toString() - Method in class chemaxon.standardizer.actions.AliasToGroupAction
 
toString() - Method in class chemaxon.standardizer.actions.AromatizeAction
 
toString() - Method in enum class chemaxon.standardizer.actions.AromatizeAction.Type
 
toString() - Method in class chemaxon.standardizer.actions.ClearStereoAction
 
toString() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
 
toString() - Method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
 
toString() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
toString() - Method in class chemaxon.standardizer.actions.ExpandAction
 
toString() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
toString() - Method in class chemaxon.standardizer.actions.MapAction
 
toString() - Method in class chemaxon.standardizer.actions.MapReactionAction
 
toString() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
 
toString() - Method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
 
toString() - Method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
 
toString() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
 
toString() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
 
toString() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
 
toString() - Method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
 
toString() - Method in class chemaxon.standardizer.actions.TautomerizeAction
 
toString() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
 
toString() - Method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
 
toString() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
 
toString() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
toString() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
 
toString() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
toString() - Method in class chemaxon.standardizer.advancedactions.TransformAction
 
toString() - Method in class chemaxon.standardizer.Changes
 
toString() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
 
toString() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
 
toString() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
 
toString() - Method in class chemaxon.struc.CTransform3D
Gets a string representation of the matrix.
toString() - Method in class chemaxon.struc.DPoint3
Gets a string representation of the point
toString() - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
toString() - Method in class chemaxon.struc.graphics.MFont
 
toString() - Method in class chemaxon.struc.graphics.MMidPoint
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
toString() - Method in class chemaxon.struc.graphics.MTextAttributes
Returns the string representation of the attributes.
toString() - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Gets the string representation of the portion.
toString() - Method in class chemaxon.struc.graphics.MTextDocument
Gets the string representation of the document.
toString() - Method in class chemaxon.struc.MDocument
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MObject
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MolAtom
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MolBond
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MoleculeGraph
Overrides MoleculeGraph.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MPoint
 
toString() - Method in class chemaxon.struc.MProp
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.prop.MBooleanProp
 
toString() - Method in class chemaxon.struc.prop.MDoubleArrayProp
 
toString() - Method in class chemaxon.struc.prop.MDoubleProp
 
toString() - Method in class chemaxon.struc.prop.MHashProp
 
toString() - Method in class chemaxon.struc.prop.MHCoords3DProp
 
toString() - Method in class chemaxon.struc.prop.MIntegerArrayProp
 
toString() - Method in class chemaxon.struc.prop.MIntegerProp
 
toString() - Method in class chemaxon.struc.prop.MListProp
 
toString() - Method in class chemaxon.struc.prop.MMoleculeProp
String representation of this object: number of atoms, number of bonds.
toString() - Method in class chemaxon.struc.prop.MObjectProp
Create the serialized object base64 string representation.
toString() - Method in class chemaxon.struc.prop.MStringProp
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.RgMolecule
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.RxnMolecule
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.Sgroup
Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.StereoActivePart
 
toString() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
 
toString() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport
 
toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Creates a string representation.
toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
 
toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
toString() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
 
toString(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Returns a string representation of the group.
toString(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Returns a string representation of the group.
toString(int) - Method in class chemaxon.struc.Sgroup
Gets a string representation of the S-group.
toString(Object) - Static method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
toString(Object, int) - Static method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
toString(Object, DecimalFormat) - Static method in class chemaxon.jep.Evaluator
Deprecated, for removal: This API element is subject to removal in a future version.
Was only intended for internal use, will be removed.
toString(String) - Method in class chemaxon.sss.search.SearchOptions
Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
toString(String, boolean) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
Creates the string representation of the pharmacophore fingerprint.
toString(Node) - Method in class chemaxon.descriptors.MDParameters
Returns parts of the parameter values in string.
touchObject(int) - Method in class chemaxon.marvin.space.GraphicComponent
Returns the z coordinate of the nearest component.
touchObject(int) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Returns the z coordinate of the component being nearest to the viewing point.
TOXIC - Enum constant in enum class com.chemaxon.calculations.admet.HergClass
 
TPSA - Class in chemaxon.descriptors.scalars
Implements TPSA (Topological Polar Surface Area) value as a scalar descriptor.
TPSA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
Topological polar surface area.
TPSA - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Topological polar surface area.
TPSA() - Constructor for class chemaxon.descriptors.scalars.TPSA
Creates a new, empty logD descriptor.
TPSA(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.TPSA
Copy constructor.
TPSA(SDParameters) - Constructor for class chemaxon.descriptors.scalars.TPSA
Creates a new instance according to the parameters given.
TPSA(String) - Constructor for class chemaxon.descriptors.scalars.TPSA
Creates a new instance according to the parameters given.
TPSAPlugin - Class in chemaxon.marvin.calculations
Plugin class for TPSA (topological polar surface area) calculation.
TPSAPlugin() - Constructor for class chemaxon.marvin.calculations.TPSAPlugin
Constructor.
TRANS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
2 dimension: The rigid part's maximal indexed ligands placed in different half-plane according to the rigid part.
0 dimension: TRANS stereo value was set on the double bond for it's maximal indexed ligands.
TRANS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
Deprecated, for removal: This API element is subject to removal in a future version.
TRANS - Static variable in interface chemaxon.struc.StereoConstants
Trans double bond.
TransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
Filter for TRANS double bonds.
TransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter
 
transDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the TRANS double bonds.
transfer - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
The Transferable which represents the clipboard data.
TRANSFER_BUTTON_ICON - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "transferButtonIcon".
TRANSFER_BUTTON_TEXT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "transferButtonText".
TRANSFER_BUTTON_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "transferButtonVisible".
TransferableDescriptor - Class in chemaxon.marvin.modules.datatransfer
Data object to store lookup information for MTransferable objects.
TransferableDescriptor(String, String, Integer, Integer, boolean, boolean) - Constructor for class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Deprecated.
since 5.3.3 new descriptor parameter added.
TransferableDescriptor(String, String, Integer, Integer, boolean, boolean, boolean) - Constructor for class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Constructs a TransferableDescriptor object.
transform(CTransform3D) - Method in class chemaxon.struc.MDocument
Transforms all object's coordinates.
transform(CTransform3D) - Method in class chemaxon.struc.MoleculeGraph
Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D) - Method in interface chemaxon.struc.MTransformable
Transformation.
transform(CTransform3D) - Method in class chemaxon.struc.NoStructure
Transforms the location of the object
transform(CTransform3D) - Method in class chemaxon.struc.prop.MHCoords3DProp
Transforms the coordinates.
transform(CTransform3D) - Method in class chemaxon.struc.SelectionMolecule
Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.MolAtom
Apply a transformation matrix to the coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.Molecule
Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.MoleculeGraph
Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.RgMolecule
Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.RxnMolecule
Apply a transformation matrix to the atomic coordinates and the reaction arrow.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom
Apply a transformation matrix to the coordinates.
transform(CTransform3D, int) - Method in class chemaxon.struc.MDocument
Transforms all object's coordinates.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Does not perform any operation.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
Transforms the bracket.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
Transforms all points.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Does not perform any operation.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint
Transforms all points.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Transforms all points, scales the arrow head widths and lengths.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Transforms the rectangle.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint
Transforms all points.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MTextBox
Transforms all points and scales the font size.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MDocument
Transforms all object's coordinates.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MObject
Transforms the object.
transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MPoint
Transforms all points.
transform(CTransform3D, CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MDocument
Transforms all object's coordinates.
transform(DPoint3) - Method in class chemaxon.struc.CTransform3D
Transforms a point.
transform(Molecule) - Method in interface chemaxon.standardizer.ConcurrentStandardizerProcessor.MolTransformer
Transforms and returns the molecule (the transformed input molecule is returned, no new molecule object is created).
transform(Molecule) - Method in interface com.chemaxon.search.transformation.Transformer
Transforms a Molecule.
transform(Molecule) - Method in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
TRANSFORM_DISTORT - Static variable in class chemaxon.struc.MObject
Distorting transformations are allowed.
TransformAction - Class in chemaxon.standardizer.advancedactions
Transformation standardizer action
TransformAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.TransformAction
Initializes the action with parameters
TRANSFORMATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
transformByParent(CTransform3D, boolean) - Method in class chemaxon.struc.sgroup.DataSgroup
Applies a transformation matrix to the Data Sgroup coordinates.
transformByParent(CTransform3D, boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Applies a transformation matrix to the Sgroup coordinates.
transformByParent(CTransform3D, boolean) - Method in class chemaxon.struc.Sgroup
Applies a transformation matrix to the coordinates.
transformCT(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond
Transform cis/trans stereo information into the `reference frame' of this bond.
Transformer - Interface in com.chemaxon.search.transformation
Transformer.
TRANSFORMER_SET_DIM_0 - Static variable in class chemaxon.standardizer.ConcurrentStandardizerProcessor
Transformer: sets the molecule dimension to 0.
TransformerFactory - Class in com.chemaxon.search.transformation
Creates Molecule Transformer objects.
TransformerFactory() - Constructor for class com.chemaxon.search.transformation.TransformerFactory
 
transformReactionArrow(CTransform3D) - Method in class chemaxon.struc.RxnMolecule
Apply a transformation matrix to the reaction arrow.
transformTo2D() - Method in class chemaxon.struc.graphics.MRectangle
Rotate to the XY plane.
translate(float[]) - Method in class chemaxon.marvin.space.BoundingBox
A box can be translated in space.
translate(float[]) - Method in class chemaxon.marvin.space.GraphicComponent
Translates the component by changing its coordinates, and not just the view.
translate(float[]) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Translates its selected ligand by changing its coordinates, and not just the view.
translate(float[]) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Translates the component with the given translation vector.
translate(float[]) - Method in class chemaxon.marvin.space.MoleculeComponent
Translates the molecule with the parameter as a vector.
translate(float[]) - Method in class chemaxon.marvin.space.PharmacophoreArrow
Translates the component with the parameter as a translation vector.
translate(float[]) - Method in class chemaxon.marvin.space.PharmacophorePoint
Translates the component with the given translation vector.
TRANSLATE_ROTATE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType
Translate and rotate only as a rigid body.
TRANSLATE_ROTATE_FLEXIBLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType
Translate and rotate, and tweak rotatable bonds to adapt conformation.
TRANSLATE_ROTATE_FLEXIBLE_EXTRA - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType
As of AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).
TRANSPARENT_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
TRIPLE - Static variable in class chemaxon.struc.MolBond
Triple bond type.
tripletIndex(int, int, int) - Method in class chemaxon.descriptors.PFParameters
Calculates the index of a feature pair and distance triplet in the linearised representation of histograms.
TRIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Trivalent radical center.
TRIVALENT_DOUBLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Trivalent radical center with doublet electronic configuration.
TRIVALENT_QUARTET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
Trivalent radical center with quartet electronic configuration.
TRUE - Static variable in class chemaxon.jep.ChemJEP
Logical result value: TRUE.
TRUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
 
tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated.
 
tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.CubeRecognizer
Deprecated.
 
tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated.
 
tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
 
tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.Recognizer
Checks whether the parameter line can be part of a valid (format specified) file on the given file position.
tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated.
 
tryToRecognize(String, int, RecognizerList) - Method in class chemaxon.formats.recognizer.Recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
Not used in recognition and will be removed. Implement Recognizer.tryToRecognize(String, int) instead.
Ts - Static variable in class chemaxon.core.ChemConst
 
tversky(float[], float, float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates Tversky dissimilarity for floating point values.
tversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates Tversky dissimilarity index for integer values.
TVERSKY - Enum constant in enum class chemaxon.descriptors.MetricsType
 
tverskyA - Variable in class chemaxon.descriptors.MDParameters
alpha values for tversky dissimilarity
tverskyB - Variable in class chemaxon.descriptors.MDParameters
beta values for tversky dissimilarity
twicesumbonds(boolean, boolean) - Method in class chemaxon.struc.MolAtom
Calculates the total number of bonding electrons, excluding implicit hydrogens.
TWO_HEADED_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule
Two headed double reaction arrow type.
TWO_HEADED_SINGLE - Static variable in class chemaxon.struc.RxnMolecule
Two headed single reaction arrow type.
TXT - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
 
type - Variable in class chemaxon.checkers.StructureCheckOptions
The output type of the structure check (one or two files)
type - Variable in class chemaxon.marvin.services.ServiceArgument
type of the argument
TYPE - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the type of source for the structure.
TYPE_3D_COORDS - Static variable in class chemaxon.struc.MProp
 
TYPE_ARRAY_BYTE - Static variable in class chemaxon.struc.MProp
 
TYPE_ARRAY_DOUBLE - Static variable in class chemaxon.struc.MProp
 
TYPE_ARRAY_INTEGER - Static variable in class chemaxon.struc.MProp
 
TYPE_BOOLEAN - Static variable in class chemaxon.struc.MProp
 
TYPE_CAS - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a CAS Registry Number®.
TYPE_CDX - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is an embedded ChemDraw structure.
TYPE_COLLECTION_HASH - Static variable in class chemaxon.struc.MProp
 
TYPE_COLLECTION_LIST - Static variable in class chemaxon.struc.MProp
 
TYPE_COMMON - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a common name.
TYPE_CONFORMER_DESCRIPTOR - Static variable in class chemaxon.struc.MProp
 
TYPE_COUNT - Static variable in class chemaxon.struc.RxnMolecule
Number of structure types.
TYPE_DISTR - Static variable in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Type constant for microspecies distribution.
TYPE_DISTR - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Type constant for microspecies distribution.
TYPE_DOUBLE - Static variable in class chemaxon.struc.MProp
 
TYPE_EC - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is an EC Number.
TYPE_FONT - Static variable in class chemaxon.struc.MProp
 
TYPE_GENERIC - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a generic name, for instance "C1-C4 alkyl".
TYPE_INCHI - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is an InChI string.
TYPE_INTEGER - Static variable in class chemaxon.struc.MProp
 
TYPE_ION - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is an ion abbreviation, for instance K+ or Ca2+.
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.AromatizeAction
Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.ClearStereoAction
Key of type for parsing
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction
Key of type for parsing and property change
TYPE_MASK - Static variable in class chemaxon.struc.MolBond
The lowest bits of the flags that store the bond type.
TYPE_MASK - Static variable in class chemaxon.struc.RxnMolecule
Component type mask.
TYPE_MDOCUMENT_PROP - Static variable in class chemaxon.struc.MProp
 
TYPE_MOLECULE - Static variable in class chemaxon.struc.MProp
 
TYPE_MRV - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is an embedded Chemaxon MRV structure.
TYPE_OBJECT - Static variable in class chemaxon.struc.MProp
 
TYPE_OSR - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a structure image recognized by Optical Structure Recognition.
TYPE_PEPTIDE - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a peptide notation, for instance Val-Gly-Ser-Ala.
TYPE_SMILES - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a SMILES string.
TYPE_STRING - Static variable in class chemaxon.struc.MProp
 
TYPE_SYMYX - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is an embedded Symyx/ISIS draw structure.
TYPE_SYSTEMATIC - Static variable in class chemaxon.naming.document.DocumentToStructure
Possible value for the DocumentToStructure.TYPE property: the source is a systematic name.
TYPE_VOLUMETRIC_DATA - Static variable in class chemaxon.struc.MProp
 
TypeConverter() - Constructor for class chemaxon.checkers.StructureCheckOptions.TypeConverter
 
typeLabel(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
types - Variable in class chemaxon.checkers.AtomTypeChecker
A List of String which represents the types should be checked in the molecule

U

U - Static variable in class chemaxon.core.ChemConst
 
UI_DISABLED_GROUP_TYPES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 
UNBALANCED_REACTION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing reactions scheme having more atoms on one side of the reaction arrow than on the other.
UnbalancedReactionChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting reaction schemes having more atoms on one side of the reaction arrow than on the other.
UnbalancedReactionChecker() - Constructor for class chemaxon.checkers.UnbalancedReactionChecker
Creates a new UnbalancedReactionChecker instance.
UNDECIDED - Static variable in class chemaxon.jep.ChemJEP
Logical result value: UNDECIDED.
UNDEF_R_MATCHING_ALL - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
UNDEF_R_MATCHING_GROUP - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
UNDEF_R_MATCHING_GROUP_H - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
UNDEF_R_MATCHING_GROUP_H_EMPTY - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
UNDEF_R_MATCHING_UNDEF_R - Static variable in interface chemaxon.sss.SearchConstants
Option value constant.
UndefinedSolubilityCategory() - Constructor for class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
 
UNDETACH_BY_X - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "undetachByX".
undo() - Method in class chemaxon.marvin.beans.MSketchPane
Invokes an undo command.
UNDO - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "undo".
UngroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which ungroups all abbreviated groups in the molecule
UngroupFixer() - Constructor for class chemaxon.fixers.UngroupFixer
 
ungroupSgroup(int) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.
ungroupSgroup(int, int) - Method in class chemaxon.struc.Molecule
Deprecated.
as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.
ungroupSgroup(Sgroup) - Method in class chemaxon.struc.Molecule
Ungroups the specified S-group and expands it if it is an Expandable S-group.
ungroupSgroup(Sgroup, int) - Method in class chemaxon.struc.Molecule
Expand and ungroup the specified S-group.
ungroupSgroups() - Method in class chemaxon.struc.Molecule
Expands and ungroups all S-groups.
ungroupSgroups(int) - Method in class chemaxon.struc.Molecule
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 6.3. use Molecule.ungroupSgroups(EnumSet) instead.
ungroupSgroups(EnumSet<SgroupType>) - Method in class chemaxon.struc.Molecule
Ungroups all S-groups of the specified types in this molecule.
UngroupSgroupsAction - Class in chemaxon.standardizer.actions
Standardizer action un-groups s-groups of the target molecule
UngroupSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.UngroupSgroupsAction
Initializes the action
unhighlight(MObject) - Method in class chemaxon.struc.MDocument
Unhighlights an object.
unhighlightAll() - Method in class chemaxon.struc.MDocument
Unhighlights all objects.
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
 
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
 
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
 
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
 
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
 
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
2 dimension: the maximal indexed ligand's bonds angle is close to 180 degrees.
0 dimension: no stereo configuration was set on the double bond, or the rigid part is not just one double bond.
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
 
UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
 
UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
Deprecated, for removal: This API element is subject to removal in a future version.
UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
Deprecated, for removal: This API element is subject to removal in a future version.
UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
Deprecated, for removal: This API element is subject to removal in a future version.
UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
Deprecated, for removal: This API element is subject to removal in a future version.
UnknownAtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop
Filter for unknown atrop stereo centers.
UnknownAtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter
 
unknownAtropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the UNKNOWN atrop stereocenters.
UnknownAxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial
Filter for unknown axial centers.
UnknownAxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter
 
unknownAxialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the UNKNOWN axial stereocenters.
unknownResolvedStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the unknown, resolved tetrahedral stereogenic centers.
unknownResolvedStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the unknown, resolved tetrahedral stereogenic centers (with attached data).
UnknownResolvedTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral
Filter for unknown, resolved tetrahedral centers.
UnknownResolvedTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter
 
UNKONWN_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
unmap(Molecule) - Static method in class com.chemaxon.mapper.AutoMapper
Remove atom maps from the given structure
UnmapAction - Class in chemaxon.standardizer.actions
Unmap reaction standardizer action
UnmapAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.UnmapAction
Initializes the action
unorderedIterator() - Method in class chemaxon.struc.prop.MCollectionProp
Gets an unordered iterator for the entries.
unorderedIterator() - Method in class chemaxon.struc.prop.MHashProp
Gets an iterator for the entries.
unorderedIterator() - Method in class chemaxon.struc.prop.MListProp
Gets an iterator for the entries.
unresolvedStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the unresolved tetrahedral stereogenic centers.
unresolvedStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the unresolved tetrahedral stereogenic centers (with attached data).
UnresolvedTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral
Filter for unresolved tetrahedral centers.
UnresolvedTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter
 
unRgroupAtoms(Set<?>) - Method in class chemaxon.struc.RgMolecule
Ungroup R-groups consisting of the specified atoms and make them be part of root.
unSelect() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the component not to be selected.
unSelect() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
unSelect() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets all parts of all visualizers not to be selected.
unSelect() - Method in class chemaxon.marvin.space.MoleculeComponent
Unselects the component, say sets all parts to be unselected.
unSelect() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Sets the monitor to be unselected and destroys the DihedralControl.
unSelect() - Method in class chemaxon.marvin.space.monitor.Label
The color of the label changes by selection.
unSelect() - Method in class chemaxon.marvin.space.monitor.Monitor
Sets the component not to be selected.
unSelect() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Sets the component to be unselected.
unSelect() - Method in class chemaxon.marvin.space.PharmacophorePoint
Sets the component to be unselected.
unSelect(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the specific part of the component not to be selected.
unSelect(ComponentElement) - Method in class chemaxon.marvin.space.monitor.Label
The color of the label changes by selection.
unSelectAllAtoms() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets all atoms to be unselected.
unSelectAtom(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
unSelectAtom(int) - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the atom with the given index to be unselected.
unselectContents() - Method in class chemaxon.struc.graphics.MChemicalStruct
Unselects atoms.
unselectContents() - Method in class chemaxon.struc.graphics.MPolyline
Unselects the points.
unselectContents() - Method in class chemaxon.struc.graphics.MTextBox
Unselects text.
unselectContents() - Method in class chemaxon.struc.MObject
Unselects sub-objects.
unSelectInDocument(MDocument) - Static method in class chemaxon.struc.NoStructure
Removes the selection from all NoStructure labels in the document.
UNSPECIFIED_AROMATICITY - Static variable in class chemaxon.struc.MolAtom
Atom aromaticity is not specified explicitly.
UNSUPPORTED - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
 
UNUSED_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that molecule with unused R-group definition found
UnusedRGroupChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting unused R-group definitions.
UnusedRGroupChecker() - Constructor for class chemaxon.checkers.UnusedRGroupChecker
Initializes the checker
uoid - Variable in class chemaxon.marvin.space.GraphicComponent
internal index of the component
UP - Static variable in class chemaxon.struc.MolBond
Single bond up flag.
updateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated.
as of Marvin 6.2, use SuperatomSgroup.calculateAttachmentPoints() instead
updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.graphics.MBracket
 
updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Calculate the bounding rectangle.
updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.MObject
Calculate the bounding rectangle.
updateBoundingRect(double[], CTransform3D, double) - Method in class chemaxon.struc.MObject
Calculate the bounding rectangle.
updateColors() - Method in class chemaxon.marvin.space.SurfaceColoring
Useful fast updating method when the atom properties have not changed, but there is a change in the way of coloring.
updateComponentRoles() - Method in class chemaxon.struc.RxnMolecule
Updates fragment roles in the molecule.
updateDim(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Updates the dimensions when fusing two structures.
updateFields(MDocument) - Method in class chemaxon.marvin.view.swing.TableOptions
Update fields of SDF table
updateFields(MDocument[]) - Method in class chemaxon.marvin.view.swing.TableOptions
Update fields of SDF table
updatePropertyMapping() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
updateRotationMatrix() - Method in class chemaxon.marvin.space.GraphicCell
 
updateStatistics(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator
Updates statistics gathered on fingerprints generated.
updateStatistics(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeGenerator
 
updateSubLevel(double[], double, int) - Method in class chemaxon.struc.graphics.MTextDocument
 
UpperBoundCalculator - Interface in com.chemaxon.search.mcs.upperbound
An interface for providing upper bound calculation for MaxCommonSubstructure (MCS) search.
USE_DEFAULT_SALTS_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
Property key for use default salts modification
USE_DEFAULT_SOLVENTS_KEY - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
Property key for use default solvent modification
USE_WARNINGS - Static variable in class chemaxon.marvin.common.ParameterConstants
Constant key to set wether the user wants to see warnings or not.
useCorrectionLibrary(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin
USED_JARS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "usedJars".
USEFUL - Static variable in class chemaxon.sss.search.MolComparator
Describes that the MolComparator should be used with the current search object and the current query, regardless of the target.
useOnlyFirstAtomInStereoCalculation - Variable in class chemaxon.struc.MoleculeGraph
 
useOnlyFirstAtomInStereoCalculation(boolean) - Method in class chemaxon.struc.MoleculeGraph
Set how parity module should interpret wedes.
useOpticalCharacterRecognition - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions
Whether to use Optical Character Recognition on images.
useOpticalCharacterRecognition(Boolean) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
usePopups(boolean) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
 
USER_CHECKERS_CONFIG_PATH - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
Deprecated, for removal: This API element is subject to removal in a future version.
Configuration file URL can be set in MarvinSketch preferences, and stored in UserSettings.
USER_DEFINED_CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Users checker configuration file name
USER_DEFINED_STANDARDIZERCONFIG_XML - Static variable in class chemaxon.standardizer.StandardizerActionFactory
Users standardizer action configuration file name
USER_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader
path to user-defined standardizer action configuration list
UserSettings - Class in chemaxon.marvin.common
Represents the settings of the MarvinSketch and MarvinView applications.
UserSettings() - Constructor for class chemaxon.marvin.common.UserSettings
Construct a UserSettings object based on the default configuration, and the marvin.properties file stored in the chemaxon settings directory in the home directory of the user.
UserSettings(UserSettings) - Constructor for class chemaxon.marvin.common.UserSettings
Copy consturctor.
UserSettings(InputStream) - Constructor for class chemaxon.marvin.common.UserSettings
 
UserSettings(String) - Constructor for class chemaxon.marvin.common.UserSettings
Construct a UserSettings object based on the default configuration, and the file stored in the chemaxon settings directory in the home of the user.
UUID - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
 

V

V - Static variable in class chemaxon.core.ChemConst
 
VAGUE_BOND_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for vague bond level HALF.
VAGUE_BOND_LEVEL_HALF - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1.
VAGUE_BOND_LEVEL1 - Static variable in interface chemaxon.sss.SearchConstants
Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries.
VAGUE_BOND_LEVEL2 - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search.
VAGUE_BOND_LEVEL3 - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search.
VAGUE_BOND_LEVEL4 - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search.
VAGUE_BOND_OFF - Static variable in interface chemaxon.sss.SearchConstants
Option value constant to disable vague bond matching.
VALENCE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that valence error had found in the molecule
VALENCE_CHECK - Static variable in class chemaxon.struc.MoleculeGraph
Valence check calculation bit in flags.
VALENCE_CHECK_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph
Deprecated, for removal: This API element is subject to removal in a future version.
As of Marvin 6.0, replaced by ValenceCheckOptions.
VALENCE_CHECK_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "valenceCheckEnabled".
VALENCE_CHECKED - Static variable in class chemaxon.struc.MolAtom
Valence checked if this flag is set.
VALENCE_ERROR - Static variable in class chemaxon.struc.MolAtom
The atom has valence error if this flag is set.
VALENCE_ERROR_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "valenceErrorVisible".
VALENCE_ERROR_VISIBLE_IN_VIEW - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "valenceErrorVisibleInView".
VALENCE_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that an atom has a valence property set.
VALENCE_PROPERTY_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "valencePropertyVisible".
valenceCheck() - Method in class chemaxon.struc.MolAtom
Valence checking.
valenceCheck() - Method in class chemaxon.struc.MoleculeGraph
Check valence and query property errors for atoms.
valenceCheck(List<MolAtom>) - Method in class chemaxon.struc.MoleculeGraph
Check valence and query property errors.
ValenceCheckOptions - Class in chemaxon.core.calculations.valencecheck
Class created to make valence calculation configurable.
ValenceCheckOptions(boolean, boolean) - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
Deprecated, for removal: This API element is subject to removal in a future version.
since Marvin 6.2, Use ValenceCheckOptions.Builder for building ValenceCheckOptions.
ValenceCheckOptions.Builder - Class in chemaxon.core.calculations.valencecheck
Builder for ValenceCheckOptions.
VALENCEERROR_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom(s) connected to an atom which have valence error.
ValenceErrorChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms with invalid valences.
ValenceErrorChecker() - Constructor for class chemaxon.checkers.ValenceErrorChecker
Default constructor
ValenceErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ValenceErrorChecker
Parameterized constructor.
ValenceFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which fixes valence problem in the molecule if it is possible with removing explicit hydrogens or by adding charge
ValenceFixer() - Constructor for class chemaxon.fixers.ValenceFixer
 
ValencePropertyChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms having an explicitly set valence property.
ValencePropertyChecker() - Constructor for class chemaxon.checkers.ValencePropertyChecker
Creates a new ValencePropertyChecker instance.
ValencePropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ValencePropertyChecker
Creates a new ValencePropertyChecker instance.
value - Variable in class chemaxon.marvin.services.ServiceArgument
value of the argument
value() - Method in class chemaxon.calculations.bbb.BBB.Property
 
value() - Method in class chemaxon.calculations.cnsmpo.CnsMpo.Property
 
value() - Element in annotation interface chemaxon.fixers.Fixes
The error type values
value() - Element in annotation interface chemaxon.fixers.FixesExternal
The error code values
value() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunctionContainer
 
valueOf(String) - Static method in enum class chemaxon.calculations.bbb.BBBFunction
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.dipole.DipoleResult.Unit
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculator.CalculatorTag
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.CheckerSeverity
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.FixMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckerErrorType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckOptions.Mode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckOptions.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.descriptors.MetricsType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.io.MolImportModule.PreferredView
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.sss.search.options.HaltOnErrorOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.sss.search.options.HomologyTranslationOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.AtomProperty.Radical
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.SgroupType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.admet.HergClass
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.solubility.SolubilityUnit
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.common.annotations.RemovalDate
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.mapper.Mapper.MappingStyle
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.search.mcs.RingHandlingMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.search.mcs.SearchMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class com.chemaxon.search.transformation.transformers.Aromatizer
Returns the enum constant of this class with the specified name.
values() - Static method in enum class chemaxon.calculations.bbb.BBBFunction
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.dipole.DipoleResult.Unit
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculator.CalculatorTag
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.CheckerSeverity
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.FixMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.StructureCheckerErrorType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.StructureCheckOptions.Mode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.StructureCheckOptions.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.descriptors.MetricsType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.io.MolImportModule.PreferredView
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.sss.search.options.HaltOnErrorOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.sss.search.options.HomologyTranslationOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.AtomProperty.Radical
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.SgroupType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.admet.HergClass
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.solubility.SolubilityUnit
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.common.annotations.RemovalDate
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.mapper.Mapper.MappingStyle
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.search.mcs.RingHandlingMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.search.mcs.SearchMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class com.chemaxon.search.transformation.transformers.Aromatizer
Returns an array containing the constants of this enum class, in the order they are declared.
VAN_DER_WAALS - Static variable in class chemaxon.marvin.calculations.MSAPlugin
Surface area type: 3D van der Waals surface area.
VARARG - Static variable in interface chemaxon.jep.ChemContext
A possible value for ChemContext.ProvidesFunction.maxParameterCount(), signaling that there is no maximum.
verbose - Static variable in class chemaxon.marvin.space.MSpaceEasy
 
verbose - Variable in class chemaxon.sss.search.SearchOptions
For debugging purposes.
verbose(Object) - Method in interface chemaxon.marvin.calculations.StructuralFrameworksPlugin.VerbosePrinter
Log a verbose message
VERBOSE_LEVEL_BASIC - Static variable in class chemaxon.marvin.space.GraphicScene
 
VERBOSE_LEVEL_DEVEL - Static variable in class chemaxon.marvin.space.GraphicScene
 
VERBOSE_LEVEL_NONE - Static variable in class chemaxon.marvin.space.GraphicScene
 
verify3d() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Returns true if 3D structure will be checked for a valid stereo conformation.
verifyParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel
Verifies parameters on the parameter panel.
verifyParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler
Verifies parameters on the parameter panel.
VERSION - Static variable in class chemaxon.marvin.beans.MarvinPane
Marvin version.
VersionInfo - Class in com.chemaxon.version
Provides version information of ChemAxon products.
VersionInfo() - Constructor for class com.chemaxon.version.VersionInfo
 
VH_AUTO - Static variable in class chemaxon.marvin.view.swing.TableOptions
Automatic view selection.
VH_GRIDBAG - Static variable in class chemaxon.marvin.view.swing.TableOptions
Molecule matrix view.
VH_SPREADSHEET - Static variable in class chemaxon.marvin.view.swing.TableOptions
Record oriented view.
VIEW_ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "viewAnyBond".
VIEW_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "viewCarbonVisibility".
VIEW_EXPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated, for removal: This API element is subject to removal in a future version.
As of release 5.3, this feature is deprecated and has no replacement. It will be removed in a future version of Marvin.
VIEW_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "viewHelp".
VIEW_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "viewLigandOrderVisibility".
VIEW_NAVIGATION_MODE_2D - Static variable in class chemaxon.marvin.common.ParameterConstants
 
VIEW_NAVIGATION_MODE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
 
VIEW_ONLY - Static variable in class chemaxon.marvin.beans.MViewPane
Editing mode identifier meaning the structures cannot be edited.
VIEW_ONLY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "viewonly".
VIEW_PANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.view.ViewParameterConstants
 
VIEW_PANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.view.ViewParameterConstants
 
ViewParameterConstants - Class in chemaxon.marvin.view
Parameters of MarvinView Applet and Bean.
The parameters of the JMView applet can be set using the <param> HTML tag.
visible - Variable in class chemaxon.marvin.space.GraphicComponent
Indicates if component is visible or hidden.
VISIBLE_COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "visibleCols".
VISIBLE_ROWS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "visibleRows".
visitAt(AtropStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor
Visit atrop stereo centers.
visitAx(AxialStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor
Visit axial stereo centers.
visitCT(CisTransStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor
Visit cis trans stereo centers.
visitTH(TetrahedralStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor
Visit tetrahedral stereo centers.
VMN - Static variable in class chemaxon.formats.MFileFormat
 

W

W - Static variable in class chemaxon.core.ChemConst
 
waitForAll() - Method in interface chemaxon.marvin.view.TaskScheduler
Waits for all tasks to finish.
WARNING - Enum constant in enum class chemaxon.checkers.CheckerSeverity
This severity level should used for StructureChecker implementations which search for problematic features in a Molecule
warningMsgOn - Static variable in class chemaxon.marvin.calculations.TautomerizationPlugin
 
WAVY - Static variable in class chemaxon.struc.MolBond
Single bond wavy flag.
WEB_SERVICES_SERVER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Web Services Server
WedgeCleanAction - Class in chemaxon.standardizer.actions
Wedge clean standardizer action
WedgeCleanAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.WedgeCleanAction
Initializes the action
WedgeCleanFixer - Class in chemaxon.fixers
Deprecated.
WedgeCleanFixer() - Constructor for class chemaxon.fixers.WedgeCleanFixer
Deprecated.
 
WEDGED_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom(s) with wedge bonds.
WedgeErrorChecker - Class in chemaxon.checkers
Deprecated.
WedgeErrorChecker() - Constructor for class chemaxon.checkers.WedgeErrorChecker
Deprecated.
Default constructor
WEIGHT - Static variable in class chemaxon.marvin.alignment.MinMaxDistance
 
weightedAsymmetricEuclidean(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric Euclidean distance.
weightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric Euclidean distance.
weightedAsymmetricNormalizedEuclidean(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric normalized Euclidean distance.
weightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted asymmetric normalized Euclidean distance.
weightedEuclidean(float[], float[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted Euclidean distance.
weightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted Euclidean distance.
weightedNormalizedEuclidean(float[], float[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted normalized Euclidean distance.
weightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics
Calculates the weighted normalized Euclidean distance.
weights - Variable in class chemaxon.descriptors.MDParameters
weights for parametrized metrics
wienerIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
wienerPolarity() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.
WIGGLY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that wiggly bond had found in the molecule
WIGGLY - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
Wiggly double bond type
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue
 
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
 
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue
 
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
 
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
 
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
Equals to CIS | TRANS
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue
 
WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
 
WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
Deprecated, for removal: This API element is subject to removal in a future version.
WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
Deprecated, for removal: This API element is subject to removal in a future version.
WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
Deprecated, for removal: This API element is subject to removal in a future version.
WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
Deprecated, for removal: This API element is subject to removal in a future version.
WIGGLY_BOND_TETRAHEDRAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents molecules having wiggly bonds on tetrahedral stereo centers
WigglyBondChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting wiggly bonds on tetrahedral stereo centers.
WigglyBondChecker() - Constructor for class chemaxon.checkers.WigglyBondChecker
Initializes a wiggly bond checker
WigglyDoubleBondChecker - Class in chemaxon.checkers
A descendant of BondChecker detecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.
WigglyDoubleBondChecker() - Constructor for class chemaxon.checkers.WigglyDoubleBondChecker
Default constructor
WigglyDoubleBondFixer - Class in chemaxon.fixers
Deprecated, for removal: This API element is subject to removal in a future version.
WigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.WigglyDoubleBondFixer
Deprecated.
 
WINDOW_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "winScale".
windowActivated(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Do nothing.
windowClosed(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Do nothing.
windowClosing(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Close the window.
windowDeactivated(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Do nothing.
windowDeiconified(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Do nothing.
windowIconified(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Do nothing.
windowOpened(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Do nothing.
WIRE_THICKNESS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "wireThickness".
withoutType(int, int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
WORD_SEPARATORS - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Word separators used to form multi-line text if the text is too long.
worked(long) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Notifies that a given number of work units has been completed.
workUnit(String) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
wrapTextAndSetActualPoints(CTransform3D, double) - Method in class chemaxon.struc.graphics.MTextBox
 
write(Molecule) - Method in class chemaxon.formats.MolExporter
Writes a molecule into the stream.
write16doubles(ObjectOutput) - Method in class chemaxon.struc.CTransform3D
Writes the 4x4 matrix components as double precision floating point numbers.
write16floats(ObjectOutput) - Method in class chemaxon.struc.CTransform3D
Writes the 4x4 matrix components as single precision floating point numbers.
writeConfiguration(OutputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory
Writes the factory configuration to the output stream
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MarvinPane
Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MSketch
Saves the sketcher's state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MSketchPane
Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MView
Saves the viewer's state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MViewPane
Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.CTransform3D
Serializes a transformation matrix.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.DPoint3
Serializes a 3D point.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.graphics.MTextAttributes
 
writeExternal(ObjectOutput) - Method in class chemaxon.struc.graphics.MTextDocument
Saves the document.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.MPropertyContainer
Saves the property container's state.
writeMetricParameter(ArrayList, String, int, boolean) - Method in class chemaxon.descriptors.MDParameters
Writes a given parameter of the specified metric into the corresponding tree node.
writeMol(ObjectOutput, Molecule) - Static method in class chemaxon.marvin.beans.MarvinPane
 
writeServiceDescriptors(List<ServiceDescriptor>, OutputStream) - Method in interface chemaxon.marvin.services.ServiceDescriptorWriter
Writes the descriptors to the specified output
WSDL - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor
Property key for Service descriptor as String
WSmolecule - Interface in chemaxon.struc
Writable abstract molecule class.

X

x - Variable in class chemaxon.marvin.space.monitor.Control
 
x - Variable in class chemaxon.struc.DPoint3
The x coordinate.
xCoordinate - Variable in class chemaxon.struc.MolAtom
X coordinate.
xCoords - Variable in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
Xe - Static variable in class chemaxon.core.ChemConst
 
XML - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType
 
XML_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
xml token of the action
XMLBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader
A descendant of ConfigurationReader which can read CheckerRunner configuration described Chemaxon's own checker configuration XML format (schema in jar: chemaxon/checkers/runner/configuration /reader/resoruce/checkerconfiguation.xsd)
XMLBasedConfigurationReader(InputStream) - Constructor for class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
Initiate an XMLBasedConfigurationReader instance with the given inputSteam with the configuration
XMLBasedConfigurationReader(InputStream, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
Initiate an XMLBasedConfigurationReader instance with the given inputSteam with the configuration
XMLRPCServiceDescriptor - Class in chemaxon.marvin.services.xmlrpcservice
ServiceDescriptor implementation for XML-RPC services.
XMLRPCServiceDescriptor() - Constructor for class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
 
xmlToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the XML tokens of the action as a string, divided by comma characters
XSTATE_C - Static variable in class chemaxon.struc.Sgroup
S-group is contracted (useful only in GUI!).
XSTATE_NONE - Static variable in class chemaxon.struc.Sgroup
S-group is in an undetermined state.
XSTATE_X - Static variable in class chemaxon.struc.Sgroup
S-group is expanded.
XSTATE_XC - Static variable in class chemaxon.struc.Sgroup
S-group is expanded but its atoms have the same coordinates as in contracted state.
xyz - Variable in class chemaxon.descriptors.PFParameters
The calculateXYZ() methods (in PharmacophoreFingerprint sub-classes) calculate three numbers (denoted by x,y and z), but methods in java cannot have output parameters.
XYZ - Static variable in class chemaxon.formats.MFileFormat
XYZ files.

Y

y - Variable in class chemaxon.marvin.space.monitor.Control
 
y - Variable in class chemaxon.struc.DPoint3
The y coordinate.
Y - Static variable in class chemaxon.core.ChemConst
 
Yb - Static variable in class chemaxon.core.ChemConst
 
yCoordinate - Variable in class chemaxon.struc.MolAtom
Y coordinate.
yCoords - Variable in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
YES - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption
Stop on any errors during the search.

Z

z - Variable in class chemaxon.struc.DPoint3
The z coordinate.
Z - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
 
zCoordinate - Variable in class chemaxon.struc.MolAtom
Z coordinate.
zCoords - Variable in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
 
ZERO_BASED_ATOM_INDEXING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier for parameter: "zeroBasedAtomIndexing" See Parameters and Events documentation.
ZERO_VECTOR - Static variable in class chemaxon.struc.DPoint3
 
Zn - Static variable in class chemaxon.core.ChemConst
 
zoom(double) - Method in class chemaxon.marvin.space.GraphicCell
 
zoom(double) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given zoom factor in the active cell or in every cells in case of synchronous mode.
ZOOM_TO_SCAFFOLD_ON_LOAD - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "zoomToScaffoldOnLoad".
zoomAnimated(double, int) - Method in class chemaxon.marvin.space.GraphicScene
Sets the given zoom factor dividing by n parts.
Zr - Static variable in class chemaxon.core.ChemConst
 
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