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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
 
AbstractSgroupAction - Class in chemaxon.standardizer.actions
Abstract class for standardizer actions modifying S-groups.
AbstractSgroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AbstractSgroupAction
Initializes an abstract s-group action with the exclude list
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 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 - Enum constant in enum class chemaxon.marvin.collecting.Consent
 
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.
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.
actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView
Handles window closing and format choice events.
actionPerformed(ActionEvent) - Method in class chemaxon.marvin.swing.MAction
Sets the action state, performs a custom action, then propagates the event.
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
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(CheckerFixerFactory.CheckerClassDescriptor) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
Adds a checker class descriptor to the factory
add(CheckerFixerFactory.FixerClassDescriptor) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
Adds a fixer class descriptor to the factory
add(InputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds an input stream containing standardizer specifications to be stored by the output factory
add(InputStream) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
Adds an input stream containing checker and fixer specifications to be stored by the output factory
add(String) - Method in class chemaxon.checkers.util.AtomLabels
Adds an atom label to the atom labels
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(URL) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
Adds an input stream containing checker and fixer 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(Properties) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
Adds a property map containing properties of checkers and fixers 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.
addArgument(ServiceArgument<?>) - Method in class chemaxon.marvin.services.ServiceDescriptor
Adds a new argument to the end of the argument list
addAtom(int) - Method in class chemaxon.calculations.nmr.Multiplet
Adds a new atom to this multiplet.
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.
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.MAnalysisBox
 
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.MElectron
 
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectronContainer
 
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MNameTextBox
Adds the attribute names to the specified list.
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.
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.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox
 
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(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.
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.
addCouplingConstants(double[]) - Method in class chemaxon.calculations.nmr.Multiplet
Adds a new coupling constant array.
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.
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.
addItemListener(ItemListener) - Method in class com.chemaxon.calculations.gui.MChart
 
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.
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.
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, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment
Add molecule to align
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.MElectronContainer
 
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.
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.
addRGroupsInPlaceOfImplHs(Molecule) - Static method in class chemaxon.sss.search.RGroupDecomposition
Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s.
addRGroupsInPlaceOfImplHs(Molecule, int) - Static method in class chemaxon.sss.search.RGroupDecomposition
Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s.
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
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.
addTo(Container) - Method in class chemaxon.marvin.swing.MAction
Add menu item to the specified menu.
addTo(Container, int) - Method in class chemaxon.marvin.swing.MAction
Add menu item to the specified menu.
addTo(Container, int, Object) - Method in class chemaxon.marvin.swing.MAction
Add menu item to the specified menu.
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
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
adjustTautomerizationPlugin(TautomerizationPlugin) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode
 
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.
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 - Static variable in class chemaxon.marvin.services.ServiceDescriptor
Property key for Service alias as String
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
Executes the 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(Molecule, Molecule, int[]) - Static method in class chemaxon.marvin.alignment.MolAligner
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
align(Molecule, Molecule, int[][]) - Static method in class chemaxon.marvin.alignment.MolAligner
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
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
 
AlignmentAccuracyMode - Enum Class in chemaxon.marvin.alignment
Settings for the representation of a molecular shape.
AlignmentException - Exception in chemaxon.marvin.alignment
 
AlignmentException() - Constructor for exception chemaxon.marvin.alignment.AlignmentException
 
AlignmentException(String) - Constructor for exception chemaxon.marvin.alignment.AlignmentException
 
AlignmentException(Throwable) - Constructor for exception chemaxon.marvin.alignment.AlignmentException
 
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
 
AMBIGUOUS - Enum constant in enum class com.chemaxon.search.AromatizationMethod
Aromatization for ambiguous 5-membered rings.
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.
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".
ANTI - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, anti (relative configuration).
ANY - Enum constant in enum class chemaxon.struc.BondType
Any bond type.
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
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() - 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.
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?
ArgumentException - Exception in chemaxon.common.util
Checked exception to indicate that a tool has been passed an illegal argument, typically used for CLI.
ArgumentException() - Constructor for exception chemaxon.common.util.ArgumentException
Creates a new instance of ArgumentException without detail message.
ArgumentException(String) - Constructor for exception chemaxon.common.util.ArgumentException
Constructs an instance of ArgumentException with the specified detail message.
ARGUMENTS - Static variable in class chemaxon.marvin.services.ServiceDescriptor
Property key for Arguments as an Unmodifiable List
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 - Enum constant in enum class chemaxon.struc.BondType
Aromatic bond type.
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
 
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)
aromatization(GeneralExportOptions.AromatizationMethod) - Method in class chemaxon.formats.GeneralExportOptions.Builder
Sets the aromatization method.
AROMATIZATION_AMBIG - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
Ambiguous aromatizatization.
AROMATIZATION_BASIC - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
Aromatization using the basic method.
AROMATIZATION_GENERAL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
Aromatization using the general method.
AROMATIZATION_LOOSE - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
Aromatization using the loose method.
AromatizationMethod - Enum Class in com.chemaxon.search
Enum for aromatization methods used during the search process.
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.
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.
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_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
atomChanged(MolAtom) - Method in interface chemaxon.calculations.clean.AtomChangeEventListener
 
AtomChangeEventListener - Interface in chemaxon.calculations.clean
 
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.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
AtomIndexMapper - Interface in com.chemaxon.search.transformation
Atom index mapper.
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.
AtomLabels - Class in chemaxon.checkers.util
The atom labels storage class.
AtomLabels() - Constructor for class chemaxon.checkers.util.AtomLabels
Initializes the atom labels
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(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether atom map numbers should be considered in search.
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.struc
Class for storing atom property enumerations.
AtomProperty() - Constructor for class chemaxon.struc.AtomProperty
 
AtomProperty.Radical - Enum Class in chemaxon.struc
Enumeration of the supported radicals.
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 interface chemaxon.core.calculations.valencecheck.MoleculeWithValence
Returns list for the atom references in the molecule.
atoms() - Method in class chemaxon.struc.MoleculeGraph
Provides an unmodifiable list view of the atoms in the molecule.
AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters
Selection which contains atom indexes.
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(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether atom types should be considered in search.
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).
AttachmentPoint - Class in chemaxon.struc.sgroup
Attachment Point class for the Superatom S-group.
AttachmentPoint(MolAtom, int, MolBond) - Constructor for class chemaxon.struc.sgroup.AttachmentPoint
Constructs an AttachmentPoint object
Au - Static variable in class chemaxon.core.ChemConst
 
AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Automatic check for structures.
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
Deprecated, for removal: This API element is subject to removal in a future version.
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".
AUTORM - Static variable in class chemaxon.marvin.swing.MAction
Remove menu items automatically when the menu becomes invisible.
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
 
Ba - Static variable in class chemaxon.core.ChemConst
 
BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "background".
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".
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.AromatizationMethod
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
 
Beta - Annotation Interface in com.chemaxon.common.annotations
Indicates that a public API entity (public class, method, or field) is subject to incompatible changes, or even removal, in a future release.
Bh - Static variable in class chemaxon.core.ChemConst
 
Bi - Static variable in class chemaxon.core.ChemConst
 
BicycloStereoDescriptor - Class in chemaxon.struc
This class is the atom index based representation which can be assigned to 'endo', 'exo', 'syn', 'anti' ligands of bicyclo[x.y.z]alkanes in case of 0 dimension molecules.
BicycloStereoDescriptor(MolAtom, int, MolAtom[], MolAtom[]) - Constructor for class chemaxon.struc.BicycloStereoDescriptor
Creates a new stereo descriptor for bicyclo stereo.
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_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_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.
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.
bonds() - Method in class chemaxon.struc.MolAtom
Provides an unmodifiable list view of the connected bonds of the atom.
bonds() - Method in class chemaxon.struc.MoleculeGraph
Provides an unmodifiable 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.
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)
BondType - Enum Class in chemaxon.struc
General chemical bond types.
bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether bond types should be considered in search.
bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom
Calculates the average of the bond unit vectors pointing out of this atom.
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".
BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
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.GeneralExportOptions.Builder
Builds an unmodifiable export option.
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.marvin.plugin.gui.ResultView
Sets sizes, builds split panes.
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 chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
Builds a CheckerFixerFactory based no the previously added InputStream and Properties instances
build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a search options object with the settings specified by this builder instance.
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.GeneralExportOptions.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 chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
 
Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object with the default settings.
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.
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.MElectronContainer
 
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie
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.
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.
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
 
CalculatorPluginCachedResults - Class in com.chemaxon.calculations.cli
Provides plugin cached results.
CalculatorPluginCachedResults(String, String, Molecule[], Molecule, String, String, Throwable, boolean) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginCachedResults
Constructor.
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
 
CalculatorResultAccess - Interface in com.chemaxon.calculations.cli
Interface providing plugin result access.
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.
calcWidth(Graphics2D) - Method in class chemaxon.struc.graphics.MNameTextBox
Calculates the width of the string in the name text box.
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.
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(HTTPServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.httpservice.HTTPServiceHandler
 
callService(JsonServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.json.JsonServiceHandler
 
callService(LocalServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.localservice.LocalServiceHandler
 
callService(SoapServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.soap.SoapServiceHandler
 
callService(XMLRPCServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceHandler
 
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
CANCELLED - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult
 
CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
canonicalName(String) - Static method in class chemaxon.marvin.io.Encoding
Standardize a Java encoding.
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)
caretUpdate(CaretEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView
 
CBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType
 
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".
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
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.
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.
CHAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType
 
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.
changes - Variable in class chemaxon.standardizer.actions.AbstractSgroupAction
 
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).
characters(char[], int, int) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter
 
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_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(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether formal charges of atoms should be considered in search.
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(Stack<Object>) - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI
Deprecated.
Checks the stack.
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
CheckerClassDescriptor() - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor
Initializes an empty checker class descriptor
CheckerClassDescriptor(String, String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor
Initializes a checker class descriptor
CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Chemaxon's default checker configuration file name
CheckerFixerFactory - Class in chemaxon.structurechecker.factory
Factory for structure checkers and structure fixers.
CheckerFixerFactory.Builder - Class in chemaxon.structurechecker.factory
Builder class for CheckerFixerFactory.
CheckerFixerFactory.CheckerClassDescriptor - Class in chemaxon.structurechecker.factory
Descriptor of a checker class
CheckerFixerFactory.ClassDescriptor - Class in chemaxon.structurechecker.factory
Descriptor of a class
CheckerFixerFactory.FixerClassDescriptor - Class in chemaxon.structurechecker.factory
Descriptor of a fixer class
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.MElectronContainer
 
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?
CHEMAXON - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod
Chemaxon logP calculation method.
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.pka - package chemaxon.calculations.pka
 
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.checkers.util - package chemaxon.checkers.util
 
chemaxon.common.swing.io.output - package chemaxon.common.swing.io.output
 
chemaxon.common.util - package chemaxon.common.util
Provides general utility classes.
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.collecting - package chemaxon.marvin.collecting
 
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.fieldaccess - package chemaxon.marvin.io.fieldaccess
 
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.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.swing - package chemaxon.marvin.swing
 
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.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.nfunk.jep.function - package chemaxon.nfunk.jep.function
 
chemaxon.sss - package chemaxon.sss
 
chemaxon.sss.formula - package chemaxon.sss.formula
 
chemaxon.sss.screen - package chemaxon.sss.screen
Classes for screeening.
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.struc.stereo - package chemaxon.struc.stereo
 
chemaxon.structurechecker.factory - package chemaxon.structurechecker.factory
 
chemaxon.util - package chemaxon.util
 
chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
 
chemaxon.util.iterator - package chemaxon.util.iterator
Provides iterator classes for molecules and their components.
chemaxon.util.progress - package chemaxon.util.progress
Common components of Calculator APIs.
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.
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()
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
ClassDescriptor(String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor
 
className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
 
className - Variable in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor
 
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".
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.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
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.
clearMark() - Method in class chemaxon.marvin.io.PositionedInputStream
Disables the mark (if any) on this stream.
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
 
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
clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Clipboard operation type.
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.AbstractSgroupAction
 
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.MAnalysisBox
 
clone() - Method in class chemaxon.struc.graphics.MAssigner
 
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.MElectron
 
clone() - Method in class chemaxon.struc.graphics.MElectronContainer
 
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.MMoleculeMovie
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MNameTextBox
 
clone() - Method in class chemaxon.struc.graphics.MPolyline
 
clone() - Method in class chemaxon.struc.graphics.MRArrow
 
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.PageSettings
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).
cloneAsMTextBox() - Method in class chemaxon.struc.graphics.MAnalysisBox
 
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.MFontProp
 
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.MMoleculeStringProp
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 interface chemaxon.marvin.io.formats.MoleculeImporterIface
Close the underlying input stream.
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 interface chemaxon.util.progress.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.cli.CalculatorPluginOutput
Closes the output.
close() - Method in interface com.chemaxon.util.concurrent.CloseableIterator
 
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.
closeableIterator(Iterator<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper
Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator.
NOTE: the returned iterator provides the same molecule instances with maps added
closeableIterator(Iterator<Molecule>, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.
closeableIterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
Returns an auto-closeable 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
closeableIterator(Iterator<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator using the specified mappers for mapping.
CloseableIterator<T> - Interface in com.chemaxon.util.concurrent
An auto-closeable wrapper for the Iterator class, so you should use this class with try-with-resources statements!
closeableResultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.
closeableResultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String, boolean) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.
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
 
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
 
codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Add mass number information to the given code.
COL_MOLECULE - Static variable in class chemaxon.sss.search.RGroupDecomposition
Constant for adding query-target column to ligand table.
COL_SCAFFOLD - Static variable in class chemaxon.sss.search.RGroupDecomposition
Constant for adding scaffold column to ligand table.
colDec - Variable in class chemaxon.descriptors.PFParameters
atom set colors
collectLonePairContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
 
collectLonePairsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
 
collectMElectronContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
Collects all MElectronContainers of an atom, if the atom is part of a Molecule, which has an MDocument.
collectMElectronsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectron
Deprecated, for removal: This API element is subject to removal in a future version.
collectRadicalContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
 
collectRadicalsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
 
color() - Method in class chemaxon.sss.search.Decomposition
Colors ligands, scaffold, query and target by setting color data in atoms by calling MolAtom.setSetSeq(int).
color(Molecule) - Static method in class chemaxon.sss.search.Decomposition
Colors a molecule by setting color data in atoms by calling MolAtom.setSetSeq(int).
color(Molecule, String) - Static method in class chemaxon.sss.search.Decomposition
Colors a molecule by setting color data in the specified molecule property (SDF tag).
color(String) - Method in class chemaxon.sss.search.Decomposition
Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag).
COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "colorScheme".
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_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.
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.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.common.annotations - package com.chemaxon.common.annotations
Provides annotations for Chemaxon classes.
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.search.transformation.util - package com.chemaxon.search.transformation.util
 
com.chemaxon.util.concurrent - package com.chemaxon.util.concurrent
This package contains an Iterator wrapper that can be used to perform calculations simultaneously on multiple elements provided by the wrapped iterator, and returns the calculation results while preserving the original order of elements.
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(BicycloStereoDescriptor) - Method in class chemaxon.struc.BicycloStereoDescriptor
Compares two bicyclostereo descriptors.
compareTo(RgroupBridgeId) - Method in class chemaxon.struc.RgroupBridgeId
 
compareTo(AttachmentPoint) - Method in class chemaxon.struc.sgroup.AttachmentPoint
Compares two attachment points by their order.
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 - Enum constant in enum class chemaxon.struc.SgroupType
 
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.
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
 
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
 
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
 
CONJUGATED - Enum constant in enum class chemaxon.struc.BondType
Conjugation state of the bond.
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
 
CONSENSUS - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod
Consensus model using Chemaxon and Klopman's models and the PhysProp database.
Consent - Enum Class in chemaxon.marvin.collecting
 
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.
contains(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer
 
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.
contains(String) - Method in class chemaxon.checkers.util.AtomLabels
Gets whether the atom labels contain the specified atom label
contains(String) - Method in class chemaxon.checkers.util.DataExclusionList
 
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.MElectronContainer
 
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MMoleculeMovie
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.
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
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(byte[], int, int) - Method in class chemaxon.marvin.io.Encoding
Converts a byte array to a string.
convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
 
convert(double, double) - Method in class chemaxon.calculations.nmr.Multiplet
Multiplies the parameters of this multiplet (unit conversion).
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
 
convertToBondType(int) - Static method in enum class chemaxon.struc.BondType
Creates BondType from the given number.
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.MFontProp
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 - Enum constant in enum class chemaxon.struc.BondType
Coordinate bond.
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
copyOf(ShapeData) - Static method in class chemaxon.marvin.alignment.ShapeData
 
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(MAssigner) - Method in class chemaxon.struc.graphics.MAssigner
Copies the assigner properties to another assigner object.
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.
copyProperties(MRArrow) - Method in class chemaxon.struc.graphics.MRArrow
Copies arrow properties to another arrow 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.mcs.McsCustomMatcherFactory
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.marvin.plugin.CalculatorPlugin
Loads a plugin from the classpath based on its fully qualified name.
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
Deprecated, for removal: This API element is subject to removal in a future version.
Loading plugins from plugin-specific jars is no longer supported, use CalculatorPlugin.create(String) instead.
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.
createBondType(int) - Static method in enum class chemaxon.struc.BondType
Deprecated, for removal: This API element is subject to removal in a future version.
since 2014.06.04. use BondType.convertToBondType(int) instead.
createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
 
createChecker(String, Map<String, String>) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory
This method creates a requested (type represented in checkerId) StructureChecker instance with the give parameters
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.
createFixer(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory
This method creates a StructureFixer instance identified by fixerId parameters
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
createImporter(InputStream) - Method in interface chemaxon.formats.ImportOptions
Creates a MolImporter from the given input stream.
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.
createMElectronContainer(DPoint3[], MolAtom, boolean) - Static method in class chemaxon.struc.graphics.MElectronContainer
 
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.
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.
createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
Creates identical attributes for the next section.
createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates the parameter panel.
createPreConcatenatedAffineTransform(Graphics2D) - Method in class chemaxon.struc.graphics.MTextBoxTransformation
 
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).
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.ServiceDescriptor
Creates a new service handler for this descriptor.
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
createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a sub-panel with a title.
createTautomerMoleculeBasedOnDecoration(Molecule, boolean) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode
 
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(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
 
createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter
Constructs the specified visitor implementation.
createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter
 
createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
 
createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter
 
createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter
 
createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
 
createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
 
createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter
 
createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter
 
createVisitor(Consumer<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter
 
createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter
 
createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
 
createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter
 
createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter
 
createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter
 
createVisitor(Consumer<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.
CustomFunction - Interface in chemaxon.jep
Base interface for custom Chemical Terms functions.
CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "customizationEnabled".
customMatching(McsCustomMatcherFactory) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets the factory to be used to create a custom matcher.
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
 
DataExclusionList - Class in chemaxon.checkers.util
A list of Strings to be excluded by AttachedDataChecker.
DataExclusionList(String) - Constructor for class chemaxon.checkers.util.DataExclusionList
 
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.
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.
DEAROMATIZATION_GENERAL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
General dearomatization method.
DEAROMATIZATION_HUCKEL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
Dearomatization method with Hückel rule checking.
DEAROMATIZATION_HUCKEL_EX - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
Dearomatization method with Hückel rule checking.
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
DECLINE - Enum constant in enum class chemaxon.marvin.collecting.Consent
 
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.
Decomposition - Class in chemaxon.sss.search
Class storing RGroupDecomposition results.
Decomposition(Molecule, Molecule, int[][], Molecule[], Molecule) - Constructor for class chemaxon.sss.search.Decomposition
Constructor.
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.
decorateTautomerRegions(Molecule, int, OptionalInt) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode
 
decQProp(String) - Method in class chemaxon.struc.MolAtom
Decrements the value of a query property.
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.formats.GeneralExportOptions.AromatizationMethod
No aromatization.
DEFAULT - Enum constant in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption
No change in hydrogens.
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.marvin.io.Encoding
The system's default encoding.
DEFAULT - Static variable in class chemaxon.standardizer.StandardizerActionFactory
default factory id
DEFAULT - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default attributes object.
DEFAULT - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory
default factory id
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_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_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_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_PATH - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory
Chemaxon's default checker 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_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_LOWER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters
default values for parameters
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_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_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_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_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_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_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.marvin.services.ServiceDescriptor
Property key for Service description as String
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
Deprecated.
detectRecordPositions(IntVector) - Method in interface chemaxon.marvin.io.MRecordReader
Deprecated.
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
 
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_ACCELERATOR - Static variable in class chemaxon.marvin.swing.MAction
Disables the keyboard shortcut while still displaying its name in the menu.
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_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.
displayInMarvinSpace - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Display in MarvinSpace is enabled or not.
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.
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.MElectronContainer
 
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie
Gets the 2D distance from the specified point.
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.
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
doAction(ActionEvent) - Method in class chemaxon.marvin.swing.MAction
Performs a custom action.
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.
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.
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 chemaxon.util.progress.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.
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
 
DOT_DISCONNECTED_FRAGMENTS - Enum constant in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule
Dot-disconnected molecular formula of a multifragment molecule.
For example: C7H5O2.Na for sodium benzoate.
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.
DOUBLE - Enum constant in enum class chemaxon.struc.BondType
Double bond type.
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 - Enum constant in enum class chemaxon.struc.BondType
Double or aromatic query bond type.
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".
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 - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration
 
E_OR_UNSPEC - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration
 
E_OR_Z - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration
 
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.
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.
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.
Encoding - Class in chemaxon.marvin.io
File encoding information.
Encoding(String, int, ByteOrder) - Constructor for class chemaxon.marvin.io.Encoding
Creates an Encoding for the specified name, word length and byte order.
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).
endElement(String, String, String) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter
 
endGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream
Deprecated, for removal: This API element is subject to removal in a future version.
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.
ensureValidity() - Method in class chemaxon.struc.graphics.MElectronContainer
 
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(Encoding) - Method in class chemaxon.marvin.io.Encoding
Tests whether two encodings are equal.
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.calculations.pka.PKaTrainingResult
 
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.util.AtomLabels
 
equals(Object) - Method in class chemaxon.checkers.util.DataExclusionList
 
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.io.Encoding
Tests whether two encodings are equal.
equals(Object) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
 
equals(Object) - Method in class chemaxon.sss.search.Decomposition
Returns true if this decomposition is equivalent to the specified decomposition.
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.MElectron
 
equals(Object) - Method in class chemaxon.struc.graphics.MElectronContainer
 
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.MFontProp
 
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.MMoleculeStringProp
 
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.RgroupBridgeId
 
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.
estimateNumRecords() - Method in class chemaxon.marvin.plugin.PluginMDocSource
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(Map<String, String>, List<Object>, ChemContext) - Method in interface chemaxon.jep.CustomFunction
Evaluates this function.
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 for internal use only.
Evaluator(File) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File, Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor for internal use only.
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 for internal use only.
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 - Static variable in class chemaxon.sss.formula.FormulaSearch
Constant value specifying the exact search type.
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".
EXACT_SUBFORMULA - Static variable in class chemaxon.sss.formula.FormulaSearch
Constant value specifying the exact sub formula search type.
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(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether generic query atoms should be matched only to atoms of exactly the same type.
exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether generic query bonds should be matched only to bonds of exactly the same type.
EXCLUDE_KEY - Static variable in class chemaxon.standardizer.actions.AbstractSgroupAction
Key of exclude for parsing and property change
EXCLUDE_XX - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
excludeString - Variable in class chemaxon.standardizer.actions.ContractSgroupsAction
 
excludeString - Variable in class chemaxon.standardizer.actions.ExpandSgroupsAction
 
excludeString - Variable in class chemaxon.standardizer.actions.UngroupSgroupsAction
 
exit() - Method in class chemaxon.marvin.beans.MarvinPane
Closes all windows opened by this MarvinPane and saves user initialization file.
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.AbstractStructureC