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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.
as of Marvin 2014.07.21.0 intended for internal use only
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_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Absolute stereoconfiguration label visibility flag.
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.
AbsentChiralFlagFixer() - Constructor for class chemaxon.fixers.AbsentChiralFlagFixer
Deprecated.
 
ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show absolute stereo label.
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
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
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
 
AbstractShapeComparator<T extends ShapeDescriptor> - Class in com.chemaxon.descriptors.alignment
 
AbstractShapeComparator(DescriptorGenerator<T>) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
AbstractShapeGenerator<D extends ShapeDescriptor,P extends AbstractShapeGeneratorParameter> - Class in com.chemaxon.descriptors.alignment
 
AbstractShapeGenerator(P) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
AbstractShapeGeneratorParameter - Class in com.chemaxon.descriptors.alignment
Helper class without the requested getDescriptorGenerator method.
AbstractShapeGeneratorParameter(AtomTyping) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 
AbstractStandardizerAction - Class in chemaxon.standardizer
Abstract implementation of the StandardizerAction.
AbstractStandardizerAction(Map<String, String>) - Constructor for class chemaxon.standardizer.AbstractStandardizerAction
Initializes the functionality of the abstract implementation.
AbstractStereoFilter<T extends StereoCenter> - Class in com.chemaxon.calculations.stereoanal.filters
Abstract class for Filter interface.
AbstractStereoFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
 
AbstractStructureChecker - Class in chemaxon.checkers
Abstract base class of all functions checking and repairing chemical structures.
AbstractStructureChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AbstractStructureChecker
Constructor to create a Structure checker instance with the given errorType
AbstractStructureFixer - Class in chemaxon.fixers
This class is the default abstract implementation of StructureFixer interface
AbstractStructureFixer() - Constructor for class chemaxon.fixers.AbstractStructureFixer
Constructor to create a Structure fixer
Ac - Static variable in class chemaxon.core.ChemConst
 
accept(Molecule) - Method in class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter
Accepts molecule if the number of R-group attachments in the molecule is exactly the attachment count specified in the constructor of this filter.
accept(Molecule) - Method in interface chemaxon.util.MolFilter
Returns true if molecule is accepted by the filter.
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
accept(StereoCenterVisitor) - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Accepts visitors.
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
accept(T) - Method in interface com.chemaxon.calculations.io.Sink
Deprecated.
 
ACCEPT_ONLY_SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
 
Accepted - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
Indicates, that the structure checker puts valid or fixed structures to the output file.
ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
Acceptor sign displayed in GUI.
ACCEPTOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
ACCESS - Static variable in class chemaxon.jchem.db.DatabaseConstants
 
ACCESS_DRIVER - Static variable in class chemaxon.jchem.db.DatabaseConstants
JDBC driver for MS Access database
ACCESS_TYPE_NAME - Static variable in class chemaxon.jchem.db.DatabaseConstants
 
ACCESS_URL_EXAMPLE - Static variable in class chemaxon.jchem.db.DatabaseConstants
JDBC URL example for Access database
ACCESS_URL_TEMPLATE - Static variable in class chemaxon.jchem.db.DatabaseConstants
JDBC URL template for Access database
ACCORD - Static variable in class chemaxon.formats.MFileFormat
ACCORD file format
ACCP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
Atomic contribution with correction terms.
ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
 
ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Constant denoting acidic pKa.
ACT_KEY - Static variable in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
Key of type for parsing and property change
actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Action handler.
ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
action string token of the checker
ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor
action string tokens of the fixer
ACTIONSTRING_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
action string token of the action
ActionStringBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader
An implementation of ConfigurationReader for parsing action strings
ActionStringBasedConfigurationReader(String) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
Default constructor
ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
ActionStringBasedConfigurationReader(String, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
Constructor with custom checker factory
actionStringToken() - Element in annotation interface chemaxon.checkers.CheckerInfo
Returns the action string token of the checker
actionStringToken() - Element in annotation interface chemaxon.fixers.FixerInfo
Returns the action string token of the fixer.
actionStringToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
Returns the action string tokens of the action as a string, divided by comma characters
activateContainerCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
The containing cell of the GraphicComponent will be the active cell of the scene.
active - Variable in class chemaxon.marvin.space.GraphicComponent
Is this component selected or not.
adaptiveSPHEX(int, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Sphere exclusion clustering with sphere radius inference.
add(MDSet) - Method in interface chemaxon.descriptors.MDHypothesisGenerator
Adds a MDSet component to be considered in the hypothesis.
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
Adds a bond to the molecule.
add(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond to the molecule.
add(MolBond) - Method in class chemaxon.struc.RgMolecule
Adds a bond to the root structure.
add(MolBond) - Method in class chemaxon.struc.RxnMolecule
Adds a bond to a reactant, product, agent.
add(MolBond) - Method in class chemaxon.struc.SelectionMolecule
Adds a bond to the graph.
add(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
Add an edge if it had not been already added.
add(MolBond, boolean) - Method in class chemaxon.struc.MoleculeGraph
Add a bond to the molecule.
add(MolBond, boolean) - Method in class chemaxon.struc.SelectionMolecule
Add a bond to the molecule.
add(MolBond, MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
Add an edge to the given atom of the sgroup, if it had not been already added.
add(MProp) - Method in class chemaxon.struc.prop.MListProp
Adds an element.
add(InputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds an input stream containing standardizer specifications to be stored by the output factory
add(URL) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds an input stream containing standardizer specifications to be stored by the output factory
add(Properties) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
Adds a property map containing properties of standardizer actions to be stored by the output factory
ADD - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
Deprecated.
Add absolute stereo
ADD_REMOVE_H_ATOMS_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "addRemoveHatomsEnabled".
addAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds an action to the configuration
addActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane
Adds an action listener.
addActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions
Adds an action listener.
addActions(List<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds actions to the configuration
addActionToGroup(String, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds an action to the group
addActionToGroups(Collection<String>, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
Adds an action to a list of groups
addAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "added atom" list.
addAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes
Adds atoms to the "added atom" list.
addAtom(int) - Method in interface chemaxon.struc.WSmolecule
Adds an atom.
addAtom(MolAtom) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "added atom" list.
addAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes
Adds an atom to the "added atom" list.
addAtom(Smolecule, int) - Method in interface chemaxon.struc.WSmolecule
Adds an atom from another Smolecule.
addAtom0(MolAtom) - Method in class chemaxon.struc.Molecule
Adds an atom.
addAtom0(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom.
addAtom0(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom.
addAtomPair(int, int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Adds an alignment constraint between the reference and aligned molecule.
addAtomPair(int, int, double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Adds an alignment constraint between the reference and aligned molecule.
addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Adds all atoms and bonds to the specified molecule.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.Molecule
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RgMolecule
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Adds an atom to a fragment.
addAtomWithBonds(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom to the molecule.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom without setting its parentGraph and index fields.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom without setting its parentGraph and index fields.
addAttachmentPoint(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point for an atom.
addAttachmentPoint(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point of the given attachment atom and order.
addAttachmentPoint(MolAtom, int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MBracket
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MEFlow
 
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MPolyline
Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRectangle
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRoundedRectangle
Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
Adds the attribute names to the specified list.
addBond(int, int, int) - Method in interface chemaxon.struc.WSmolecule
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.Molecule
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.SelectionMolecule
Adds a bond.
addBondWithoutChangingIt(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond without setting its parentGraph and index fields.
addBracket(MBracket) - Method in class chemaxon.struc.Sgroup
Adds a bracket to this S-group.
addCanvas(Container) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace viewer to the container.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
Adds attribute names to the specified list.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
Adds attribute names to the specified list.
addCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Adds a central atom to this sgroup.
addChar(char) - Method in class chemaxon.struc.graphics.MTextBox
Adds a character to the text.
addCheckerMark(MDocument.CheckerMark) - Method in class chemaxon.struc.MDocument
Adds a checker mark to the document.
addChildCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Add a cluster to another cluster as a child cluster.
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.
addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Adds a new component to this cell.
addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to the active or to the first cell.
addComponent(GraphicComponent, int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to the cell having the given index.
addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule
Adds a reactant, product or agent.
addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule
Adds a reactant, product or agent.
addComponentToEmptyCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to an empty cell.
addConstraintsFromUserMappedAtoms() - Method in class chemaxon.marvin.alignment.Alignment
An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.
addCoordinateSystem(int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a dummy graphic component that represents the coordinate system.
addCrossingBonds(List<MolBond>, List<MolBond>) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the crossing bonds (head and tail) of a ladder-type polymer.
addData(Molecule, MolAtom, String, String) - Method in class chemaxon.marvin.io.MolExportModule
Adds a data sgroup to the given atom in the given molecule with fieldName and value.
addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Adds a line to the data stored in the field.
addDataPoint(double, double) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot
Add new point to put.
addDescriptor(MolecularDescriptor) - Method in class chemaxon.descriptors.MDSet
Appends the next component to the MDSet object.
addDihedralStep(DihedralScanStep) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Add a new step.
addDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent
Forces the component to set all drawing property stored in drawProperties, and leaves the old settings which are not overidden.
addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
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.
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.
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
Adds a new function to the parser.
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.
since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph) instead
addHAtoms(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead
addHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) instead
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.
addHydrogens() - Method in class chemaxon.util.MolHandler
Adds explicit H atoms instead of the current implicit ones.
addHydrogensToAromaticHeteroAtoms() - Method in class chemaxon.util.MolHandler
Adds the implicit Hydrogen atoms to heteroatoms in aromatic rings.
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.
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.
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.
addInputChecker(CalculatorInputChecker) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Adds the specified input checker to this plugin.
additionalInformation - Variable in class chemaxon.jchem.db.Updater.UpdateInfo
Additional information for the entities in same order, if needed.
addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a label component inside the MarvinView table.
addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a label component inside the MarvinView table.
addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MTextBox
 
addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage
Adds a listener if it is not yet added.
addListToDelete(int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a gl list id to the deletion list
addLogger(ProgressWriter.Logger) - Method in class chemaxon.jchem.file.ProgressWriter
Adds a ProgressWriter.Logger to retrieve suppressed (error) messages.
addLonePairs(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead
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.
addMDConfig(String, String, File) - Method in class chemaxon.descriptors.GenerateMD
Adds a new parameter configuration to the descriptor.
addMDConfig(String, String, String) - Method in class chemaxon.descriptors.GenerateMD
Adds a new parameter configuration to the descriptor.
addMenuBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace menubar to the container.
addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane
Adds a menubar change listener.
addMessage(int, String, Throwable) - Method in interface chemaxon.jchem.file.ProgressWriter.Logger
 
addMolecule(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a molecule viewer component inside the MarvinView table.
addMolecule(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a molecule viewer component inside the MarvinView table.
addMolecule(Molecule) - Method in class chemaxon.clustering.libmcs.LibraryMcs
Adds a new molecule to the set of structures to be clustered.
addMolecule(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds a Molecule object to the actual cell of the viewer.
addMolecule(Molecule) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add a new structure.
addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment
Add molecule to align
addMolecule(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.
addMolecules(Collection<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures.
addMolecules(Iterator<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures.
addMolecules(Iterator<? extends Molecule>, StandardizerWrapper) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures with preprocessing.
addMoleculeTo(Molecule, int) - Method in class chemaxon.marvin.space.MSpaceEasy
Makes the given cell to be the active cell, and adds the molecule to it.
addMoleculeToEmptyCell(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.
addMoleculeToEmptyCell(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.
addMoleculeWithoutChange(Molecule, boolean) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds a Molecule object to the actual cell of the viewer and resets the view only if required.
addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Allocate a new cluster.
addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Allocate a new cluster.
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.Alignment
User may define extra weights between colors defined at setColoringScheme.
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
addNodeColorWeight(int, int, double) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint
Point added to a document.
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint
Point added to a document.
addNotify(MDocument) - Method in class chemaxon.struc.MObject
Called when the object is added to a document.
addNumbering - Variable in class chemaxon.marvin.io.MolExportModule
Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.
addObject(MObject) - Method in class chemaxon.struc.MDocument
Adds an object to the document.
addObject(MObject) - Method in class chemaxon.struc.MSelectionDocument
Adds an object to the document.
addOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Adds an owner, that should be notified about the changes in the properties.
addParameters(File) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML config file keeping all previous settings.
addParameters(String) - Method in class chemaxon.descriptors.MDParameters
Sets parameters from an XML string representation keeping all previous settings.
addParametrizedMetric(String, String, String) - Method in class chemaxon.descriptors.MDParameters
Expands the set of parametrized metrics with a new item.
addParametrizedMetricNode(String, String, String) - Method in class chemaxon.descriptors.MDParameters
Adds a ParametrizedMetric node to the DOM tree.
addParametrizedMetricsNode() - Method in class chemaxon.descriptors.MDParameters
Adds the ParametrizedMetrics node to the DOM tree.
addPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
addPopupMenu() - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace popup menu to the JPanel.
addProperty(String, String) - Method in class chemaxon.jchem.db.DatabaseProperties
Inserts the property with the specified key and value into the JChemProperties table.
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.
addPropertyColumnName(String, String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
Sets the displayed name in the header column of the given property
addQueries(MDReader) - Method in class chemaxon.descriptors.MDSimilarity
Adds new query molecules as their set of descriptors from a chemical descriptor reader.
addQueries(MDSet[]) - Method in class chemaxon.descriptors.MDSimilarity
Adds new query molecules as their set of descriptors from an array.
addQuery(MDSet) - Method in class chemaxon.descriptors.MDSimilarity
Adds a new query molecule as its set of descriptors.
addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Adds an atom to the list of paradigmatic repeating unit atoms.
addResultWriter(MDSimilarityResultWriter) - Method in class chemaxon.descriptors.MDSimilarity
Adds a MDSimilarityResultWriter object.
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
addSelectionPanel(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
addSelectionPanelAndProgressBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
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
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.
addStructure(byte[], String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(byte[], String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(byte[], String, Map<String, String>) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(byte[], String, Map<String, String>, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(IMoleculeData) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
Adds the molecule and its properties into the predefined template.
addStructure(IMoleculeData) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the molecule structure to the end of the document without it's properties
addStructure(IMoleculeData, ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the molecule structure to the the document with the given settings without properties
addStructure(IMoleculeData, ITemplateWriterOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
Adds the molecule and its properties into the predefined template.
addStructure(Molecule, String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(Molecule, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(String, int, int, byte[]) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, byte[], String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, byte[], String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, byte[], String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, Molecule, String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, Molecule, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, String, String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, int, int, String, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
Adds a structure to the cell in the given column/row on the sheet with the given name.
addStructure(String, String, String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(String, String, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(String, String, String, Map<String, String>) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructure(String, String, String, Map<String, String>, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
A single structure can be added to the worksheet, in the current row
addStructureAndProperties(IMoleculeData, ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the molecule structure and all corresponding properties to the document with the give settings
addStructures(IMoleculeData[]) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
Adds the array of molecule structures and their corresponding properties to the predefined template.
addStructures(IMoleculeData[]) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the array of molecule structures and their corresponding properties to the end of the document.
addStructures(IMoleculeData[], ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the array of molecule structures and their corresponding properties to the location given in the settings.
addStructures(IMoleculeData[], ISettings, int) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the array of molecule structures and their corresponding properties to the document with the give settings
addStructures(IMoleculeData[], ITemplateWriterOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
Adds the array of molecule structures and their corresponding properties to the predefined template.
addStructuresToCluster(Collection<Integer>, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Add multiple structures to a cluster.
addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Set a structure to be a part of a cluster as a leaf.
addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Add a structure to a cluster as an immediate leaf.
addTable(ITableModel) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Adds the table custom table to the and of the Document
addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
Add a thread-local name to structure converter.
addTimestamp(String, Connection) - Method in class chemaxon.jchem.db.CacheRegistrationUtil
 
addToolBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace toolbar to the container.
addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated.
Not used.
addToSelection(MDocument, MSelectionDocument) - Static method in class chemaxon.struc.NoStructure
Adds the selected NoStrutures from the document to the selectionDocument
addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
Add an element to marvinsketch's recent file list
addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
Add an element to marvinview's recent file list
addTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Add a TransferableDescriptor to the MTransferable Registry.
addTransferable(String, String, Integer, Integer, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Add a TransferableDescriptor to the registry, and constructing it by the given parameters.
addUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
Adds the given user-defined comparator to the search.
addUserConstraint(int, int, int, int) - Method in class chemaxon.marvin.alignment.Alignment
Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph
Checks whether the molecule has multiple chiral centres
AdvancedCheckerRunner - Class in chemaxon.checkers.runner
CheckerRunner implementation with advanced fixing capabilities.
StructureFixer selection is based on provided fixer class if available, or falls back to StructureCheckerResult based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts.
AdvancedCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(ConfigurationReader, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
Ag - Static variable in class chemaxon.core.ChemConst
 
AGENT - Static variable in class chemaxon.jep.context.ReactionContext
 
AGENTS - Static variable in class chemaxon.struc.RxnMolecule
"Agent" structure type.
Al - Static variable in class chemaxon.core.ChemConst
 
alias - Variable in class chemaxon.marvin.services.ServiceArgument
the alias of the argument
alias() - Element in annotation interface chemaxon.checkers.Persistent
Returns the alias name of the annotated property
ALIAS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias values had found in the molecule
ALIAS_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias value that could be converted to an element had found in the molecule
ALIAS_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias value that could be converted to an abbreviated group had found in the molecule
ALIAS_NONE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that alias value had found in the molecule
AliasChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting atoms with alias labels.
AliasChecker() - Constructor for class chemaxon.checkers.AliasChecker
Default constructor.
AliasToAtomAction - Class in chemaxon.standardizer.actions
Alias to Atom standardizer action.
AliasToAtomAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToAtomAction
Initializes the action
AliasToGroupAction - Class in chemaxon.standardizer.actions
Alias to Group standardizer action
AliasToGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToGroupAction
Initializes the action with parameters
align() - Method in class chemaxon.marvin.alignment.Alignment
3D alignment on two or more molecules.
align() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
align() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
does a simple one-to-one atom mappin and aligns.
align() - Method in class chemaxon.marvin.alignment.MolAligner
Execute best alignment based on hit map provided earlier
align(int[]) - Method in class chemaxon.marvin.alignment.MolAligner
Calculates and performs the best alignment possible specified by the hit map array.
align(int[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
Rigid alignment on the user defined atom index
align(Molecule) - Method in interface chemaxon.marvin.alignment.MCSAlignment
Align the given molecule to the reference.
align(Molecule, int[]) - Method in class chemaxon.util.MolHandler
Alignes (rotates) a specified molecule realtive to the contained molecule according to the specified atom pairs.
ALIGN_AS_IS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
 
ALIGN_BOTTOM - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to bottom of box.
ALIGN_CENTER - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to center of box.
ALIGN_LEFT - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to left edge of box.
ALIGN_RIGHT - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to right edge of box.
ALIGN_TOP - Static variable in class chemaxon.struc.graphics.MTextBox
Align text to top of box.
Alignment - Class in chemaxon.marvin.alignment
3D Alignment aligns two or more 3D molecules onto each other.
Alignment() - Constructor for class chemaxon.marvin.alignment.Alignment
 
Alignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.Alignment
 
ALIGNMENT - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
 
ALIGNMENT - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Alignment
ALIGNMENT_OFF - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
The structure is displayed with the original coordinates.
ALIGNMENT_PARTIAL_CLEAN - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
The substructure part of the target will get the exact coordinates of the query, and new coordinates will be generated for the remainder of the structure.
ALIGNMENT_ROTATE - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
The structure is rotated according to the substructure.
AlignmentAccuracyMode - Enum Class in chemaxon.marvin.alignment
Settings for the representation of a molecular shape.
AlignmentMolecule - Class in chemaxon.marvin.alignment
 
AlignmentMoleculeFactory - Class in chemaxon.marvin.alignment
Creates an AlignmentMolecule form a Molecule based on the settings.
AlignmentMoleculeFactory() - Constructor for class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.marvin.alignment
 
AlignmentPlugin - Class in chemaxon.marvin.calculations
Plugin layer for the AlignmentAPI
AlignmentPlugin() - Constructor for class chemaxon.marvin.calculations.AlignmentPlugin
 
AlignmentProperties - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.ColoringScheme - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.ColorNotSpecifiedCase - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.DegreeOfFreedomType - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.FlexibilityMode - Enum Class in chemaxon.marvin.alignment
Conformational flexibility treatment during the alignment for a pair of a molecule.
AlignmentProperties.NodeType - Enum Class in chemaxon.marvin.alignment
 
AlignmentProperties.OrientationType - Enum Class in chemaxon.marvin.alignment
 
AlignOnPairedAtoms - Class in chemaxon.marvin.alignment
Overlays two molecules using the user defined atom pairs
Example:
AlignOnPairedAtoms() - Constructor for class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
AlignRigidEasy - Class in chemaxon.marvin.alignment
Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.
AlignRigidEasy() - Constructor for class chemaxon.marvin.alignment.AlignRigidEasy
 
ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
Aliphatic query atom.
ALIPHATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
aliphaticAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.
aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
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.
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.
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.
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.
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.
as of release 5.5, replaced by Ring.aliphaticRings(int)
ALL - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption
All atoms can have translation.
ALL - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
 
ALL_H - Static variable in class chemaxon.struc.MolAtom
Include any Hydrogen atom.
ALL_MATCH_AMBIG - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
Ambiguous aromatic parts of the target Markush structure can be matched by aliphatic and aromatic forms as well.
ALL_PERM - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
 
allringsystems - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
allStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
All stereo centers of molecule.
allStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
All stereo centers with attached data.
Am - Static variable in class chemaxon.core.ChemConst
 
ambient - Static variable in class chemaxon.marvin.space.monitor.Control
 
AMBIGUOUS - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
AMBIGUOUS_AROMATIC_ATOMS_IGNORED - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.DEFAULT.
Usage:
             molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             
AMINOACID - Enum constant in enum class chemaxon.struc.SgroupType
 
AMINOACID_BOND_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "aminoAcidBondColoringEnabled".
ANCHOR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
and(StandardizerWrapper) - Method in interface com.chemaxon.overlap.io.StandardizerWrapper
Create a new wrapper representing an additional step.
AND - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
Stereogenic centers belonging to an ANDn group (e.g.
AND - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
AND_OR - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Set of enhanced stereo flags.
ANGLE_STEP - Static variable in class chemaxon.struc.MolAtom
 
angle2D(double, double) - Method in class chemaxon.struc.DPoint3
Calculates the absolute angle in the XY plane of the vector pointing from this point to the other point.
angle3D(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculate the angle of two vectors (this and p) in the range 0.0 through pi.
AngleMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring angle between 3 components, the first 2 determines a line, the second 2 another.
AngleMonitor() - Constructor for class chemaxon.marvin.space.monitor.AngleMonitor
Creates a new instance of AngleMonitor
ANIMATE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animate".
ANIMATION_DELAY - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animDelay".
ANIMATION_FPS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animFPS".
ANIMATION_SYNCHRONIZATION - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animSync".
ANIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
ANTI - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, anti (relative configuration).
ANY - Enum constant in enum class chemaxon.struc.SgroupType
 
ANY - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the any atom A.
ANY - Static variable in class chemaxon.struc.MolBond
Any bond type.
ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
 
anybond_auto - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues
 
ANYBOND_AUTO - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_AUTO_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
anybond_dashed - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues
 
ANYBOND_DASHED - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_DASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
anybond_solid - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues
 
ANYBOND_SOLID - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
anyBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the drawing style for ANY bonds.
AnyBondStyle - Enum Class in chemaxon.marvin.paint.constants
Holds the values for the possible rendering styles for Any bonds.
anyBooleanPropertyTrue(Map<String, String>, String...) - Method in class chemaxon.standardizer.AbstractStandardizerAction
Check the given map, whether there is a String 'true' (case in-sensitive) value for any of the given keys
anyCancelled(CancelObserver...) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a cancel observer which cancels when any of the specified observer is cancelled.
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.
APPEND_TO_RESULT_TABLE - Static variable in class chemaxon.jchem.db.JChemSearch
Constant for the generation of result tables.
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.
appendLongAsBinaryString(StringBuilder, long) - Method in enum class com.chemaxon.descriptors.common.BinaryVectors.Endianness
Convert 64 bit long to binary string.
appendMEnd(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Appends the "M END" line to the string buffer.
appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.MDParameters
Extends internal data with a new parametrized metric.
appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.PFParameters
 
appendpHText(String) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Appends the pH text.
appendRight(int, int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append an integer to the buffer in the right hand side of an n-characters wide field.
appendRight(String, int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append a string to the buffer in the right hand side of an n-characters wide field.
apply(Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker
Checks the given molecule and returns the found errors, or an empty list of the molecule is valid.
apply(BinaryVectorMetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory.ToLinenote
 
apply(MetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.MetricFactory.ToLinenote
 
APPLY_DEPTH_CUE - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
As of Marvin 5.4.1, replaced by DispOptConsts.AUTOMATIC_FOG
applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane
Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.
applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane
Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.
Ar - Static variable in class chemaxon.core.ChemConst
 
ARC_BRACES - Static variable in class chemaxon.struc.graphics.MBracket
The default arc angle of the Braces Rectangle in degrees.
ARC_ROUND - Static variable in class chemaxon.struc.graphics.MBracket
The default arc angle of the Rounded Rectangle in degrees.
areArrowsAndLikelyTheSame(MPolyline, MPolyline) - Static method in class chemaxon.marvin.modules.reaction.ReactionEditUtils
Compares type and checks perfect equality of location.
areAttachmentPointsVisible() - Method in class chemaxon.marvin.MolPrinter
Gets the attachment points visibility.
areChildSgroupsVisible() - Method in class chemaxon.struc.Sgroup
Checks whether the child S-groups are visible.
areChildSgroupsVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the child S-groups are visible.
areMonomersTransformed() - Method in class chemaxon.sss.search.SearchOptions
Obtain monomer transformation information.
areNeighbors(int, int) - Method in interface chemaxon.struc.Smolecule
Tests whether two atoms are connected.
arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Are popup menus enabled?
areRGroupsHidden() - Method in class chemaxon.marvin.io.image.ImageExporter
 
ARO_R - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
Number of aromatic rings.
AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph
Aromatization type for ambiguous 5-membered rings.
AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph
Basic aromatization.
AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph
Huckel aromatization.
AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
General (Daylight conform) aromatization.
AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph
Loose aromatization.
AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph
Substructure aromatization.
AROMATIC - Static variable in class chemaxon.struc.MolAtom
Aromatic query atom.
AROMATIC - Static variable in class chemaxon.struc.MolBond
Aromatic bond type.
AROMATIC_ATOM - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
Aromatic or aliphatic query atom.
AROMATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AROMATIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
aromaticAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic atoms in the molecule.
aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
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.
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.
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.
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.
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.
as of release 5.5, replaced by Ring.aromaticRings(int)
aromatize - Variable in class chemaxon.marvin.io.MolExportModule
Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, etc, dearomatize if -1, do nothing if 0.
aromatize() - Method in class chemaxon.struc.MoleculeGraph
Aromatize molecule using the default general aromatization method.
aromatize() - Method in class chemaxon.util.MolHandler
Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.
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) - Method in class chemaxon.util.MolHandler
Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.
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.
aromatizeBasic() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap basic aromatization.
aromatizeGeneral() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap general aromatization.
aromatizeLoose() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap loose aromatization.
Aromatizer - Enum Class in com.chemaxon.search.transformation.transformers
Aromatizer transformer.
arrangeComponents() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
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.
arrangeCrossingBonds(MolBond, Molecule, boolean) - Static method in class chemaxon.marvin.util.MoleculeUtil
Deprecated.
as of Marvin 5.11.1 use MoleculeGraph.setBond(int, MolBond)
arrangeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange data attached to DataSgroup.
arrangeHydrogenIncerments(Molecule, int, String, double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
arrangeMolecules(MoleculeGraph[], int, int) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice.
arrangeReaction(RxnMolecule) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges reaction components nicely
arrangeRelativeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange data attached to DataSgroup.
arrangeRgroupMembers(RgMolecule) - Method in class chemaxon.marvin.util.MolFragLoader
Arranges R-group definition member coordinates.
arrangeSgBrackets(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange sgroup brackets in the molecule.
ArrayMDocSource - Class in chemaxon.marvin.io
MDocSource implementation for an array of documents or molecules.
ArrayMDocSource(MDocument[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for an array of documents.
ArrayMDocSource(Molecule[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for an array of molecules.
ArrayMDocSource(List<?>) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for a list of documents or molecules.
ARROW - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.LineType
 
ARROW - Enum constant in enum class chemaxon.marvin.paint.constants.CoordinateBondStyle
Arrow is used when rendering Coordinate bonds.
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
 
Assign(ICellFormat) - Method in interface chemaxon.formats.documents.jchemoffice.ICellFormat
Assign an existing cell format to the cell
Assign(IMoleculeData) - Method in interface chemaxon.formats.documents.jchemoffice.ICellData
Assigns the structure to the cell and sets the molecule data and format
Assign(String) - Method in interface chemaxon.formats.documents.jchemoffice.ICellData
Assigns the string content and string format to the cell
associate(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
The given component will depend on this component.
associatedComponents - Variable in class chemaxon.marvin.space.GraphicComponent
Strores components that depend on this component.
asymmetricAtomCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of atoms having four different ligands.
asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
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.
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
 
ATMAP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom mapping flag.
ATNUM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom numbers flag.
atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
The atom whose the neighbours are processed.
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_COUNT_UPPER_BOUND - Static variable in class chemaxon.clustering.libmcs.LibraryMcs
structures above this size are not searched for pair-wise mcs as it would take to long to calculate the MCS
ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomFont".
ATOM_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Sets the atom font.
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_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Displays atom mapping.
ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomNumberingType".
ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Atom numbering type
ATOM_NUMBERS - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.AtomNumberingType
 
ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
in 6.2.0 use atomNumberingType parameter instead.
ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Displays atom numbers.
ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomPropertiesVisible".
ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
 
ATOM_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by mapping atom based property values to the surface.
ATOM_QUERY_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that an atom has a query property set.
ATOM_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "atomSet".
ATOM_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomSetColor".
ATOM_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomsize".
ATOM_STRINGS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "atomStrings".
ATOM_SYMBOL_VISIBLE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
 
ATOM_SYMBOLS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomSymbolsVisible".
ATOM_TYPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom with the specified symbol had found in the molecule
ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom
Number of atom types in the elements array
ATOM_TYPE_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum atom number.
ATOM_TYPES - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
 
ATOM_VALUE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that atom values had found in the molecule
atomA - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
atomAndBondColors(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Set the atom and bond colors.
atomB - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
AtomChecker - Class in chemaxon.checkers
Descendants of the abstract AtomChecker class check every atom for a specific error or property.
AtomChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomChecker
Constructor to create a Structure checker instance with the given errorType.
AtomContext - Class in chemaxon.jep.context
Expression evaluation context containing an input molecule and an input atom.
AtomContext() - Constructor for class chemaxon.jep.context.AtomContext
Constructor.
atomCount - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
atomCount - Variable in class chemaxon.struc.MoleculeGraph
The number of atoms.
atomCount() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms in the molecule.
atomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of atoms in the molecule including implicit hydrogens.
atomCount() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms in the molecule.
atomCount(int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms of a given element in the molecule.
atomCount(int, int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms of a given element in the molecule.
ATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
Atom count of the molecule
atomFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Atom font type.
AtomIdentifier - Class in chemaxon.reaction
The identifier of an atom in the input of the reaction.
AtomIdentifier(int, int) - Constructor for class chemaxon.reaction.AtomIdentifier
Initializes an atom identifier based on the input molecules of the reaction.
AtomIdentifier(int, int, int) - Constructor for class chemaxon.reaction.AtomIdentifier
Initializes an atom identifier based on the input molecules of the reaction.
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.
atomLabelSize(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the atom label font size.
ATOMLIST - Static variable in class chemaxon.sss.search.MarkushFeature
Expansion type: atom list.
AtomMapChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atom maps.
AtomMapChecker() - Constructor for class chemaxon.checkers.AtomMapChecker
Default constructor
atomMapMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
atomMapMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether atom map numbers should be considered in search.
atomMapMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
atomMapping() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
Array of atom - atom mapping.
atomMapping() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Displays 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.
atomNumber() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Displays atom numbers.
atomNumberType(ImageExporter.AtomNumberingType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the type of atom numbering: Atom numbers or IUPAC numbering.
AtomProperty - Class in chemaxon.marvin.space
The AtomProperty class provides access to chemical properties of Molecule atoms by atom index.
AtomProperty - Class in chemaxon.struc
Class for storing atom property enumerations.
AtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty
 
AtomProperty() - Constructor for class chemaxon.struc.AtomProperty
 
AtomProperty.MoleculeAtomProperty - Class in chemaxon.marvin.space
 
AtomProperty.Radical - Enum Class in chemaxon.struc
Enumeration of the supported radicals.
AtomProperty.SmoleculeAtomProperty - Class in chemaxon.marvin.space
 
AtomQueryPropertyChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms having an query property set.
AtomQueryPropertyChecker() - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.
AtomQueryPropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
Creates a new AtomQueryPropertyChecker instance to detect the given query properties.
AtomQueryPropertyCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying atom query properties, thus errorType property is StructureCheckerErrorType.ATOM_QUERY_PROPERTY by default.
AtomQueryPropertyCheckerResult(StructureChecker, List<MolAtom>, Molecule, String, List<String>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
Constructor which initialize all the properties.
atoms() - Method in class chemaxon.struc.MoleculeGraph
Provides a list view of the atoms in the molecule.
AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters
Selection which contains atom indexes.
AtomSelection(int[], int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated.
AtomSelection(int, int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated.
AtomSelection(List<Integer>, List<Integer>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Constructs an AtomSelection from lists.
atomSet - Variable in class chemaxon.struc.Sgroup
Set for storing the atoms of the s-group's graph.
ATOMSIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of atom label font size parameter.
ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants
Either stereo atom type.
ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants
Stereo atom type mask.
ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants
No stereo atom type specified.
ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants
Specific stereo atom type.
AtomTypeChecker - Class in chemaxon.checkers
A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.
AtomTypeChecker() - Constructor for class chemaxon.checkers.AtomTypeChecker
Default constructor.
AtomTypeChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomTypeChecker
Parameterized constructor providing the possibility for descendants to initialize with their own error type.
AtomTypeChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomTypeChecker
Parameterized constructor.
atomTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
atomTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether atom types should be considered in search.
atomTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
AtomTyping - Enum Class in com.chemaxon.descriptors.alignment
Settings for shape associated atom typing.
atomTypizer(EcfpAtomTypizers) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Set atom typizer to use.
AtomValueChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms with atom value.
AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker
Default constructor.
ATPROP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom properties flag.
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.
AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Deprecated.
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
 
ATSYM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom symbols in 3D flag.
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).
ATTR_OPERATION - Static variable in class chemaxon.jchem.db.RegenerationChecker
 
Au - Static variable in class chemaxon.core.ChemConst
 
AUTO - Enum constant in enum class chemaxon.marvin.paint.constants.AnyBondStyle
Automatically decide whether Dashed or Solid rendering is used.
AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Automatic check for structures.
AUTO_RESOLUTION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
AUTO_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "autoscale".
AUTO_TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "autoTabScale".
AUTO_UNGROUP - Static variable in class chemaxon.struc.MoleculeGraph
Automatic ungroup bit in flags.
autoGzip(InputStream) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Detect gzipped InputStream.
AutoMapper - Class in com.chemaxon.mapper
AutoMapper is a tool that performs automated chemical reaction mapping.
AutoMapper() - Constructor for class com.chemaxon.mapper.AutoMapper
Initializes an AutoMapper object
AutoMapper.Options - Class in com.chemaxon.mapper
Option object for set common options when mapping called by static way.
AUTOMATIC_FOG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated. 
AUTOMATIC_FOG_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "automaticFogEnabled".
AUTOMATIC_REACTION_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "automaticReactionEnabled".
automaticSettingOfGridSize - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
AverageLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
 
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.
AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Deprecated.
axialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the axial stereocenters.
axialStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the axial stereocenters with attached data.
AxialStereoDescriptor - Class in chemaxon.struc
 
AxialStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AxialStereoValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AxialStereoDescriptor
 

B

B - Static variable in class chemaxon.core.ChemConst
 
B_FACTOR_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
Ba - Static variable in class chemaxon.core.ChemConst
 
BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "background".
BACKGROUND_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
 
BACKGROUND_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColor - Variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColorMode - Variable in class chemaxon.marvin.space.monitor.Label
 
BACKGROUNDLOAD_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bgloadEnabled".
BACKGROUNDLOAD_PRIORITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bgload".
backgroundThread - Variable in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
balabanIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
BALL_AND_STICK - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.Rendering
 
BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "ballRadius".
ballPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
ballRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
ballRadius(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the ball radius in ball and stick mode.
BALLRADIUS - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Ball radius for ball and stick mode.
ballstick - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.renderingValues
 
BALLSTICK - Enum constant in enum class chemaxon.marvin.paint.constants.RenderingStyle
Stick rendering style with balls at atoms
BALLSTICK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
use RenderingStyle instead.
BALLSTICK_RENDERING_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
use RenderingStyle instead.
BASE64 - Static variable in class chemaxon.formats.MFileFormat
BASE64 encoded file.
BaseColor16 - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
16 base colors defined with a palette, image data contains 2 bits/pixel
BaseColor256 - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
256 colors defined with a palette, image data contains 2 bits/pixel
BaseShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment
 
BaseShapeComparatorParameter(AlignmentProperties.FlexibilityMode, ShapeFunction, Optional<Integer>) - Constructor for class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
BASIC - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type
Basic aromatization
BASIC - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
 
BASIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Constant denoting basic pKa.
BasicStandardizerRunner - Class in chemaxon.standardizer.runner
This is the default implementation of StandardizerActionRunner interface.
BasicStandardizerRunner(StandardizerConfigurationReader) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner
Initialize a BasicStandardizerRunner instance with the StandardizerConfiguration read from the provided configuration reader.
BasicStandardizerRunner(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner
Initialize a BasicStandardizerRunner instance with specified StandardizerConfiguration.
BBB - Class in chemaxon.calculations.bbb
BBB score calculator.
BBB.Property - Class in chemaxon.calculations.bbb
Simple DTO that contains the predicted value, its BBB score and the BBB score multiplied with the corresponding BBB multiplier.
BBBFunction - Enum Class in chemaxon.calculations.bbb
Base phys-chem property calculators and its score functions for BBB score calculation.
BCUT - Class in chemaxon.descriptors
Implements BCUT descriptors.
BCUT() - Constructor for class chemaxon.descriptors.BCUT
Creates a new, empty BCUT descriptor.
BCUT(BCUT) - Constructor for class chemaxon.descriptors.BCUT
Copy constructor.
BCUT(BCUTParameters) - Constructor for class chemaxon.descriptors.BCUT
Creates a new instance according to the parameters.
BCUT(String) - Constructor for class chemaxon.descriptors.BCUT
Creates a new instance according to the parameters.
BCUTGenerator - Class in chemaxon.descriptors
Descriptor generator class for the BCUT descriptor.
BCUTGenerator() - Constructor for class chemaxon.descriptors.BCUTGenerator
Creates and initializes a BCUT descriptor generator object.
BCUTParameters - Class in chemaxon.descriptors
Manages parameters for the BCUT descriptor class.
BCUTParameters() - Constructor for class chemaxon.descriptors.BCUTParameters
Creates an empty object.
BCUTParameters(File) - Constructor for class chemaxon.descriptors.BCUTParameters
Creates a new object based on a given configuration file.
BCUTParameters(String) - Constructor for class chemaxon.descriptors.BCUTParameters
Creates a new object based on a given configuration string.
Be - Static variable in class chemaxon.core.ChemConst
 
beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
Changes the cursor to hourglass at the beginning of a long operation.
bemismurcko - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
BemisMurckoClustering - Class in com.chemaxon.clustering.framework
Convenience utilities for using Bemis-Murcko clustering.
bemismurckoloose - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
 
bgColor(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the background color.
bgColorAlpha(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the background color with alpha value.
Bh - Static variable in class chemaxon.core.ChemConst
 
Bi - Static variable in class chemaxon.core.ChemConst
 
BIG_ENDIAN - Enum constant in enum class com.chemaxon.descriptors.common.BinaryVectors.Endianness
Decreasing numeric significance with increasing addresses/indices.
BINARY_COMMONPART - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
Commonly set bits.
BINARY_COMMONPART_NORMALIZED - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
Common set bit ratio.
BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
descriptor type constants
BINARY_DICE - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
Dice's similarity measure.
BINARY_EUCLIDEAN - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
Euclidean distance.
BINARY_EUCLIDEAN_NORMALIZED - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
Normalized Euclidean distance.
BINARY_TANIMOTO - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
Tanimoto coefficient.
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.
BinaryMetrics - Enum Class in com.chemaxon.descriptors.metrics
Simple metrics suitable for finite length binary vectors.
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.
BinaryVectorComparator - Interface in com.chemaxon.descriptors.metrics
Basic functionality for finite binary vector based calculations.
BinaryVectorComparator.Util - Class in com.chemaxon.descriptors.metrics
Simple consistency check utility.
BinaryVectorDescriptor - Interface in com.chemaxon.descriptors.common
BinaryVectorDescriptor is a Descriptor which holds a fixed length binary fingerprint.
BinaryVectorMetricFactory<C> - Interface in com.chemaxon.descriptors.metrics
Represents available metrics for binary vector based descriptors.
BinaryVectorMetricFactory.ToLinenote<C> - Class in com.chemaxon.descriptors.metrics
Utility for creating a default linenote.
BinaryVectors - Class in com.chemaxon.descriptors.common
Utility methods related to bit string descriptors.
BinaryVectors.Endianness - Enum Class in com.chemaxon.descriptors.common
Order of components in packed representations.
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.
bitsPerPattern(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Set bits per pattern.
Bk - Static variable in class chemaxon.core.ChemConst
 
BlackWhite - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
Black and white colors defined with a palette, image data contains 1 bit/pixel
BlackWhiteGray - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
Black, white, light, and dark gray colors defined with a palette, image data contains 2 bits/pixel
BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Constant storing the blue rgb value (the basic pKa result color).
Bold - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
 
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".
BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bold bond width parameter.
BoldItalic - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
 
BoldItalicUnderline - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
 
BoldUnderline - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
 
bond - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
BOND_ANGLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents that bond angle problem had found in the molecule
BOND_BOND_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
This String represents the key of cloned bond, original bond map
BOND_DRAGGED_ALONG - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bondDraggedAlong".
BOND_DRAW_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_FACING - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondHashSpacing".
BOND_HASH_SPACING - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bondHashSpacing parameter.
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 - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bond length parameter.
BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondLengthVisible".
BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show bond lengths.
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.
bondCount(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Set bond count to consider.
bondDistance - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bondFacing - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bondHashSpacing() - Method in class chemaxon.marvin.io.image.ImageExporter
 
bondHashSpacing(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
The spacing of the hash in hashed bonds in C-C bond length units.
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.
BONDLEN_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show bond lengths flag.
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
Expansion type: bond list.
BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
Constructs an iterator to process the bonds connecting to the specified atom.
bondRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bonds() - Method in class chemaxon.struc.MolAtom
Provides a list view of the connected bonds of the atom.
bonds() - Method in class chemaxon.struc.MoleculeGraph
Provides a list view of the bonds in the molecule.
bondSkipped(BondInfo, String) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when visited bond is skipped.
bondSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BondTable - Class in chemaxon.core.util
Provides easy lookup of bonds between pair of atoms in a molecule graph.
BondTopologyChecker - Class in chemaxon.checkers
Checker detects bonds with reacting center bond marks.
BondTopologyChecker() - Constructor for class chemaxon.checkers.BondTopologyChecker
Default constructor
bondType(int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines the type of a bond (aromatic bonds are automatically recognized)
bondTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
bondTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether bond types should be considered in search.
bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom
Calculates the average of the bond unit vectors pointing out of this atom.
bondWidth - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bondWidth(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the width of the double bond.
BONDWIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bond width parameter.
BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor
Boolean option.
BOOLEAN - Enum constant in enum class com.chemaxon.apidiscovery.ParameterWrapper.ParameterType
A boolean parameter (primitive type).
booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp
Gets the boolean value.
BORDER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "border".
BORDER_MODE_BRIGHTER_FOREGROUND - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_FOREGROUND_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
borderColor - Variable in class chemaxon.marvin.space.monitor.Label
 
borderColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
borderColorMode - Variable in class chemaxon.marvin.space.monitor.Label
 
BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
Bottom - Enum constant in enum class chemaxon.formats.documents.jchemoffice.PropertyTablePosition
 
BottomCenter - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontAlignment
 
BottomLeft - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontAlignment
 
BottomRight - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontAlignment
 
boundingBox - Variable in class chemaxon.marvin.space.GraphicComponent
The smallest box containing the graphic component.
BoundingBox - Class in chemaxon.marvin.space
Class for representing a bounding box of any component in the 3D space.
BoundingBox() - Constructor for class chemaxon.marvin.space.BoundingBox
Creates a new instance of BoundingBox but does not set anything.
BoundingBox(float, float, float, float, float, float) - Constructor for class chemaxon.marvin.space.BoundingBox
Creates a bounding box with the given coordinates, computes the center and radius of the box.
Br - Static variable in class chemaxon.core.ChemConst
 
brackets - Variable in class chemaxon.struc.Sgroup
 
BRACKETS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type representing that the molecule contains brackets (S-groups).
BracketsChecker - Class in chemaxon.checkers
Detects brackets (S-groups) in molecules.
BracketsChecker() - Constructor for class chemaxon.checkers.BracketsChecker
Default constructor.
BRIDGEHEAD_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom which is connected to a bridgehead atom.
brightness - Variable in class chemaxon.descriptors.ChemicalFingerprint
number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less pausible)
brightness - Variable in class chemaxon.descriptors.ECFP
The number of bits set in the binary vector storage
brightness - Variable in class chemaxon.descriptors.ReactionFingerprint
number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)
btab - Variable in class chemaxon.struc.MoleculeGraph
Bond table.
bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream
Reads a character and writes into the buffer.
build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
 
build() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
Builds a ValenceCheckOptions object.
build() - Method in class chemaxon.formats.MolConverter.Builder
Builds the MolConverter.
build() - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
build() - Method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.exporter.JpegExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.exporter.PngExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Builds an unmodifiable export option.
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 interface com.chemaxon.apidiscovery.interfaces.ParameterBuilder
Constructs an immutable instance of T.
build() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Build immutable clustering representation.
build() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Build the immutable clustering representation.
build() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
Build a new instance of MaccsParameters.
build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
 
build() - Method in class com.chemaxon.search.MatchingOptions.Builder
Creates a search options object with the settings specified by this builder instance.
build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
build(IDBasedAssignerBuilder) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Build an immutable snapshot of the clustering.
build(DescriptorGenerator<D>, DescriptorComparator<D>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Build immutable input descriptor.
buildButtonBar() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
 
buildContentPanel() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
 
builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter
Creates a builder for this class.
builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter
Creates a builder for this class.
builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter
Creates a builder for this class.
builder() - Static method in class chemaxon.marvin.io.image.exporter.JpegExporter
Creates a builder for this class.
builder() - Static method in class chemaxon.marvin.io.image.exporter.MsbmpExporter
Creates a builder for this class.
builder() - Static method in class chemaxon.marvin.io.image.exporter.PngExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder
 
Builder() - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
 
Builder() - Constructor for class chemaxon.formats.MolConverter.Builder
Constructs an empty Builder object.
Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.image.exporter.JpegExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.image.exporter.PngExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.image.ImageExporter.Builder
 
Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder
 
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Constructor with default settings.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Constructor with default settings.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
Constructor mandated by descriptors API contracts.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Constructor with default settings.
Builder() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate builder with default values.
Builder() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Constructor with default settings.
Builder() - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Constructor with default settings.
Builder() - Constructor for class com.chemaxon.search.MatchingOptions.Builder
Creates a Builder object with the default settings.
Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object with the default settings.
Builder(double, double) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate with weights.
Builder(CfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Constructor based on a parameter object.
Builder(EcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Constructor based on a parameter object.
Builder(MaccsParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
Constructor mandated by descriptors API contracts.
Builder(PfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Constructor based on a parameter object.
Builder(TverskyParameters) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate builder based on an actual parameter instance.
Builder(BvParameters) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Construct to represent the state of a parameter object instance.
Builder(FvParameters) - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Construct to represent the state of a parameter object instance.
Builder(MatchingOptions) - Constructor for class com.chemaxon.search.MatchingOptions.Builder
Creates a Builder object containing the settings of the given search options object.
Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object containing the settings of the given search options object.
builderClass() - Element in annotation interface com.chemaxon.apidiscovery.annotations.BuilderClass
Associated builder class for this immutable object.
BuilderClass - Annotation Interface in com.chemaxon.apidiscovery.annotations
This annotation gives information about the associated ParameterBuilder for this class.
BuildupMcs - Class in com.chemaxon.search.mcs.buildup
Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
BuildupMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.buildup.BuildupMcs
Creates a new BuildupMcs object with the given search options.
BUILT_IN_CHAIN_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in chain colors.
BUILT_IN_CPK_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in cpk colors.
BUILT_IN_RAINBOW_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in rainbow colors.
BUILT_IN_RESIDUE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in residue colors.
BUILT_IN_SECONDARY_STRUCTURE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in secondary structure colors.
BUTTON_MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "buttonmenubar".
BvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
Generator for generic binary vector descriptors.
BvParameters - Class in com.chemaxon.descriptors.vectors.binary
Parameters for generic binary vector descriptor.
BvParameters() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters
Construct with default values.
BvParameters(BvParameters.Builder) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters
Constructor based on a builder.
BvParameters.Builder - Class in com.chemaxon.descriptors.vectors.binary
Builder for BvParameters.
BvParameters.ConstructBvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
Interface representing BvGenerator implementation constructor
BvParameters.StringFormat - Enum Class in com.chemaxon.descriptors.vectors.binary
Fingerprint textual representation.
BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure
For internal usage only.
BYTES_IN_INT - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
Number of bytes in an int.
BYTES_IN_LONG - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
Number of bytes in a long.

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_REGISTRATION_SENSITIVITY_EXCEPTION - Static variable in class chemaxon.jchem.db.CacheRegistrationUtil
Error sensitivity - exception.
CACHE_REGISTRATION_SENSITIVITY_LOG - Static variable in class chemaxon.jchem.db.CacheRegistrationUtil
Error sensitivity - log
CACHE_REGISTRATION_SENSITIVITY_NONE - Static variable in class chemaxon.jchem.db.CacheRegistrationUtil
Error sensitivity - none.
CACHE_REMOVAL_METHOD_LOADTIME - Enum constant in enum class chemaxon.jchem.db.cache.CacheManager.CacheRemovalMethodImplementation
 
CACHE_REMOVAL_METHOD_LRU - Enum constant in enum class chemaxon.jchem.db.cache.CacheManager.CacheRemovalMethodImplementation
 
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.
CacheManager - Enum Class in chemaxon.jchem.db.cache
Singleton for managing cache-related functions.
CacheManager.CacheRemovalMethodImplementation - Enum Class in chemaxon.jchem.db.cache
For internal use only.
cacheMemory - Variable in class chemaxon.struc.MoleculeGraph
 
CacheRegistrationUtil - Class in chemaxon.jchem.db
Utility class for cache registration.
CacheRegistrationUtil(ConnectionHandler) - Constructor for class chemaxon.jchem.db.CacheRegistrationUtil
 
calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates a "badness" value for the atomic coordinates.
calcBitCount(int) - Static method in class chemaxon.descriptors.Metrics
Counts the number of bits set (1) in the integer parameter.
calcBitCount(int[]) - Static method in class chemaxon.descriptors.Metrics
Counts the number of bits set (1) in a bit vector.
calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the bracket endpoints from the base line of the bracket.
calcCenter() - Method in class chemaxon.struc.MDocument
Calculates the geometrical center.
calcCenter() - Method in class chemaxon.struc.MoleculeGraph
Calculates the geometrical center.
calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument
Calculates the geometrical center.
calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
Calculates the geometrical center.
calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
Calculates the graph invariants with the assumption that hydrogens are removed.
calcDissimilarity(MDReader, MDReader) - Method in class chemaxon.descriptors.MDHitEvaluator
Precalculates dissimilarity values.
calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the division point of a segment with a given ratio.
calcExpTime() - Method in class chemaxon.jchem.file.ProgressWriter
Recalculates expected time.
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
 
calcMetricDistribution(int, int, float, float, int, float[]) - Method in class chemaxon.descriptors.MDHitEvaluator
Retrieves the distribution of the given metric from the dissimilarity values calculated by a previous call to calcDissimilarity().
calcMetricDistribution(int, int, float, float, int, float[], MDReader, MDReader) - Method in class chemaxon.descriptors.MDHitEvaluator
Retrieves the distribution of the given metric from the dissimilarity values calculated by a screen using the given two molecular descriptor readers.
calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
Calculates the minimum distance between two atoms in the molecule.
calcMolFormula() - Method in class chemaxon.util.MolHandler
Calculates the molecular formula of the molecule.
calcMolWeight() - Method in class chemaxon.util.MolHandler
Calculates the molecular weight of the molecule.
calcMolWeightInDouble() - Method in class chemaxon.util.MolHandler
Calculates the molecular weight of 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, SubProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculate(Molecule, SubProgressObserver, 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.
calculateBinaryVectorDissimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
Calculate represented dissimilarity score from binary vector parameters.
calculateBinaryVectorDissimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
calculateBinaryVectorSimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
Calculate represented similarity score from binary vector parameters.
calculateBinaryVectorSimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
 
calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
 
calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
 
calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
Calculates the stereo descriptors of the given molecule.
calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Calculates the coordinates during expand and contract.
calculateCosAFromScalarMul(MolBond, MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.
calculateDarkness() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Calculate the darkness of this fingerprint.
calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateDissimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors in serialized form.
calculateDissimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors.
calculateDissimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateDissimilarityMatrix(DissimilarityInput, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Distance matrix calculation.
calculateFloatVectorDissimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Calculate dissimilarity.
calculateFloatVectorSimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Deprecated.
In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
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.
calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateSimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors in serialized form.
calculateSimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors.
calculateSimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateSimilarityUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.
calculateUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.
CALCULATIONS_PACK - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Calculations Pack
CalculatorError - Interface in chemaxon.calculator
An error that might occur when a calculator is initialized.
CalculatorInputChecker - Interface in chemaxon.calculator
Instances of this interface are used by calculators to check if they can process an input molecule.
CalculatorPlugin - Class in chemaxon.marvin.plugin
Common base class for calculator plugins.
CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin(Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin(Consumer<Molecule>, Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin
 
CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin
Deprecated, for removal: This API element is subject to removal in a future version.
This class has been moved to a new package, import and use it from its new location: CalculatorPluginDisplay
CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.gui
Common base class for calculator plugin displays.
CalculatorPluginDisplay() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginDisplay
Deprecated.
 
CalculatorPluginDisplay() - Constructor for class com.chemaxon.calculations.gui.CalculatorPluginDisplay
 
CalculatorPluginOutput<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin
Deprecated, for removal: This API element is subject to removal in a future version.
This class has been moved to a new package, import and use it from its new location: CalculatorPluginOutput
CalculatorPluginOutput<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.cli
Class providing plugin output in table form.
CalculatorPluginOutput() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
Deprecated.
 
CalculatorPluginOutput() - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput
Default constructor.
CalculatorPluginOutput(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
Deprecated.
 
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
 
calcWidth() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecule width.
call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Performs the calculation and returns the result returned by PluginWorkUnit.getResult().
call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Performs the calculation and returns the result returned by ReusablePluginWorkUnit.getResult().
callback(String, Object) - Method in interface chemaxon.jep.ChemContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.jep.ChemJEP
Delegates CallbackIface.callback(String, Object) to the context.
callback(String, Object) - Method in class chemaxon.jep.context.AtomContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.jep.context.MolContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.jep.context.ReactionContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.marvin.space.GraphicScene
 
callback(String, Object) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
callback(String, Object) - Method in class chemaxon.marvin.space.MSpaceEasy
Callback function to make avoiding direct calls easier.
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.
Line can be in the given format.
CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated.
Line can be in the given format.
canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
Tests whether a string can be one-letter-abbreviated peptide name.
A valid name contains only uppercase letters.
canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
Tests whether a string can be three-letter-abbreviated peptide name.
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.
Tests whether a string can be SMARTS.
canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated.
Tests whether a string can be SMILES.
cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner
Stops the background thread
cancel() - Method in class chemaxon.jchem.db.Importer
Stops the importing progress.
cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment
Cancel the ongoing calculation
cancel() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
cancel() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
Stops the background thread
CancelObserver - Interface in com.chemaxon.calculations.common
Callback to propagate cancel requests into long running tasks.
canHandle(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
Returns true if this factory can handle the given xml.
CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
 
canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.
carboaliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
carboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
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.
as of release 5.5, replaced by Ring.carboaromaticRingCount()
CARBON_VIS_INCHAIN - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility is switched on in chain.
CARBON_VIS_INCHAIN_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
String constant for switching on carbon-visibility in chain.
CARBON_VIS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility mask.
CARBON_VIS_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility is switched off.
CARBON_VIS_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
String constant for switching off carbon-visibility.
CARBON_VIS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility offset.
CARBON_VIS_ON - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility is switched on.
CARBON_VIS_ON_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
String constant for switching on carbon-visibility.
CARBON_VIS_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Array of carbon-visibility styles.
carbonDisplay(ImageExporter.CarbonDisplay) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Show the atom labels on carbon atoms.
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.
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.
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.
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.
as of release 5.5, replaced by Ring.carboRings(int)
CardLayoutArrangement - Enum Class in chemaxon.formats.documents.jchemoffice
 
CARTRIDGE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem Cartridge
CATIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
CCLENGTH - Static variable in class chemaxon.struc.MolBond
Default bond length.
Cd - Static variable in class chemaxon.core.ChemConst
 
CDParameters - Class in chemaxon.descriptors
Manages parameters the CustomDescriptor class.
CDParameters() - Constructor for class chemaxon.descriptors.CDParameters
Creates an empty object.
CDParameters(int) - Constructor for class chemaxon.descriptors.CDParameters
Creates an empty object of the given type.
CDParameters(File) - Constructor for class chemaxon.descriptors.CDParameters
Creates a new descriptor configured from the given file.
CDParameters(String) - Constructor for class chemaxon.descriptors.CDParameters
Creates a new object based on a given configuration string.
CDX - Static variable in class chemaxon.formats.MFileFormat
ChemDraw CDX file.
CDXML - Static variable in class chemaxon.formats.MFileFormat
ChemDraw CDXML file.
Ce - Static variable in class chemaxon.core.ChemConst
 
CELL - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "cell".
CELL_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
CellOrComponentId - Class in chemaxon.marvin.space
Class to identify cells and components.
CellOrComponentId(int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
Creates a cell id.
CellOrComponentId(int, int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
Creates an id.
cellSize - Variable in class chemaxon.descriptors.MDParameters
size - number of bits - of one descriptor cell
CELLSIZE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
The default viewer cell size.
cellwiseWeights - Variable in class chemaxon.descriptors.MDParameters
is cell weights for parametrized metrics
center - Variable in class chemaxon.marvin.space.monitor.Control
 
center - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
centerx() - Method in class chemaxon.marvin.space.BoundingBox
Returns the x coordinate of the center of the box.
centery() - Method in class chemaxon.marvin.space.BoundingBox
Returns the y coordinate of the center of the box.
centerz() - Method in class chemaxon.marvin.space.BoundingBox
Returns the z coordinate of the center of the box.
centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane
Puts the molecule into the center of the display.
Cf - Static variable in class chemaxon.core.ChemConst
 
CFGenerator - Class in chemaxon.descriptors
The CFGenerator class generates topological fingerprints of molecular graphs.
CFGenerator() - Constructor for class chemaxon.descriptors.CFGenerator
Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.
CFGenerator(int) - Constructor for class chemaxon.descriptors.CFGenerator
Deprecated.
since 5.4
CFNS - Static variable in class chemaxon.jep.context.AtomContext
The context function names.
CFNS - Static variable in class chemaxon.jep.context.ReactionContext
The context function names.
Cfp - Interface in com.chemaxon.descriptors.fingerprints.cfp
Folded fixed length bit string representation of the CFP descriptor.
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.
CfpComparator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Comparator for Cfp descriptor representation.
CfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Calculates CFP (fixed length folded binary vector representation) descriptors.
CfpParameters - Class in com.chemaxon.descriptors.fingerprints.cfp
CFP parameters class.
CfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Constructor using the default settings.
CfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.cfp
Builder class for the immutable parameter object.
CfpParameters.ConstructCfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Interface representing CFP generator constructor.
CfpTableReader - Class in com.chemaxon.descriptors.fingerprints.cfp
MDTable reader for CFP.
CfpTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
 
CfpTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.cfp
Factory class.
CHAIN - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.CarbonDisplay
 
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.
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.
as of release 5.5, replaced by Ring.chainBondCount()
chainOf(StandardizerWrapper...) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Create a chained wrapper.
chainTransformers(Transformer...) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a chain transformer.
chainTransformers(List<Transformer>) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a chain transformer.
changeColorMapperColors(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.
Changes - Class in chemaxon.standardizer
The change set of the standardization procedure.
Changes(Molecule) - Constructor for class chemaxon.standardizer.Changes
Initializes the changes object.
Changes(Molecule, StandardizerAction) - Constructor for class chemaxon.standardizer.Changes
Initializes the changes object.
Changes(Molecule, Molecule) - Constructor for class chemaxon.standardizer.Changes
Initializes the changes object.
CHANGING - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
Only reaction center will be mapped
CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).
charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a character of the document.
CHARGE_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Sets the circled charge's font.
CHARGE_FONT_SIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Sets the circled charge's font.
CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).
CHARGE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).
CHARGE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignore charge searching (charge information is ignored during searching).
CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup
Charge is located on atoms and displayed on atoms.
CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup
Charge is located on atoms but displayed on the whole group (bracket).
CHARGE_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Charge Plugin Group
CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "chargeWithCircle".
CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show charge symbols in a circle.
CHARGE_WITH_CIRCLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
 
CHARGE_WITH_CIRCLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
 
CHARGED_H - Static variable in class chemaxon.struc.MolAtom
Include charged Hydrogen atom(s).
chargeFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Font type in circled charge display.
chargeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
chargeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether formal charges of atoms should be considered in search.
chargeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
ChargePlugin - Class in chemaxon.marvin.calculations
Plugin class for partial charge calculation.
ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin
Constructor.
check() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
check() - Method in interface chemaxon.checkers.runner.CheckerRunner
Invokes a background thread which will run all checkers on the given molecule
check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
 
check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
 
check(Molecule) - Method in class chemaxon.checkers.InvalidChecker
 
check(Molecule) - Method in interface chemaxon.checkers.StructureChecker
Detects a specific error in the molecule.
check(Molecule) - Method in interface chemaxon.jep.MolCondition
Deprecated.
Returns true if molecule should be processed, false otherwise.
check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AliasChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker
Detects atom of the molecule has atom map.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker
Detects if the current atom of the molecule has atom value.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker
Check the atom of the molecule with index i has no atom map.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker
Detects atom of the molecule is a query atom.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker
Detects if the current atom has free electrons.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.BondTopologyChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker
Examines if the bond is a crossed double bond.
check(Molecule, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker
Detects bond of the molecule is crossing another bond or closer than the limit distance.
check(Molecule, MolBond) - Method in class chemaxon.checkers.QueryBondChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker
 
check(Molecule, E) - Method in class chemaxon.checkers.ComponentChecker
Checks if the component with index i has problem
Check - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Mode
Indicates, that the structurechecker does not automatically fixes.
check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker
Determines if a non chiral molecule contains a chiral flag.
check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker
Determines if all asymmetric centers have absolute stereo configuration
check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
This method contains the current checking mechanism.
check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker
Detects attached data in the molecule
check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker
 
check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker
 
check1(Molecule) - Method in class chemaxon.checkers.BracketsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker
Determines if a non chiral molecule contains a chiral flag.
check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker
Iterates through the components and checks every component.
check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Detects implicitizable hydrogen atoms.
check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.IncorrectTetrahedralStereoChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker
Detects if molecule has charge
check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker
 
check1(Molecule) - Method in class chemaxon.checkers.NonStandardWedgeSchemeChecker
 
check1(Molecule) - Method in class chemaxon.checkers.NonStereoWedgeBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RatomChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RgroupBridgeRatomChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.SolventChecker
 
check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker
 
check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker
 
check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker
Deprecated.
In version 15.8.3 the checker logic was replaced with the logic implemented in Molecule's stereoClean() method.
check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker
 
checkAndWait() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
checkAndWait() - Method in interface chemaxon.checkers.runner.CheckerRunner
Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems
checkAtno(int) - Static method in class chemaxon.struc.MolAtom
Check if the given atomic number is positive and less then atomic type maximum value.
checkBitCounts(int, int, int, int) - Static method in class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util
Check that descriptor comparison parameters are consistent.
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.
checkChemTermColValue(Object) - Static method in class chemaxon.jchem.db.UpdateHandler
 
checkConsistency() - Method in class chemaxon.struc.Molecule
Deprecated.
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.
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.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistencyInEmbeddings() - Method in class chemaxon.struc.Sgroup
Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.
checkDocumentVersion(String, String) - Method in class chemaxon.descriptors.MDParameters
Checks if the document is the right version
CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
Chemaxon's default checker configuration file name
CheckerInfo - Annotation Interface in chemaxon.checkers
This annotation is responsible for adding GUI based meta data for StructureChecker implementations
CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark
 
checkError() - Method in class chemaxon.util.ErrorHandler
Throws the exception stored in the object.
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
checkException() - Method in class chemaxon.jchem.db.JChemSearch
 
checkException() - Method in class chemaxon.util.ErrorHandler
Throws the exception stored in the object.
checkFilter(String) - Static method in class chemaxon.sss.search.MolSearch
Checks the syntax of the filtering expression.
checkFilter(String, File) - Static method in class chemaxon.sss.search.MolSearch
Checks the syntax of the filtering expression.
checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Checks the input molecule.
checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.
checkSgroupConsistency() - Method in class chemaxon.struc.Molecule
Checks the internal consisitency of S-groups.
checkSgroupConsistency() - Method in class chemaxon.struc.RgMolecule
Checks the consistency of S-groups.
checkSgroupConsistency() - Method in class chemaxon.struc.RxnMolecule
Checks the consistency of S-groups.
checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.Sgroup
Checks whether the parameter s-group contains the atoms of this s-group.
checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup.
checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Checks result types.
checkValence(MolAtom) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
 
checkValence(MoleculeGraph) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
 
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject
Is it a valid object in the document?
CHEM_CURATOR_COMPOUND - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Compound
CHEM_CURATOR_FULL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Full
chemaxon.calculations - package chemaxon.calculations
Contains chemical computation modules.
chemaxon.calculations.bbb - package chemaxon.calculations.bbb
BBB score calculator.
chemaxon.calculations.cip - package chemaxon.calculations.cip
 
chemaxon.calculations.clean - package chemaxon.calculations.clean
 
chemaxon.calculations.cnsmpo - package chemaxon.calculations.cnsmpo
CNS MPO score calculator.
chemaxon.calculations.dipole - package chemaxon.calculations.dipole
 
chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize
 
chemaxon.calculations.nmr - package chemaxon.calculations.nmr
 
chemaxon.calculations.nmr.io - package chemaxon.calculations.nmr.io
 
chemaxon.calculations.stereo - package chemaxon.calculations.stereo
 
chemaxon.calculator - package chemaxon.calculator
 
chemaxon.checkers - package chemaxon.checkers
Structure checkers can be used to filter drawing mistakes or special structural elements.
chemaxon.checkers.result - package chemaxon.checkers.result
This package is used to identify problems found in molecules.
chemaxon.checkers.runner - package chemaxon.checkers.runner
This package supports the automatic running of structure checkers.
chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader
Extension package of the automatic runner functionality.
chemaxon.clustering - package chemaxon.clustering
Provides classes for clustering.
chemaxon.clustering.adapter - package chemaxon.clustering.adapter
 
chemaxon.clustering.libmcs - package chemaxon.clustering.libmcs
 
chemaxon.clustering.libmcs.adapter - package chemaxon.clustering.libmcs.adapter
Adapter to expose LibraryMcs clustering through the (com.chemaxon.clustering) API.
chemaxon.common.util - package chemaxon.common.util
 
chemaxon.core - package chemaxon.core
 
chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo
 
chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck
 
chemaxon.core.util - package chemaxon.core.util
 
chemaxon.descriptors - package chemaxon.descriptors
Classes for virtual screening using Molecular 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.documents.jchemexcel - package chemaxon.formats.documents.jchemexcel
 
chemaxon.formats.documents.jchemoffice - package chemaxon.formats.documents.jchemoffice
 
chemaxon.formats.recognizer - package chemaxon.formats.recognizer
Provides classes to recognize files of various file formats.
chemaxon.jchem.db - package chemaxon.jchem.db
Provides classes for database operations.
chemaxon.jchem.db.cache - package chemaxon.jchem.db.cache
 
chemaxon.jchem.file - package chemaxon.jchem.file
 
chemaxon.jep - package chemaxon.jep
Chemical Terms Evaluator classes.
chemaxon.jep.context - package chemaxon.jep.context
Specific chemical terms evaluation contexts.
chemaxon.license - package chemaxon.license
Classes related licenses, license handling, validating, GUI and documentation.
chemaxon.marvin - package chemaxon.marvin
Contains utility classes for rendering molecules.
chemaxon.marvin.alignment - package chemaxon.marvin.alignment
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
chemaxon.marvin.alignment.atrop - package chemaxon.marvin.alignment.atrop
Utilities for AtropIsomerDetector.
chemaxon.marvin.beans - package chemaxon.marvin.beans
Provides bean classes for creating Marvin based user interface.
chemaxon.marvin.calculations - package chemaxon.marvin.calculations
Provides specific plugin, plugin loader and table form output implementations.
chemaxon.marvin.common - package chemaxon.marvin.common
Contains a class for handling user settings.
chemaxon.marvin.io - package chemaxon.marvin.io
Provides classes for molecule import and export through data streams.
chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats
Core package of any import/export module.
chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles
 
chemaxon.marvin.io.formats.vectgraphics - package chemaxon.marvin.io.formats.vectgraphics
 
chemaxon.marvin.io.image - package chemaxon.marvin.io.image
 
chemaxon.marvin.io.image.exporter - package chemaxon.marvin.io.image.exporter
 
chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.
chemaxon.marvin.modules.reaction - package chemaxon.marvin.modules.reaction
 
chemaxon.marvin.paint - package chemaxon.marvin.paint
Defines display options constants.
chemaxon.marvin.paint.constants - package chemaxon.marvin.paint.constants
 
chemaxon.marvin.plugin - package chemaxon.marvin.plugin
Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.
chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent
Classes to achieve concurrent processing of calculator plugins.
chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
Calculator plugin common GUI classes.
chemaxon.marvin.services - package chemaxon.marvin.services
Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.
chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice
 
chemaxon.marvin.services.json - package chemaxon.marvin.services.json
 
chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice
 
chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap
 
chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice
 
chemaxon.marvin.sketch - package chemaxon.marvin.sketch
Contains the sketcher's core classes and various sketching modes.
chemaxon.marvin.sketch.swing.modules.documentstyle - package chemaxon.marvin.sketch.swing.modules.documentstyle
 
chemaxon.marvin.space - package chemaxon.marvin.space
Contains the core classes of MarvinSpace including the graphic canvas and the basic visualizer classes.
chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
chemaxon.marvin.uif.dialog - package chemaxon.marvin.uif.dialog
 
chemaxon.marvin.util - package chemaxon.marvin.util
Contains some utilities for example for molecule cleaning and Swing.
chemaxon.marvin.util.codeassist - package chemaxon.marvin.util.codeassist
 
chemaxon.marvin.view - package chemaxon.marvin.view
Control records in MarvinView.
chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing
Swing support for MarvinView tables.
chemaxon.naming - package chemaxon.naming
Name to Structure conversion.
chemaxon.naming.document - package chemaxon.naming.document
Document to Structure (D2S) conversion.
chemaxon.naming.document.annotate - package chemaxon.naming.document.annotate
 
chemaxon.pharmacophore - package chemaxon.pharmacophore
Classes for pharmacophore point perception, pharmacophore fingerprint generation and pharmacophore dissimilarity calculations.
chemaxon.reaction - package chemaxon.reaction
Classes for reaction processing related tasks.
chemaxon.sss - package chemaxon.sss
Contains packages for structure search and screening.
chemaxon.sss.formula - package chemaxon.sss.formula
 
chemaxon.sss.screen - package chemaxon.sss.screen
Classes for screeening.
chemaxon.sss.search - package chemaxon.sss.search
Provides structural search capabilities.
chemaxon.sss.search.options - package chemaxon.sss.search.options
 
chemaxon.standardizer - package chemaxon.standardizer
Contains packages for structure standardization.
chemaxon.standardizer.actions - package chemaxon.standardizer.actions
Contains basic standardizer actions.
chemaxon.standardizer.advancedactions - package chemaxon.standardizer.advancedactions
Contains advanced standardizer actions.
chemaxon.standardizer.concurrent - package chemaxon.standardizer.concurrent
Contains classes for concurrent execution of standardization.
chemaxon.standardizer.configuration - package chemaxon.standardizer.configuration
Contains classes for handling configurations of standardizer.
chemaxon.standardizer.configuration.reader - package chemaxon.standardizer.configuration.reader
Contains classes for handling configuration deserialization.
chemaxon.standardizer.runner - package chemaxon.standardizer.runner
Contains classes for executing standardization based on a configuration.
chemaxon.struc - package chemaxon.struc
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.
chemaxon.struc.graphics - package chemaxon.struc.graphics
Contains graphics MDocument elements.
chemaxon.struc.prop - package chemaxon.struc.prop
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
chemaxon.struc.sgroup - package chemaxon.struc.sgroup
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.
chemaxon.util - package chemaxon.util
Provides general utility classes.
chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
 
chemaxon.util.iterator - package chemaxon.util.iterator
Provides iterator classes for molecules and their components.
ChemConst - Class in chemaxon.core
 
ChemConst() - Constructor for class chemaxon.core.ChemConst
 
ChemContext - Interface in chemaxon.jep
Interface of expression evaluation contexts.
CHEMICAL_ATOM_TYPES - Enum constant in enum class com.chemaxon.descriptors.alignment.AtomTyping
 
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 - Class in chemaxon.jep
Expression parser and evaluator for chemical expressions.
ChemJEP() - Constructor for class chemaxon.jep.ChemJEP
Constructor.
ChemJEP(Class) - Constructor for class chemaxon.jep.ChemJEP
Constructor.
CHEMLOCATOR_PERSONAL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemLocator Personal
CHEMLOCATOR_SERVER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemLocator Server
chemTermColValues - Variable in class chemaxon.jchem.db.UpdateHandler.RowData
 
chiral_all - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
 
CHIRAL_ALL - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
 
CHIRAL_ALL_POSSIBLE - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
 
chiral_allPossible - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
 
CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
Error type represents molecules marked with "absolute stereo" flag.
chiral_off - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
 
CHIRAL_OFF - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
 
chiral_selected - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
 
CHIRAL_SELECTED - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
 
chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of chiral centers.
chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Stereochemistry.chiralCenterCount()
chiralCenterCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Calculates the number of tetrahedral stereogenic centers.
chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry
Determines the chiral center atoms.
chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
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".
chiralityDisplay(ImageExporter.ChiralityDisplayOption) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the chirality display option.
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.
If substituents located on the same side of the reference plane.
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.
CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Deprecated.
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
CLASS_NOT_FOUND_ERROR - Static variable in class chemaxon.util.ErrorHandler
 
className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
 
clean(boolean, String) - Method in class chemaxon.util.MolHandler
Calculates 2D coordinates.
clean(int) - Method in class chemaxon.formats.MolConverter.Builder
Enables cleaning.
clean(int) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder
Enables cleaning.
clean(int, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
clean(int, String) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
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.
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".
cleanResults() - Method in class chemaxon.jchem.db.JChemSearch
Cleans stored search results.
cleanup() - Method in class chemaxon.marvin.space.GraphicComponent
 
cleanup() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
cleanup() - Method in class chemaxon.marvin.space.PharmacophorePoint
 
cleanup(long) - Method in class chemaxon.reaction.ConcurrentReactorProcessor
Cancels work currently executed, awaits termination of associated worker threads and releases any resource this processor has reserved.
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.
clear() - Method in class chemaxon.jchem.file.ProgressWriter
Clears texts except main text.
clear() - Method in interface chemaxon.jep.ChemContext
Clears the context.
clear() - Method in class chemaxon.jep.context.AtomContext
Clears the context.
clear() - Method in class chemaxon.jep.context.MolContext
Clears the context.
clear() - Method in class chemaxon.jep.context.ReactionContext
Clears the context.
clear() - Method in class chemaxon.marvin.space.BoundingBox
Clears all previously set coordinate from the box.
clear() - Method in class chemaxon.marvin.space.monitor.Monitor
Deletes all items from selectedItems.
clear() - Method in class chemaxon.pharmacophore.PMap
Sets every feature for every atom to false
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
clearAllCellStyle() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
Clears all the previously set cell style of the property columns
clearAllColumnWidth() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
Clears all the previously set width of the property columns
clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
clearCache() - Method in enum class chemaxon.jchem.db.cache.CacheManager
Clears the cache that stores fingerprints and structures.
clearCachedInfo(int) - Method in class chemaxon.struc.MoleculeGraph
Deletes the cached information depending on the given options.
clearChangesInUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Used in initializing searches.
clearCheckerMarks() - Method in class chemaxon.struc.MDocument
Clears the checker marks
clearClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Clears the clipboard by creating an empty Transferable and placing it on the clipboard.
clearClipboardConditionally() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Clears the clipboard, if ClipboardHandler.isClearClipboardBeforeExport() is true.
clearComparators() - Method in class chemaxon.sss.search.MolSearch
Delete all comparator from the search object.
clearExtraLabel() - Method in class chemaxon.struc.MolAtom
Clears the extra label.
clearExtraLabels() - Method in class chemaxon.struc.Molecule
Clears extra atom labels.
clearFeatures(int) - Method in class chemaxon.pharmacophore.PMap
Clears all features corresponding to the given atom index.
clearForImport(String) - Method in class chemaxon.struc.Molecule
Initializes molecule for import.
clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph
Clears the bonds vector, the properties, the flags, and sets the origin coordinates to 0.
clearForImport(String) - Method in class chemaxon.struc.RgMolecule
Clear the edges vector and the properties.
clearForImport(String) - Method in class chemaxon.struc.RxnMolecule
Clear the edges vector and the properties.
clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane
Reset undo queue.
clearInactiveTasks(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil
Clears the inactive tasks list.
ClearIsotopesAction - Class in chemaxon.standardizer.actions
Clear isotopes standardizer action
ClearIsotopesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearIsotopesAction
Initializes the action
clearLines() - Method in class chemaxon.struc.graphics.MTextBox
Clears all lines.
clearMatch() - Method in class chemaxon.sss.search.MolSearch
 
clearMatch() - Method in class chemaxon.sss.search.Search
Clears the extra prerequisites of the structure search specified using addMatch calls.
clearObjects() - Method in class chemaxon.struc.Molecule
 
clearObjects() - Method in class chemaxon.struc.RgMolecule
 
clearObjects() - Method in class chemaxon.struc.RxnMolecule
Deletes the graphical objects from this.
clearObjects() - Method in class chemaxon.struc.Sgroup
Clears all MObject-s that belong to this S-groups.
clearProperties() - Method in class chemaxon.struc.MolAtom
Removes all properties from this atom.
clearProperties() - Method in class chemaxon.struc.MolBond
Removes all properties from this bond.
clearProperties() - Method in class chemaxon.struc.Molecule
Clears RDfile/SDfile properties.
clearPropertyColumnNames() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
Clears the display name list of properties
clearQProps() - Method in class chemaxon.struc.MolAtom
Clears query props.
clearSavedAtomIndices() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
clearSelection(int) - Method in class chemaxon.marvin.space.GraphicScene
Sets all components and parts of components to be unselected in the given cell.
clearSelections() - Method in class chemaxon.marvin.space.GraphicCell
Sets all components and parts of components to be unselected.
clearSets() - Method in class chemaxon.struc.MDocument
Clears the atomSets and the bondSets.
ClearStereoAction - Class in chemaxon.standardizer.actions
Clear stereo standardizer action
ClearStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearStereoAction
Initializes the action with parameters
ClearWedgeFixer - Class in chemaxon.fixers
Clears wedges.
ClearWedgeFixer() - Constructor for class chemaxon.fixers.ClearWedgeFixer
 
CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Flag that indicates an import operation
CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Flag that indicates an export operation
CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Undefined clipboard operation state identifier
CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Temporary property name to mark the molecule if it comes from a file via the clipboard
ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer
Facade of the Clipboard handling in Marvin.
clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Clipboard operation type.
clipSurface(BoundingBox) - Method in class chemaxon.marvin.space.SurfaceComponent
The bounding box of the surface can be used to determine 6 clipping planes and clip (do not draw) parts lying outside of the box.
clone() - Method in class chemaxon.checkers.AbstractStructureChecker
 
clone() - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
clone() - Method in class chemaxon.checkers.SubstructureChecker
 
clone() - Method in class chemaxon.core.util.BondTable
 
clone() - Method in class chemaxon.descriptors.BCUT
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.ChemicalFingerprint
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.CustomDescriptor
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.ECFP
Creates a new instance with identical internal state.
clone() - Method in class chemaxon.descriptors.MDSet
Clones the object.
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.
clone() - Method in class chemaxon.pharmacophore.PMap
Clones this PMap object.
clone() - Method in class chemaxon.sss.search.JChemSearchOptions
Makes an identical copy of this SearchObject.
clone() - Method in class chemaxon.sss.search.MolSearchOptions
 
clone() - Method in class chemaxon.sss.search.SearchOptions
Makes an identical copy of this SearchObject.
clone() - Method in class chemaxon.standardizer.AbstractStandardizerAction
 
clone() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
Deprecated.
 
clone() - Method in class chemaxon.standardizer.actions.AliasToGroupAction
 
clone() - Method in class chemaxon.standardizer.actions.AromatizeAction
 
clone() - Method in class chemaxon.standardizer.actions.ClearStereoAction
 
clone() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
 
clone() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
 
clone() - Method in class chemaxon.standardizer.actions.ExpandAction
 
clone() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
 
clone() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
 
clone() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
 
clone() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
 
clone() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
 
clone() - Method in class chemaxon.standardizer.actions.TautomerizeAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
clone() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
 
clone() - Method in class chemaxon.standardizer.advancedactions.TransformAction
 
clone() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
 
clone() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
 
clone() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
 
clone() - Method in class chemaxon.struc.CTransform3D
 
clone() - Method in class chemaxon.struc.DPoint3
Make an identical copy.
clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
clone() - Method in class chemaxon.struc.graphics.MBracket
 
clone() - Method in class chemaxon.struc.graphics.MChemicalStruct
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MEFlow
 
clone() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
clone() - Method in class chemaxon.struc.graphics.MEllipse
 
clone() - Method in class chemaxon.struc.graphics.MFont
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MMidPoint
 
clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
 
clone() - Method in class chemaxon.struc.graphics.MPolyline
 
clone() - Method in class chemaxon.struc.graphics.MRectangle
 
clone() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
 
clone() - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
clone() - Method in class chemaxon.struc.graphics.MTextBox
 
clone() - Method in class chemaxon.struc.MDocument
Creates a clone.
clone() - Method in class chemaxon.struc.MObject
Creates a clone.
clone() - Method in class chemaxon.struc.MolAtom
Clones the atom.
clone() - Method in class chemaxon.struc.MolBond
Make a copy of this object.
clone() - Method in class chemaxon.struc.Molecule
Makes an identical copy of the molecule.
clone() - Method in class chemaxon.struc.MoleculeGraph
Make an identical copy of the molecule.
clone() - Method in class chemaxon.struc.MPoint
 
clone() - Method in class chemaxon.struc.MPropertyContainer
Clones this object.
clone() - Method in class chemaxon.struc.prop.MBooleanProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MDoubleProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MHCoords3DProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MIntegerProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MMoleculeProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MObjectProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MStringProp
Clones the object.
clone() - Method in class chemaxon.struc.QueryBond
Make a copy of this object.
clone() - Method in class chemaxon.struc.RgMolecule
Clone the markush structure.
clone() - Method in class chemaxon.struc.RxnMolecule
Make an identical copy of the reaction structure.
clone() - Method in class chemaxon.struc.SelectionMolecule
Create a clone of this SelectionMolecule.
clone() - Method in class chemaxon.struc.sgroup.SgroupAtom
Clones the S-group superatom and it's SuperatomSgroup as well.
clone() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Clones the SuperatomSgroup (and not the Molecule).
clone() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
Makes an identical copy of the Options
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.JChemSearchOptions
Copies parameters to other.
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.JChemSearchOptions
 
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
cloneLeavingGroups(SuperatomSgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
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.
as of Marvin 2014.09.01.0 use Molecule.clone() instead
cloneMoleculeWithDocument() - Method in class chemaxon.struc.Molecule
Makes an identical copy of the molecule and its document.
cloneMoleculeWithDocument() - Method in class chemaxon.struc.RgMolecule
 
cloneMoleculeWithDocument() - Method in class chemaxon.struc.RxnMolecule
 
cloneProp() - Method in class chemaxon.struc.MDocument.Prop
Creates a clone.
cloneProp() - Method in class chemaxon.struc.MProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MObjectProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MStringProp
Clones the object.
cloneResult - Variable in class chemaxon.descriptors.MDReader
indicates if mdSet is cloned or not in next()
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.descriptors.GenerateMD
Closes the generator, all output files or database connection.
close() - Method in class chemaxon.descriptors.MDArrayReader
Closes the reader
close() - Method in class chemaxon.descriptors.MDDBReader
Closes down the descriptor stream.
close() - Method in class chemaxon.descriptors.MDDBWriter
Closes down the descriptor output stream.
close() - Method in class chemaxon.descriptors.MDFileReader
Closes the reader.
close() - Method in class chemaxon.descriptors.MDFileWriter
Closes the stream, after that no more operations are permitted.
close() - Method in class chemaxon.descriptors.MDReader
Closes down the descriptor stream.
close() - Method in class chemaxon.descriptors.MDSimilarityResultWriter
Closes output.
close() - Method in class chemaxon.descriptors.MDWriter
Closes down the descriptor output stream.
close() - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentReader
Closes the office document stream.
close() - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
Clear up resources collected during the report generation process.
close() - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
Closes the office Document stream.
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.jchem.db.DatabaseProperties
Should be called only if the use of prepared statements are enabled with DatabaseProperties.setUsePreparedStatement(boolean).
close() - Method in class chemaxon.jchem.db.UpdateHandler
Closes the handler (required to call).
close() - Method in class chemaxon.jchem.file.ProgressWriter
Indicate that the operation is complete.
close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Interrupts parsing.
close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
 
close() - Method in class chemaxon.marvin.io.MDocSource
Closes the underlying input stream(s).
close() - Method in class chemaxon.marvin.io.MolExportModule
Close the stream.
close() - Method in class chemaxon.marvin.io.MRecordImporter
Closes the input stream.
close() - Method in interface chemaxon.marvin.io.MRecordReader
Closes the input stream.
close() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
 
close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
Closes the importers.
close() - Method in class chemaxon.util.ConnectionHandler
Closes the connection to the database.
close() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
Closes the output.
close() - Method in interface com.chemaxon.calculations.common.ProgressObserver
close() - Method in interface com.chemaxon.calculations.io.CloseableIterator
 
close() - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
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<T> - Interface in com.chemaxon.calculations.io
Closeable iterator.
CloseableIterators - Class in com.chemaxon.calculations.io
Utility class.
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.
cluster(double[][], LanceWilliamsMerge, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Invoke clustering.
cluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
A spec for a clusterId.
cluster(LegacyLibraryMcsParameters, Iterator<Molecule>) - Static method in class chemaxon.clustering.adapter.LegacyLibraryMcsAdapter
Deprecated.
Launch clustering.
cluster(LegacyLibraryMcsParameters, Iterator<Molecule>) - Static method in class chemaxon.clustering.libmcs.adapter.LegacyLibraryMcsAdapter
Launch clustering.
cluster(DissimilarityInput, LanceWilliamsMerge, ProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Invoke clustering.
Cluster<T> - Interface in com.chemaxon.clustering.common
Cluster represents a group of structures.
ClusterEnumerator(MGraph, boolean) - Constructor for class chemaxon.clustering.libmcs.LibraryMcs.ClusterEnumerator
 
ClusterEnumerator(MGraph, boolean, boolean) - Constructor for class chemaxon.clustering.libmcs.LibraryMcs.ClusterEnumerator
 
clusterLevel(T) - Method in interface com.chemaxon.clustering.common.LevelAssigner
Level associated to a hierarchic cluster.
clusterLevelFunction() - Method in interface com.chemaxon.clustering.common.LevelAssigner
CLuster level association.
clusterOf(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Look up immediate parent of a structure present in the clustering.
clusterOf(T) - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Identify the lowest level cluster containing the given item.
clusterOf(T) - Method in interface com.chemaxon.clustering.common.SingleLevelClustering
Identify the cluster containing the given item.
clusters() - Method in interface com.chemaxon.clustering.common.HierarchicCluster
Access further grouping of the represented elements.
clusters() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster
 
clusters() - Method in interface com.chemaxon.clustering.common.SingleLevelClustering
Represented cluster.
Cm - Static variable in class chemaxon.core.ChemConst
 
CmdlineUtils - Class in com.chemaxon.calculations.util
Command line related utilities.
CML - Static variable in class chemaxon.formats.MFileFormat
Chemical Markup Language.
Cn - Static variable in class chemaxon.core.ChemConst
 
CnsMpo - Class in chemaxon.calculations.cnsmpo
CNS MPO score calculator.
CnsMpo.Property - Class in chemaxon.calculations.cnsmpo
Simple DTO that contains the predicted value and its CNS MPO score.
CnsMpoFunction - Enum Class in chemaxon.calculations.cnsmpo
Base phys-chem property calculators and its score functions for CNS MPO calculation.
Co - Static variable in class chemaxon.core.ChemConst
 
CodeAssistConfiguration() - Constructor for class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
 
CodeAssistFactory - Class in chemaxon.marvin.util.codeassist
Manages the creation of Chemical Terms related components, such as the Code Assist text field, toolbars, favorite and macro handling components, and validation response component.
CodeAssistFactory.CodeAssistConfiguration - Class in chemaxon.marvin.util.codeassist
Helper class for CodeAssistFactory to set up CodeAssist
codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Add mass number information to the given code.
coeffQuery(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Set query coefficient.
coeffTarget(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Set target coefficient.
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
collectStatisitcs(ConnectionHandler, String) - Method in class chemaxon.jchem.db.TableStatistics
 
color - Variable in class chemaxon.marvin.space.GraphicComponent
 
color - Variable in class chemaxon.marvin.space.MoleculeComponent
 
color - Variable in class chemaxon.marvin.space.SurfaceComponent
 
color() - 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, Molecule, int[], HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
Performs hit coloring on the specified structure.
color(Molecule, Molecule, HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
Performs hit coloring on the specified structure.
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_MAPPER_BLUE_TO_GREEN - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in blue-cyan-green palette will be used.
COLOR_MAPPER_BLUE_TO_RED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in blue-lightgray-red palette will be used.
COLOR_MAPPER_FIRE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in "fire" palette will be used.
COLOR_MAPPER_GREEN_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in green-cyan-blue palette will be used.
COLOR_MAPPER_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in rainbow palette will be used.
COLOR_MAPPER_RED_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in red-lightgray-blue palette will be used.
COLOR_MAPPER_REVERSE_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in reverse rainbow palette will be used.
COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "colorScheme".
COLOR_SCHEMES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Array of color schemes strings.
color3 - Variable in class chemaxon.marvin.space.SurfaceComponent
 
ColorGenerator - Class in chemaxon.marvin.util
A final class which provides a static access to a color distant color creator class.
ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator
 
colorHit(Molecule, Molecule, int[], HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
Returns the colored copy of the specified target structure, the original target is kept unchanged.
coloring(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
 
coloring(ImageExporter.Coloring) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the coloring scheme.
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.
COLORS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Color scheme mask in display option flags.
COLORS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Color scheme offset in display option flags.
colorType - Variable in class chemaxon.marvin.space.MoleculeComponent
 
COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "cols".
com.chemaxon.apidiscovery - package com.chemaxon.apidiscovery
API Discovery framework.
com.chemaxon.apidiscovery.annotations - package com.chemaxon.apidiscovery.annotations
Annotations used by the API Discovery framework.
com.chemaxon.apidiscovery.interfaces - package com.chemaxon.apidiscovery.interfaces
Interfaces introduced for the API Discovery framework.
com.chemaxon.apidiscovery.util - package com.chemaxon.apidiscovery.util
Various utilities.
com.chemaxon.calculations.cli - package com.chemaxon.calculations.cli
 
com.chemaxon.calculations.common - package com.chemaxon.calculations.common
Common components of Calculator APIs.
com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal
API of the elemental analysis functionality.
com.chemaxon.calculations.gui - package com.chemaxon.calculations.gui
 
com.chemaxon.calculations.io - package com.chemaxon.calculations.io
 
com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility
 
com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal
API of the Stereo Analysis Plugin.
com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters
Core filter classes.
com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop
Atrop stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial
Axial stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans
Cis-trans stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral
Tetrahedral stereo filter implementations.
com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters
Stereocenter implementations of Stereo Analysis API.
com.chemaxon.calculations.stereoisomers - package com.chemaxon.calculations.stereoisomers
 
com.chemaxon.calculations.util - package com.chemaxon.calculations.util
Various utilities used in calculations, descriptors, clustering and overlap analysis.
com.chemaxon.clustering.common - package com.chemaxon.clustering.common
Common components of clustering related APIs.
com.chemaxon.clustering.framework - package com.chemaxon.clustering.framework
Hierarchic structural framework based clustering.
com.chemaxon.clustering.singlelinkage - package com.chemaxon.clustering.singlelinkage
Single linkage clustering algorithm.
com.chemaxon.clustering.sphex - package com.chemaxon.clustering.sphex
Sphere exclusion clustering algorithm.
com.chemaxon.clustering.util - package com.chemaxon.clustering.util
Clustering related utilities.
com.chemaxon.clustering.wards - package com.chemaxon.clustering.wards
Ward's minimum variance implemented as a generic agglomerative hierarchical clustering algorithm.
com.chemaxon.common.annotations - package com.chemaxon.common.annotations
 
com.chemaxon.descriptors.alignment - package com.chemaxon.descriptors.alignment
3D flexible alignment based molecular shape similarity calculation.
com.chemaxon.descriptors.common - package com.chemaxon.descriptors.common
Unguarded descriptor handling.
com.chemaxon.descriptors.db - package com.chemaxon.descriptors.db
Interfaces for database import/export.
com.chemaxon.descriptors.fingerprints.cfp - package com.chemaxon.descriptors.fingerprints.cfp
API of the Chemaxon hashed fingerprint family molecular descriptors.
com.chemaxon.descriptors.fingerprints.ecfp - package com.chemaxon.descriptors.fingerprints.ecfp
API of the ECFP fingerprint family molecular descriptors.
com.chemaxon.descriptors.fingerprints.maccs - package com.chemaxon.descriptors.fingerprints.maccs
ChemAxon implementation of the MACCS 166 bit fingerprints.
com.chemaxon.descriptors.fingerprints.pf2d - package com.chemaxon.descriptors.fingerprints.pf2d
API of the 2D pharmacophore fingerprint family molecular descriptors.
com.chemaxon.descriptors.metrics - package com.chemaxon.descriptors.metrics
Common descriptor comparison metrics.
com.chemaxon.descriptors.vectors.binary - package com.chemaxon.descriptors.vectors.binary
Generic binary vector descriptors.
com.chemaxon.descriptors.vectors.floats - package com.chemaxon.descriptors.vectors.floats
Generic floating point vector descriptors.
com.chemaxon.mapper - package com.chemaxon.mapper
 
com.chemaxon.overlap.io - package com.chemaxon.overlap.io
 
com.chemaxon.search - package com.chemaxon.search
Tools for chemical search.
com.chemaxon.search.mcs - package com.chemaxon.search.mcs
Contains classes for finding the maximum common substructure (MCS) of molecular structures.
com.chemaxon.search.mcs.buildup - package com.chemaxon.search.mcs.buildup
Contains MCS algorithm implementation based on the "build up" method.
com.chemaxon.search.mcs.maxclique - package com.chemaxon.search.mcs.maxclique
Contains MCS algorithm implementation based on the "maximum clique" method.
com.chemaxon.search.mcs.upperbound - package com.chemaxon.search.mcs.upperbound
Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.
com.chemaxon.search.transformation - package com.chemaxon.search.transformation
 
com.chemaxon.search.transformation.transformers - package com.chemaxon.search.transformation.transformers
 
com.chemaxon.version - package com.chemaxon.version
 
combine(Collection<? extends CalculatorInputChecker>) - Static method in interface chemaxon.calculator.CalculatorInputChecker
Combines the given checkers into a single one that reports all errors reported by the given checkers.
Common - Class in chemaxon.clustering
Common superclass for JKlustor tools.
Common() - Constructor for class chemaxon.clustering.Common
 
compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
 
compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors in serialized form.
compare(int, int, MDSet) - Method in class chemaxon.descriptors.MDSimilarity
Compares a target descriptor against all queries added prior to the call of this method using the given metric of the given descriptor.
compare(MDReader) - Method in class chemaxon.descriptors.MDSimilarity
Compares a list of target descriptor sets (read by a molecular descriptor reader) against all queries added prior to the call of this method the same way as compareQueries( MolecularDescriptor target ) but for each target.
compare(MDSet) - Method in class chemaxon.descriptors.MDSimilarity
Compares a target descriptor set (for instance from a database) against all queries added prior to the call of this method.
compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator
 
compare(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors.
compare(T, T) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
 
Compare - Class in chemaxon.clustering
Compares two sets of objects (like compound libraries) using diversity and dissimilarity calculations.
Compare() - Constructor for class chemaxon.clustering.Compare
 
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(AtomIdentifier) - Method in class chemaxon.reaction.AtomIdentifier
 
compareTo(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
 
compareTo(Object) - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
 
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Get an unguarded context factory.
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
 
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
 
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
 
comparisonLinenote() - Method in interface com.chemaxon.descriptors.metrics.MetricFactory
Gets the string based parameterization description.
ComparisonResult - Interface in com.chemaxon.descriptors.common
Result of a descriptor comparison.
compatible(Guarded, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat
Ensure the guard object based compatibility of two objects.
compatibleWithGuard(Object, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat
Ensure the guard object based compatibility of two objects.
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, Class) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, Class, SymbolTable) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
COMPLETE - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
All atoms will be mapped
CompleteLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
 
component - Variable in class chemaxon.marvin.space.monitor.Control
 
COMPONENT - Enum constant in enum class chemaxon.struc.SgroupType
 
COMPONENT_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_ENTIRE - Static variable in class chemaxon.marvin.space.GraphicComponent
Indicates if the entire component is selected by picking.
COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
componentBecameSelected() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if a component became selected previously.
componentBecameSelected(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if a component became selected previously in the given cell.
componentBecameUnselected() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if a component became unselected previously.
componentBecameUnselected(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if a component became unselected previously in the given cell.
ComponentChecker<E> - Class in chemaxon.checkers
Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).
ComponentChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.ComponentChecker
Constructor to create a Structure checker instance with the given errorType.
ComponentElement - Class in chemaxon.marvin.space
Class to identify parts of GraphicComponents mainly during selection.
ComponentElement(ComponentElement) - Constructor for class chemaxon.marvin.space.ComponentElement
Copies the given ComponentElement.
ComponentElement(GraphicComponent, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement of a simple (not structured) GraphicComponent.
ComponentElement(GraphicComponent, int, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement of a complex (structured) GraphicComponent.
ComponentElement(GraphicComponent, int, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement.
ComponentElement(GraphicComponent, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement.
componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Hides windows if the parent frame is hidden.
componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Does nothing.
componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Does nothing.
componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MViewPane
 
componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Shows windows if the parent frame is hidden.
COMPOSITE - Static variable in class chemaxon.jchem.db.DatabaseConstants
 
COMPOSITE_DRIVER - Static variable in class chemaxon.jchem.db.DatabaseConstants
JDBC driver for Composite database
COMPOSITE_TYPE_NAME - Static variable in class chemaxon.jchem.db.DatabaseConstants
 
COMPOSITE_URL_EXAMPLE - Static variable in class chemaxon.jchem.db.DatabaseConstants
JDBC URL example for Composite database
COMPOSITE_URL_TEMPLATE - Static variable in class chemaxon.jchem.db.DatabaseConstants
JDBC URL template for Composite database
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.io.MemoizingIterator
 
computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
 
computeSurface(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MSpaceEasy
Activates the container cell of the MoleculeVisualizer, and computes its Connolly surface.
computeSurface(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Computes the given type of surface in the active cell of the viewer.
ConcurrentReactorProcessor - Class in chemaxon.reaction
Executes a chemical reaction: creates products from reactants with reaction center data.
ConcurrentReactorProcessor() - Constructor for class chemaxon.reaction.ConcurrentReactorProcessor
 
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.
ConditionalRuleOperators - Enum Class in chemaxon.formats.documents.jchemoffice
 
ConditionRule - Class in chemaxon.formats.documents.jchemoffice
 
ConditionRule() - Constructor for class chemaxon.formats.documents.jchemoffice.ConditionRule
 
ConditionRule(ConditionalRuleOperators, double) - Constructor for class chemaxon.formats.documents.jchemoffice.ConditionRule
 
ConditionRule(ConditionalRuleOperators, String) - Constructor for class chemaxon.formats.documents.jchemoffice.ConditionRule
 
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.
CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "confirmTransfer".
CONFORMATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Conformation Plugin Group
ConformerPlugin - Class in chemaxon.marvin.calculations
Plugin class for conformer calculation.
ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin
Constructor.
CONJUGATED - Static variable in class chemaxon.struc.MolBond
Conjugation state of the bond.
connectedMode(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether the common substructures should be connected or they can consist of multiple fragments.
ConnectionHandler - Class in chemaxon.util
A JavaBean for connecting to relational databases using JDBC.
ConnectionHandler() - Constructor for class chemaxon.util.ConnectionHandler
Creates new ConnectionHandler Connection will automatically be non-commitable (see ConnectionHandler.isCommitable()) to preserve compatibility with previous versions.
ConnectionHandler(boolean) - Constructor for class chemaxon.util.ConnectionHandler
Creates new ConnectionHandler
ConnectionHandler(ConnectionHandler) - Constructor for class chemaxon.util.ConnectionHandler
Creates new ConnectionHandler based on the settings of an other ConnectionHandler.
ConnectionHandler(ConnectionHandler, boolean) - Constructor for class chemaxon.util.ConnectionHandler
Creates new ConnectionHandler based on the settings of an other ConnectionHandler.
ConnectionHandler(Connection, String) - Constructor for class chemaxon.util.ConnectionHandler
Creates a new ConnectionHandler and sets the connection to an externally created Connection (e.g.
ConnectionHandler(Connection, String, boolean) - Constructor for class chemaxon.util.ConnectionHandler
Creates a new ConnectionHandler and sets the connection to an externally created Connection (e.g.
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.
connectToDatabase() - Method in class chemaxon.util.ConnectionHandler
Connects to the database.
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject
 
constant - Variable in class chemaxon.marvin.services.ServiceArgument
field indicates constant argument
constructBvGenerator(BvParameters) - Method in interface com.chemaxon.descriptors.vectors.binary.BvParameters.ConstructBvGenerator
Construct new instance
constructCfpGenerator(CfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.ConstructCfpGenerator
Constructor invocation.
constructEcfpGenerator(EcfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.ConstructEcfpGenerator
Constructor invocation.
constructMaccsGenerator(MaccsParameters) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.ConstructMaccsGenerator
Constructor invocation.
constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.ConstructPfGenerator
Constructor invocation.
containerFrame - Variable in class chemaxon.marvin.space.MSpaceEasy
 
contains(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
Tells whether the given location is inside the box.
contains(MDocument) - Method in class chemaxon.struc.MDocument
Tests whether the document contains all objects of another document.
contains(MObject) - Method in class chemaxon.struc.MDocument
Searches an object in the document.
contains(MolAtom) - Method in class chemaxon.struc.Molecule
Checks if the molecule graph contains the specified atom.
contains(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Checks if the molecule graph contains the specified atom.
contains(MolAtom) - Method in class chemaxon.struc.RgMolecule
Checks if the root structure or an R-group contains the specified node.
contains(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Checks if a reactant, agent or product structure contains the specified node.
contains(MolAtom) - Method in class chemaxon.struc.Sgroup
Is this atom contained by the s-group?
contains(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.
contains(MolBond) - Method in class chemaxon.struc.RgMolecule
Checks if the root structure or an R-group contains the specified edge.
contains(MolBond) - Method in class chemaxon.struc.RxnMolecule
Checks if a reactant, agent or product structure contains the specified edge.
contains(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Does the molecule graph contain the specified fragment?
contains(MProp) - Method in class chemaxon.struc.MPropertyContainer
Tests whether the container contains the specified property object.
contains(MProp) - Method in class chemaxon.struc.prop.MCollectionProp
Tests whether the collection contains the specified property.
containsAllAtomsOf(Sgroup) - Method in class chemaxon.struc.Sgroup
Checks if the S-group contains the atoms of another S-group.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.MObject
Checks if the object contains the specified atom reference.
containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Tells whether the component is in the cell.
containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the component exists in the scene.
containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule graph contains coordinate bonds.
containsHydrogens() - Method in class chemaxon.util.MolHandler
True if the molecule contains explicit Hydrogen atoms, false otherwise.
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
Tests whether the document contains only one object of the specified class.
containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
 
containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom
Returns true if this atom has a mapping for the specified property key.
containsPropertyKey(String) - Method in class chemaxon.struc.MolBond
Returns true if this bond has a mapping for the specified property key.
containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if molecule contains pseudo atom.
containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule contains SRU S-groups.
CONTEXT - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: the context of the structure recognized in the text.
CONTEXT_INDEX - Static variable in class chemaxon.naming.document.DocumentToStructure
Molecule property key on results: index of the hit inside the context.
contract(int) - Method in class chemaxon.struc.Sgroup
Sets the state to Sgroup.XSTATE_C.
contract(int) - Method in interface chemaxon.struc.sgroup.Expandable
Contracts the S-group.
contract(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Contracts this S-group.
contract(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Contracts this S-group.
ContractGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule
ContractGroupFixer() - Constructor for class chemaxon.fixers.ContractGroupFixer
 
contractOrExpandSgroups(int, String, boolean) - Method in class chemaxon.marvin.view.MDocStorage
Contract or expand S-groups in the specified cell.
contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.view.MDocStorage
Contract or expand S-groups in all molecules.
contractSgroups() - Method in class chemaxon.struc.Molecule
Contracts all S-groups.
contractSgroups(int) - Method in class chemaxon.struc.Molecule
Contracts all S-groups.
ContractSgroupsAction - Class in chemaxon.standardizer.actions
Standardizer action contracting s-groups of the target molecule
ContractSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ContractSgroupsAction
Initializes the action
control - Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
 
control - Variable in class chemaxon.marvin.space.monitor.Monitor
 
control(int) - Method in class chemaxon.marvin.space.monitor.Control
Does control on z event.
control(int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
One part of the molecule being in one of the end of the torsion bond will be rotated around the bond.
control(int) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Passes the control event to the control.
control(int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Changes the location say translates the component of the control in the global coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Changes the orientation that is rotates the component of the control in the global coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Changes the location say translates the component of the control in its local coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Changes the orientation say rotates the component of the control in its local coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Causes the monitor's controll to take action with 1 parameter.
control(int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
Resizes the component in z direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
control(int, int) - Method in class chemaxon.marvin.space.monitor.Control
Does control on x-y events.
control(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
Does nothing.
control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Changes the location say translates the component of the control in the global coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Changes the orientation say rotates the component of the control in the global coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Changes the location say translates the component of the control in its local coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Changes the orientation say rotates the component of the control in its local coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Causes the monitor's controll to take action with 2 parameters.
control(int, int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
Resizes the component in x, y direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
Control - Class in chemaxon.marvin.space.monitor
Transformation on a GraphicComponent that changes the coordinates, and not just the view.
Control() - Constructor for class chemaxon.marvin.space.monitor.Control
Creates a new instance of Control
ConversionOptions - Class in chemaxon.formats.documents.jchemoffice
 
ConversionOptions() - Constructor for class chemaxon.formats.documents.jchemoffice.ConversionOptions
 
ConversionOptions(boolean) - Constructor for class chemaxon.formats.documents.jchemoffice.ConversionOptions
 
convert() - Method in class chemaxon.formats.MdlCompressor
Compression/decompression
convert() - Method in class chemaxon.formats.MolConverter
Convert the next molecule.
convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor
(Un)compress the specified molfile or SDfile.
convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
 
convert(TransferDataImporter) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Convert transfer data available on clipboard in one of the requested flavors.
convert(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Creates an MDL mol or compressed mol representation of the molecule.
convert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule
Convert a molecule to a string or byte array.
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
 
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
 
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - 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
 
convertAll(ImageExporter) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
Converts the rendering settings of all molecule structures in the given document to the format given in the imageWriter parameter
convertAll(ImageExporter, IConversionOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
Converts the rendering settings of all molecule structures in the given document to the format given in the imageWriter parameter
convertAll(String) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
Converts the rendering settings of all molecule structures in the given document to the format given in the moleculeImageSettingsFormat parameter
convertAll(String, IConversionOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
Converts the rendering settings of all molecule structures in the given document to the format given in the moleculeImageSettingsFormat parameter
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
Convert explicit Hydrogen atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert explicit Hydrogen atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert 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
Convert 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.
convertForAppletParameter(String) - Static method in class chemaxon.util.HTMLTools
Converts a string to a format that can be used as a value of an applet parameter in an HTML page.
convertForJavaScript(String) - Static method in class chemaxon.util.HTMLTools
Converts a string to a format that can be used as a value of JavaScript variable in an HTML page.
convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit Hydrogen atoms of the molecule to explicit.
convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit lone pairs of the atoms of a molecule to explicit.
convertPageSettingsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX.
ConvertPiMetalBondsAction - Class in chemaxon.standardizer.actions
Convert Pi-Metal coordinate bond to coordinate bond action.
ConvertPiMetalBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertPiMetalBondsAction
Initializes a convert pi-metal bond action
ConvertPseudoToGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the pseudo informations to contracted abbreviated groups in the molecule
ConvertPseudoToGroupFixer() - Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer
 
convertResult(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
This method converts the result by changing the atoms and bonds back to the original instead of the cloned ones
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker
Handles the mapping of a cloned and expanded molecule result to the original molecule.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker
This implementation does nothing.
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker
This implementation does nothing.
ConvertToAtomFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information
ConvertToAtomFixer() - Constructor for class chemaxon.fixers.ConvertToAtomFixer
 
ConvertToCarbonFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms
ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer
 
ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond
ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
 
ConvertToElementalFormFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms
ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer
 
ConvertToEnhancedStereoAction - Class in chemaxon.standardizer.actions
Convert to enhanced stereo standardizer action
ConvertToEnhancedStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
Initializes the action with parameters
convertToFrags() - Method in class chemaxon.struc.Molecule
Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.
ConvertToIonicFormFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.
ConvertToIonicFormFixer() - Constructor for class chemaxon.fixers.ConvertToIonicFormFixer
 
ConvertToPlainDoubleBondFixer - Class in chemaxon.fixers
Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.
ConvertToPlainDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToPlainDoubleBondFixer
 
ConvertToSingleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the bond to single bond.
ConvertToSingleBondFixer() - Constructor for class chemaxon.fixers.ConvertToSingleBondFixer
 
convertToSmilingFormat(Molecule) - Static method in class chemaxon.formats.MFileFormatUtil
Tries to convert a molecule to a SMILES related format.
convertToSmilingFormat(MProp) - Static method in class chemaxon.formats.MFileFormatUtil
Try to convert a property to text with a SMILES related format argument.
convertToString(MDocument, String, int) - Static method in class chemaxon.formats.MolExporter
Converts the document to text format.
convertToString(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler
Convert key of 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.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop
Deprecated.
convertToString(String, int) - Method in class chemaxon.struc.MProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp
Deprecated.
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
 
coordBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Coordinate bond display style.
coordBondStyleAtMulticenter(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Coordinate bond display style when it connects to a multicenter atom.
COORDDEP - Static variable in class chemaxon.struc.MProp
Coordinate dependent property.
COORDINATE - Static variable in class chemaxon.struc.MolBond
Coordinate bond flag.
COORDINATE_BOND_ARROW_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_AT_MULTICENTER_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_AT_MULTICENTER_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_AT_MULTICENTER_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_HASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
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".
COORDINATE_BOND_STYLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_STYLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
CoordinateBondOnMulticenterStyle - Enum Class in chemaxon.marvin.paint.constants
Holds the values for the possible rendering styles for Coordinate bonds connected to Multicenter atoms.
CoordinateBondStyle - Enum Class in chemaxon.marvin.paint.constants
Holds the values for the possible rendering styles for Coordinate bonds.
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.
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. 
COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
since 5.3.3 has no sense
copyFrom(ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.ISettings
Copies the entire settings from another settings instance
copyFrom(ISettings) - Method in class chemaxon.formats.documents.jchemoffice.ReportSettings
 
CopyOptConstants - Interface in chemaxon.marvin.util
Deprecated.
since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this interface either non exists in the new implementation or its value has changed. See the constants own description for details.
copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket
Copies line properties to another line object.
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow
 
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline
Copies line properties to another line object.
correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
count() - Method in class chemaxon.descriptors.MDSimilarityResultWriter
Increments the counter of the results processed.
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.
countNumberOfClusters(HierarchicClustering<?, ? extends HierarchicCluster<?>>) - Static method in class com.chemaxon.clustering.util.Util
Count the number of clusters in a clustering.
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. 
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.
cpk - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.coloringValues
 
CPK - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.Coloring
 
CPK_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts
CPK color scheme in display option flags.
CPK_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
CPK color scheme.
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() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
Invoke creator method.
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.
create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
create(Molecule, Molecule) - Method in interface com.chemaxon.search.CustomMatcherFactory
Creates a custom matcher for atom and bond pairs of the given query and target structures.
create(String) - Static method in class chemaxon.descriptors.MDHypothesisCreator
Creates a hypothesis of the given type.
create(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
Creates a similarity calculator object according to the user defined parameters.
create(String) - Static method in class chemaxon.util.DotfileUtil
Opens a dotfile for writing.
create(String, int, int) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
Creates a similarity calculator object according to the user defined parameters.
create(String, PSymbols) - Static method in class chemaxon.pharmacophore.PMap
Creates a PMap object from a pharmacophore point list string.
create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
CREATE_OR_REPLACE_RESULT_TABLE - Static variable in class chemaxon.jchem.db.JChemSearch
Constant for the generation of result tables.
createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Constructs an elemental analysis from molecular formula.
createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value
createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value
createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value and type
createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value and type
createAromatizedSearcher(AromatizationMethod) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that considers aromatization differences of the input molecule.
createAromatizedSearcher(AromatizationMethod, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher which considers aromatization according to the specified rules and initializes it with the specified search options.
createArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
Creates an array property.
createArrayXSD(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
Creates an array property from the XSD type.
createAtomIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
createAtomNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an iterator to get the atom neighbours of the specified atom.
createBondIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.
createBondNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an iterator to get the bonds connecting to the specified atom.
createBondTable(int, int) - Static method in class chemaxon.core.util.BondTable
Creates a new bond table for a molecule graph with the specified number of atoms and bonds.
createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
 
createChemicalTermsTextPane() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
createChemicalTermsTextPane(boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
createChemicalTermsTextPane(CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(String, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
 
createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument
Creates a ServiceArgument constant based on string value and argument type.
Supported types are String, Integer, Long, Double, Float and Boolean
createDefaultParameterPanel(Class, String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory
 
createDefaultParameterPanel(String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory
Creates default parameter panel based on XML config.
createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph
Creates a dehydrogenized version of the molecule.
createDocumentConverter(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentConverter method instantiates a class which implements the IDocumentConverter interface.
createDocumentOLEConverter(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentOLEConverter method instantiates a class which implements the IDocumentConverter interface.
createDocumentOLEConverter(DocumentType, String, SupportedOLETypes) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentOLEConverter method instantiates a class which implements the IDocumentConverter interface.
createDocumentReader(DocumentType, InputStream) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentReader method instantiates a class which implements the IDocumentReader interface.
createDocumentReader(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentReader method instantiates a class which implements the IDocumentReader interface.
createDocumentTemplateWriter(DocumentType, InputStream, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentWriter method instantiates a class which implements the IDocumentTemplateWriter interface.
createDocumentTemplateWriter(DocumentType, String, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentTemplateWriter method instantiates a class which implements the IDocumentTemplateWriter interface.
createDocumentWriter(DocumentType, InputStream, OutputStream) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentWriter method instantiates a class which implements the IDocumentWriter interface.
createDocumentWriter(DocumentType, OutputStream) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentWriter method instantiates a class which implements the IDocumentWriter interface.
createDocumentWriter(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
The static createDocumentWriter method instantiates a class which implements the IDocumentWriter interface.
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 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.
createFeatureMap(Molecule) - Method in class chemaxon.pharmacophore.PMapper
Creates the feature ID -> atom index BitSet HashMap for the given target molecule.
createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
createGData() - Method in class chemaxon.marvin.space.SurfaceComponent
 
createGearch() - Method in class chemaxon.struc.Molecule
 
createGearch() - Method in class chemaxon.struc.MoleculeGraph
 
createGearch() - Method in class chemaxon.struc.RgMolecule
 
createGearch() - Method in class chemaxon.struc.RxnMolecule
 
createGearch() - Method in class chemaxon.struc.SelectionMolecule
 
createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
CreateGroupAction - Class in chemaxon.standardizer.advancedactions
Create Group standardizer action
CreateGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.CreateGroupAction
Initializes a create group standardizes action
createImage(Buffer, int, int) - Method in class chemaxon.marvin.space.GraphicScene
 
createImageExporterParameter(Properties, String, MDocument) - Static method in class chemaxon.util.ImageExportUtil
Creates the Image Exporter parameter String based on the values in the Properties object.
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 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.
createLabels(MDSet) - Method in class chemaxon.descriptors.MDSimilarityResultWriter
Creates labels.
createLicenseManagerPanel() - Static method in class chemaxon.license.LicenseManager
Creates the main panel which is used for end-user license managing.
createMD(String) - Method in class chemaxon.jchem.db.MDTableHandler
Creates an MolecularDescriptor based on settings stored in the database
createMDSet(String[]) - Method in class chemaxon.jchem.db.MDTableHandler
Creates an MDSet based on settings stored in the database
createMDSetComponent(int, String, String) - Method in class chemaxon.descriptors.MDReader
Creates and sets the given component of the internal MDSet object of the given type and specified parameter settings.
createMDTable(String, String, String, String) - Method in class chemaxon.descriptors.GenerateMD
Creates a database table to store the MolecularDescriptors generated.
createMDTable(String, String, String, String) - Method in class chemaxon.jchem.db.MDTableHandler
Creates a Molecular Descriptor Table.
createMDTable(String, String, String, String, boolean) - Method in class chemaxon.jchem.db.MDTableHandler
Creates a Molecular Descriptor Table.
createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
Deprecated.
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
Creates a target molecule object for import.
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 interface chemaxon.formats.documents.jchemoffice.IMoleculeData
Creates a Molecule content for the MoleculeData
createMolecule() - Method in class chemaxon.struc.Sgroup
Creates a molecule object that contains only this group.
createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Creates a molecule object that contains only one SuperatomSgroup identical to this one.
createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.
createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Creates a MoleculeIterator object for iterating through a molecule array (Molecule[]).
createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Creates a MoleculeIterator object for iterating through collection of molecules (Molecule objects).
createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter
Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.
createNeighbourBonds(Molecule, MolBond, boolean) - Static method in class chemaxon.checkers.StructureCheckerHelper
This method returns a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond
createNew() - Static method in class chemaxon.marvin.calculations.HlbPlugin.Builder
Constructs a new HlbPlugin instance.
createNew(Molecule) - Static method in class chemaxon.marvin.alignment.MCSAlignment.Factory
Constructs a new instance of ConformationAlignment class.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.binary.BvParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Construct a builder for this parameter class, initialized to default.
createNewCell() - Method in class chemaxon.marvin.space.GraphicScene
Sets an empty cell to be the active cell.
createNewReader(String) - Static method in class com.chemaxon.descriptors.db.MDTableReader
Create an MDTableReader from the xml configuration string.
createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
Create a PfTableReader from the xml configuration string.
createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
Create a PfTableReader from the xml configuration string.
createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
Create a PfTableReader from the xml configuration string.
createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
Creates identical attributes for the next section.
createNoCancelObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers
createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
Creates the parameter panel.
createPartialMappingMatcher() - Method in interface com.chemaxon.search.CustomMatcherFactory
 
createPropertyTable(ConnectionHandler) - Static method in class chemaxon.jchem.db.DatabaseProperties
Creates a new property table for storing JChem's settings.
createPropertyTable(ConnectionHandler, int) - Static method in class chemaxon.jchem.db.DatabaseProperties
Creates a new property table for storing JChem's settings.
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.
createReader(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
Generates reader object.
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader.Factory
 
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader.Factory
 
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader.Factory
 
createRecognizer() - Method in class chemaxon.formats.MFileFormat
Creates a recognizer module.
createRecognizer(String) - Method in class chemaxon.formats.MFileFormat
Deprecated.
as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead
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