Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A_ALL - Static variable in class chemaxon.struc.graphics.MTextAttributes

All identifiers.

A_ALL - Static variable in interface chemaxon.struc.Smolecule

Use all atom and bond property arrays.

A_ASTEREO - Static variable in interface chemaxon.struc.Smolecule

Use atom stereo properties arrays, equals Smolecule.A_PARITY|Smolecule.A_CHIRALITY.

A_ATOMMAP - Static variable in interface chemaxon.struc.Smolecule

Use atom type array.

A_BOLD - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font's bold subattribute.

A_BOND - Static variable in interface chemaxon.struc.Smolecule

Use arrays to store bonds.

A_CHARGE - Static variable in interface chemaxon.struc.Smolecule

Use charge array.

A_CHIRALITY - Static variable in interface chemaxon.struc.Smolecule

Chirality.

A_DX - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the x shift attribute.

A_DY - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the y shift attribute.

A_EXPLH - Static variable in interface chemaxon.struc.Smolecule

Use explicit Hydrogen count array.

A_FONT - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font attribute.

A_FONT_BITS - Static variable in class chemaxon.struc.graphics.MTextAttributes

All font bits.

A_FONTFAMILY - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font family subattribute.

A_FONTSIZE - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font size subattribute.

A_FOREGROUND - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the color attribute.

A_HYBRIDIZATION - Static variable in interface chemaxon.struc.Smolecule

Use hybridization state array.

A_IMPLH - Static variable in interface chemaxon.struc.Smolecule

Use implicit Hydrogen count array.

A_ITALIC - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font's italic subattribute.

A_MASSNO - Static variable in interface chemaxon.struc.Smolecule

Use mass number array.

A_PARITY - Static variable in interface chemaxon.struc.Smolecule

Atom parity.

A_RADICAL - Static variable in interface chemaxon.struc.Smolecule

Use radical array.

A_RGROUP - Static variable in interface chemaxon.struc.Smolecule

Use R-group ID array.

A_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font scale attribute.

A_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the subscript/superscript level attribute.

A_VALENCE - Static variable in interface chemaxon.struc.Smolecule

Use valence array.

AAMAP_MASK - Static variable in class chemaxon.struc.MolAtom

Atom map mask in flags.

AAMAP_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom-atom mapping number.

AAMAP_OFF - Static variable in class chemaxon.struc.MolAtom

Atom map offset in flags.

AATOM - Static variable in class chemaxon.jep.context.ReactionContext

ABBREV_GROUPS_KEY - Static variable in class chemaxon.standardizer.actions.AliasToGroupAction

Property Key of the abbreviated group modification

ABBREVGROUP - Static variable in class chemaxon.formats.MFileFormat

Chemaxon SMILES Abbreviated Groups.

AbbrevGroupRecognizer - Class in chemaxon.formats.recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

AbbrevGroupRecognizer() - Constructor for class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated.

ABBREVIATED_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that abbreviated groups had found in the molecule

ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that only contracted abbreviated groups had found in the molecule

ABBREVIATED_GROUP_WITH_ONLY_EXPANDED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that only expanded abbreviated groups had found in the molecule

ABBREVIATED_GROUPS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "abbrevgroups".

ABBREVIATED_GROUPS_ALLOWED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "abbrevgroupsAllowed".

AbbreviatedGroupChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.

AbbreviatedGroupChecker() - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker

Default constructor.

AbbreviatedGroupChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker

Parameterized constructor.

ABS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

Stereogenic centers belonging to ABS represent absolute stereochemistry, i.e.

ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABSENT_CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule is chiral, but flag is not added to the molecule

AbsentChiralFlagChecker - Class in chemaxon.checkers

Detects chiral molecules with no chiral flag defined

AbsentChiralFlagChecker() - Constructor for class chemaxon.checkers.AbsentChiralFlagChecker

Initializes the absent chiral flag error checker

AbsentChiralFlagFixer - Class in chemaxon.fixers

Deprecated, for removal: This API element is subject to removal in a future version.

use AddChiralFlagFixer

AbsentChiralFlagFixer() - Constructor for class chemaxon.fixers.AbsentChiralFlagFixer

Deprecated.

ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "absLabelVisible" or "absLabel".

ABSOLUTE_STEREO_CONFIGURATION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents molecules in which all asymmetric centers have absolute stereo configuration

AbsoluteStereoAction - Class in chemaxon.standardizer.actions

Deprecated, for removal: This API element is subject to removal in a future version.

use SetAbsoluteStereoAction or RemoveAbsoluteStereoAction instead

AbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

Initializes the action with parameters

AbsoluteStereoAction.Type - Enum Class in chemaxon.standardizer.actions

Deprecated.

Type of absolute stereo action

AbsoluteStereoConfigurationChecker - Class in chemaxon.checkers

Detects molecules in which all asymmetric centers have absolute stereo configuration

AbsoluteStereoConfigurationChecker() - Constructor for class chemaxon.checkers.AbsoluteStereoConfigurationChecker

Initializes the absolute stereo configuration checker

AbsoluteStereoFixer - Class in chemaxon.fixers

Deprecated, for removal: This API element is subject to removal in a future version.

use RemoveInvalidChiralFlagFixer

AbsoluteStereoFixer() - Constructor for class chemaxon.fixers.AbsoluteStereoFixer

Deprecated.

AbstractMRecordReader - Class in chemaxon.marvin.io.formats

Abstract record reader class.

AbstractMRecordReader(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader

Constructs an abstract record reader.

AbstractMRecordReader(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader

AbstractSgroupAction - Class in chemaxon.standardizer.actions

Abstract class for standardizer actions modifying S-groups.

AbstractSgroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AbstractSgroupAction

Initializes an abstract s-group action with the exclude list

AbstractStandardizerAction - Class in chemaxon.standardizer

Abstract implementation of the StandardizerAction.

AbstractStandardizerAction(Map<String, String>) - Constructor for class chemaxon.standardizer.AbstractStandardizerAction

Initializes the functionality of the abstract implementation.

AbstractStereoFilter<T extends StereoCenter> - Class in com.chemaxon.calculations.stereoanal.filters

Abstract class for Filter interface.

AbstractStereoFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter

AbstractStructureChecker - Class in chemaxon.checkers

Abstract base class of all functions checking and repairing chemical structures.

AbstractStructureChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AbstractStructureChecker

Constructor to create a Structure checker instance with the given errorType

AbstractStructureFixer - Class in chemaxon.fixers

This class is the default abstract implementation of StructureFixer interface

AbstractStructureFixer() - Constructor for class chemaxon.fixers.AbstractStructureFixer

Constructor to create a Structure fixer

Ac - Static variable in class chemaxon.core.ChemConst

accept(Molecule) - Method in interface chemaxon.util.MolFilter

Returns true if molecule is accepted by the filter.

accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter

accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter

accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter

accept(StereoCenterVisitor) - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter

Accepts visitors.

accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

ACCEPT - Enum constant in enum class chemaxon.marvin.collecting.Consent

ACCEPT_ONLY_SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase

Accepted - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type

Indicates, that the structure checker puts valid or fixed structures to the output file.

ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin

Acceptor sign displayed in GUI.

ACCORD - Static variable in class chemaxon.formats.MFileFormat

ACCORD file format

ACCP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode

Atomic contribution with correction terms.

ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy

ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin

Constant denoting acidic pKa.

ACT_KEY - Static variable in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

Key of type for parsing and property change

actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Action handler.

actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Handles window closing and format choice events.

actionPerformed(ActionEvent) - Method in class chemaxon.marvin.swing.MAction

Sets the action state, performs a custom action, then propagates the event.

ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

action string token of the checker

ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor

action string tokens of the fixer

ACTIONSTRING_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

action string token of the action

ActionStringBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader

An implementation of ConfigurationReader for parsing action strings

ActionStringBasedConfigurationReader(String) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader

Default constructor

ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader

Deprecated.

use ActionStringBasedConfigurationReader(String, CheckerFixerFactory) instead

ActionStringBasedConfigurationReader(String, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader

Constructor with custom checker factory

actionStringToken() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the action string token of the checker

actionStringToken() - Element in annotation interface chemaxon.fixers.FixerInfo

Returns the action string token of the fixer.

actionStringToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the action string tokens of the action as a string, divided by comma characters

add(NameConverter, int) - Static method in class chemaxon.naming.NameConverters

Add a name to structure converter.

add(StandardizerActionFactory.StandardizerClassDescriptor) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder

Adds a standardizer action class descriptor to the factory

add(DPoint3) - Method in class chemaxon.struc.DPoint3

Add the given point to this one.

add(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3

Calculates the sum of the two vectors

add(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Adds an atom to the molecule.

add(MolAtom) - Method in class chemaxon.struc.RgMolecule

Adds an atom to the root structure.

add(MolAtom) - Method in class chemaxon.struc.RxnMolecule

Adds an atom to a reactant, product or agent structure.

add(MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Adds an atom to the molecule.

add(MolAtom) - Method in class chemaxon.struc.Sgroup

Adds a new atom to the S-group.

add(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Adds a new atom to the S-group.

add(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Adds a new atom to the S-group.

add(MolAtom, boolean) - Method in class chemaxon.struc.SelectionMolecule

Adds an atom to the molecule.

add(MolBond) - Method in class chemaxon.struc.MolAtom

Add a bond if it had not been already added.

add(MolBond) - Method in class chemaxon.struc.Molecule

add(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Adds a bond to the molecule.

add(MolBond) - Method in class chemaxon.struc.RgMolecule

Adds a bond to the root structure.

add(MolBond) - Method in class chemaxon.struc.RxnMolecule

Adds a bond to a reactant, product, agent.

add(MolBond) - Method in class chemaxon.struc.SelectionMolecule

Adds a bond to the graph.

add(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom

Add an edge if it had not been already added.

add(MolBond, boolean) - Method in class chemaxon.struc.MoleculeGraph

Add a bond to the molecule.

add(MolBond, boolean) - Method in class chemaxon.struc.SelectionMolecule

Add a bond to the molecule.

add(MolBond, MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom

Add an edge to the given atom of the sgroup, if it had not been already added.

add(MProp) - Method in class chemaxon.struc.prop.MListProp

Adds an element.

add(CheckerFixerFactory.CheckerClassDescriptor) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Adds a checker class descriptor to the factory

add(CheckerFixerFactory.FixerClassDescriptor) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Adds a fixer class descriptor to the factory

add(InputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder

Adds an input stream containing standardizer specifications to be stored by the output factory

add(InputStream) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Adds an input stream containing checker and fixer specifications to be stored by the output factory

add(String) - Method in class chemaxon.checkers.util.AtomLabels

Adds an atom label to the atom labels

add(String, double) - Method in class chemaxon.jep.ConstantTableBuilder

Adds a double constant to this builder.

add(String, Molecule) - Method in class chemaxon.jep.ConstantTableBuilder

Adds a molecule constant to this builder.

add(String, Molecule[]) - Method in class chemaxon.jep.ConstantTableBuilder

Adds a molecule array constant to this builder.

add(String, String) - Method in class chemaxon.jep.ConstantTableBuilder

Adds a string constant to this builder.

add(URL) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder

Adds an input stream containing standardizer specifications to be stored by the output factory

add(URL) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Adds an input stream containing checker and fixer specifications to be stored by the output factory

add(Properties) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder

Adds a property map containing properties of standardizer actions to be stored by the output factory

add(Properties) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Adds a property map containing properties of checkers and fixers to be stored by the output factory

ADD - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Add absolute stereo

ADD_REMOVE_H_ATOMS_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "addRemoveHatomsEnabled".

addAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Adds an action to the configuration

addActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane

Adds an action listener.

addActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions

Adds an action listener.

addActions(List<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Adds actions to the configuration

addActionToGroup(String, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Adds an action to the group

addActionToGroups(Collection<String>, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Adds an action to a list of groups

addAll(ConstantTable) - Method in class chemaxon.jep.ConstantTableBuilder

Adds all constants in the given table to this builder.

addAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes

Adds atoms to the "added atom" list.

addAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes

Adds atoms to the "added atom" list.

addArgument(ServiceArgument<?>) - Method in class chemaxon.marvin.services.ServiceDescriptor

Adds a new argument to the end of the argument list

addAtom(int) - Method in class chemaxon.calculations.nmr.Multiplet

Adds a new atom to this multiplet.

addAtom(MolAtom) - Method in class chemaxon.standardizer.Changes

Adds an atom to the "added atom" list.

addAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes

Adds an atom to the "added atom" list.

addAtom0(MolAtom) - Method in class chemaxon.struc.Molecule

Adds an atom.

addAtom0(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Adds an atom.

addAtom0(MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Adds an atom.

addAtomPair(int, int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Adds an alignment constraint between the reference and aligned molecule.

addAtomPair(int, int, double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Adds an alignment constraint between the reference and aligned molecule.

addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Adds all atoms and bonds to the specified molecule.

addAtomToFragment(MolAtom) - Method in class chemaxon.struc.Molecule

Adds an atom to a fragment.

addAtomToFragment(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Adds an atom to a fragment.

addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RgMolecule

addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule

addAtomWithBonds(MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Adds an atom to the molecule.

addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Adds an atom without setting its parentGraph and index fields.

addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Adds an atom without setting its parentGraph and index fields.

addAttachmentPoint(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Adds a new free attachment point for an atom.

addAttachmentPoint(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Adds a new free attachment point of the given attachment atom and order.

addAttachmentPoint(MolAtom, int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Adds a new free attachment point.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MBracket

Adds the attribute names to the specified list.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MEFlow

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectron

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectronContainer

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MNameTextBox

Adds the attribute names to the specified list.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MPolyline

Adds the attribute names to the specified vector.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRectangle

Adds the attribute names to the specified list.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRoundedRectangle

Adds the attribute names to the specified vector.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox

Adds the attribute names to the specified list.

addAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject

Adds the attribute names to the specified list.

addBond0(MolBond) - Method in class chemaxon.struc.Molecule

Adds a bond.

addBond0(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Adds a bond.

addBond0(MolBond) - Method in class chemaxon.struc.SelectionMolecule

Adds a bond.

addBondWithoutChangingIt(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Adds a bond without setting its parentGraph and index fields.

addBracket(MBracket) - Method in class chemaxon.struc.Sgroup

Adds a bracket to this S-group.

addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox

addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox

Adds attribute names to the specified list.

addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject

Adds attribute names to the specified list.

addCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Adds a central atom to this sgroup.

addChar(char) - Method in class chemaxon.struc.graphics.MTextBox

Adds a character to the text.

addCheckerMark(MDocument.CheckerMark) - Method in class chemaxon.struc.MDocument

Adds a checker mark to the document.

addChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup

Adds a child S-group.

AddChiralFlagFixer - Class in chemaxon.fixers

Absent chiral flag fixer.

AddChiralFlagFixer() - Constructor for class chemaxon.fixers.AddChiralFlagFixer

addComparator(MolComparator) - Method in class chemaxon.sss.search.MolSearch

Add a comparator to the search object.

addComplex() - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Complex number support will be removed without replacement.

addComplexVariable(String, double, double) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Complex number support will be removed without replacement.

addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule

Adds a reactant, product or agent.

addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule

Adds a reactant, product or agent.

addConstraintsFromUserMappedAtoms() - Method in class chemaxon.marvin.alignment.Alignment

An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.

addCouplingConstants(double[]) - Method in class chemaxon.calculations.nmr.Multiplet

Adds a new coupling constant array.

addCrossingBonds(List<MolBond>, List<MolBond>) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the crossing bonds (head and tail) of a ladder-type polymer.

addData(Molecule, MolAtom, String, String) - Method in class chemaxon.marvin.io.MolExportModule

Adds a data sgroup to the given atom in the given molecule with fieldName and value.

addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Adds a line to the data stored in the field.

addDihedralStep(DihedralScanStep) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult

Add a new step.

addError(Exception) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.

addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:

             Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
             

addExplicitHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:

             Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
             

AddExplicitHydrogensAction - Class in chemaxon.standardizer.actions

Hydrogenization standardizer action

AddExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AddExplicitHydrogensAction

Initializes the action

addExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]).
Usage:

             Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
             

addFunction(String, PostfixMathCommandI) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The function table will not be modifiable anymore. No replacement.

addGroup(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Adds a group definition to the group list of the action

addGroup(String) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Adds a group to the list defined by its abbreviation

addHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertImplicitHToExplicit(MoleculeGraph) instead

addHAtoms(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead

addHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.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.

addHyperlinkListener(JEditorPane) - Static method in class chemaxon.marvin.util.SwingUtil

Adds HTML link handling to an editor pane.

addInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil

Adds the Standardizer tasks specified in the configuration parameter to the inactive tasks list.

addInput(File, String) - Method in class chemaxon.formats.MolConverter.Builder

Adds an input file.

addInput(File, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Builder

Adds an input stream.

addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

addInput(String, String) - Method in class chemaxon.formats.MolConverter.Builder

Adds an input file.

addInput(String, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

addInputChecker(TaggedCalculatorInputChecker) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Adds the specified input checker to this plugin.

addItemListener(ItemListener) - Method in class com.chemaxon.calculations.gui.MChart

addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a label component inside the MarvinView table.

addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a label component inside the MarvinView table.

addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MTextBox

addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage

Adds a listener if it is not yet added.

addLonePairs(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) instead

addMatch(int[], int[], int) - Method in class chemaxon.sss.search.MolSearch

addMatch(int[], int[], int) - Method in class chemaxon.sss.search.Search

Specifies extra prerequisites of the structure search that queryAtoms[0] must match to targetAtoms[0] only AND queryAtoms[1] must match to targetAtoms[1], etc.

addMatch(int, int) - Method in class chemaxon.sss.search.MolSearch

Adds a fixed matching between the given query and target atoms.

addMatch(int, int) - Method in interface com.chemaxon.search.SimpleSearcher

Adds a fixed matching between the given query and target atoms.

addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane

Adds a menubar change listener.

addMolecule(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a molecule viewer component inside the MarvinView table.

addMolecule(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a molecule viewer component inside the MarvinView table.

addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment

Add molecule to align

addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.Alignment

User may define extra weights between colors defined at setColoringScheme.

addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

addNodeColorWeight(int, int, double) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

addNotify(MDocument) - Method in class chemaxon.struc.graphics.MElectronContainer

addNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint

Point added to a document.

addNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint

Point added to a document.

addNotify(MDocument) - Method in class chemaxon.struc.MObject

Called when the object is added to a document.

addNumbering - Variable in class chemaxon.marvin.io.MolExportModule

Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.

addObject(MObject) - Method in class chemaxon.struc.MDocument

Adds an object to the document.

addObject(MObject) - Method in class chemaxon.struc.MSelectionDocument

Adds an object to the document.

addOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings

Adds an owner, that should be notified about the changes in the properties.

addParameters(File) - Method in class chemaxon.descriptors.MDParameters

Sets parameters from an XML config file keeping all previous settings.

addParameters(String) - Method in class chemaxon.descriptors.MDParameters

Sets parameters from an XML string representation keeping all previous settings.

addParametrizedMetric(String, String, String) - Method in class chemaxon.descriptors.MDParameters

Expands the set of parametrized metrics with a new item.

addParametrizedMetricNode(String, String, String) - Method in class chemaxon.descriptors.MDParameters

Adds a ParametrizedMetric node to the DOM tree.

addParametrizedMetricsNode() - Method in class chemaxon.descriptors.MDParameters

Adds the ParametrizedMetrics node to the DOM tree.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker

addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner

Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class

addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker

Add a PropertyChangeListener to the listener list.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Add a PropertyChangeListener to the listener list.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor

Add a PropertyChangeListener to the listener list.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings

Add a property change listener

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class

addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction

Add a PropertyChangeListener to the listener list.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Add a PropertyChangeListener to the listener list.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker

addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner

Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed

addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker

Add a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Add a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor

Add a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MSketchPane

Adds a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MViewPane

Adds a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed

addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction

Add a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Add a PropertyChangeListener for a specific property.

addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Adds an atom to the list of paradigmatic repeating unit atoms.

addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule

Adds an R-group member.

addRgroupAttachmentPoint(int, int) - Method in class chemaxon.struc.MolAtom

Attaches a new R-group attachment point to this atom by a bond of a specified type.

addRgroupBridgeMember(RgroupBridgeId, Molecule) - Method in class chemaxon.struc.RgMolecule

Adds a definition member to an R-group bridge.

addRGroupsInPlaceOfImplHs(Molecule) - Static method in class chemaxon.sss.search.RGroupDecomposition

Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s.

addRGroupsInPlaceOfImplHs(Molecule, int) - Static method in class chemaxon.sss.search.RGroupDecomposition

Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s.

addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule

Creates an RgMolecule containing R-groups of this object from the 'simplified molecule' object made of 'm'.

addSalt(String, Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Adds a salt to the salt list of the action

addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.Molecule

Adds an S-group to this object.

addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule

Adds an S-group to this object.

addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule

Adds an S-group to this object.

addSgroupClones(Molecule, Molecule, Molecule) - Method in class chemaxon.struc.Molecule

Adds the S-groups of a child molecule clone to the new parent molecule clone.

addSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule

Adds S-groups to this object and its parent.

addSimpleAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Adds a non-SgroupAtom atom without setting its parentGraph and index fields.

addSolvent(String, Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Adds a solvent to the solvent list of the action

addStandardConstants() - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.

addStandardFunctions() - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

These functions will be removed without replacement.

addStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Changes terminal carbon atoms to star atoms (*).

addString(String) - Method in class chemaxon.struc.graphics.MTextBox

Adds a string to the text.

addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters

Add a thread-local name to structure converter.

addTo(Container) - Method in class chemaxon.marvin.swing.MAction

Add menu item to the specified menu.

addTo(Container, int) - Method in class chemaxon.marvin.swing.MAction

Add menu item to the specified menu.

addTo(Container, int, Object) - Method in class chemaxon.marvin.swing.MAction

Add menu item to the specified menu.

addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

Not used.

addToSelection(MDocument, MSelectionDocument) - Static method in class chemaxon.struc.NoStructure

Adds the selected NoStrutures from the document to the selectionDocument

addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings

Add an element to marvinsketch's recent file list

addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings

Add an element to marvinview's recent file list

addUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions

Adds the given user-defined comparator to the search.

addUserConstraint(int, int, int, int) - Method in class chemaxon.marvin.alignment.Alignment

Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.

addVariable(String, double) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.

addVariableAsObject(String, Object) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.

adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph

Checks whether the molecule has multiple chiral centres

adjustTautomerizationPlugin(TautomerizationPlugin) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

AdvancedCheckerRunner - Class in chemaxon.checkers.runner

CheckerRunner implementation with advanced fixing capabilities.
StructureFixer selection is based on provided fixer class if available, or falls back to StructureCheckerResult based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts.

AdvancedCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner

Constructs CheckerRunner with more advanced fixing capabilities.

affectsPerformance() - Method in enum class chemaxon.calculator.CalculatorTag

Returns whether the presence of this tag affects the performance of the calculator.

Ag - Static variable in class chemaxon.core.ChemConst

AGENT - Static variable in class chemaxon.jep.context.ReactionContext

AGENTS - Static variable in class chemaxon.struc.RxnMolecule

"Agent" structure type.

Al - Static variable in class chemaxon.core.ChemConst

alias - Variable in class chemaxon.marvin.services.ServiceArgument

the alias of the argument

alias() - Element in annotation interface chemaxon.checkers.Persistent

Returns the alias name of the annotated property

ALIAS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that alias values had found in the molecule

ALIAS - Static variable in class chemaxon.marvin.services.ServiceDescriptor

Property key for Service alias as String

ALIAS_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that alias value that could be converted to an element had found in the molecule

ALIAS_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that alias value that could be converted to an abbreviated group had found in the molecule

ALIAS_NONE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that alias value had found in the molecule

AliasChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting atoms with alias labels.

AliasChecker() - Constructor for class chemaxon.checkers.AliasChecker

Default constructor.

AliasToAtomAction - Class in chemaxon.standardizer.actions

Alias to Atom standardizer action.

AliasToAtomAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToAtomAction

Initializes the action

AliasToGroupAction - Class in chemaxon.standardizer.actions

Alias to Group standardizer action

AliasToGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToGroupAction

Initializes the action with parameters

align() - Method in class chemaxon.marvin.alignment.Alignment

3D alignment on two or more molecules.

align() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

align() - Method in class chemaxon.marvin.alignment.AlignRigidEasy

does a simple one-to-one atom mappin and aligns.

align() - Method in class chemaxon.marvin.alignment.MolAligner

Executes the best alignment based on hit map provided earlier

align(int[]) - Method in class chemaxon.marvin.alignment.MolAligner

Calculates and performs the best alignment possible specified by the hit map array.

align(int[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy

Rigid alignment on the user defined atom index

align(Molecule) - Method in interface chemaxon.marvin.alignment.MCSAlignment

Align the given molecule to the reference.

align(Molecule, Molecule, int[]) - Static method in class chemaxon.marvin.alignment.MolAligner

Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.

align(Molecule, Molecule, int[][]) - Static method in class chemaxon.marvin.alignment.MolAligner

Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.

ALIGN_AS_IS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType

ALIGN_BOTTOM - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to bottom of box.

ALIGN_CENTER - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to center of box.

ALIGN_LEFT - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to left edge of box.

ALIGN_RIGHT - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to right edge of box.

ALIGN_TOP - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to top of box.

Alignment - Class in chemaxon.marvin.alignment

3D Alignment aligns two or more 3D molecules onto each other.

Alignment() - Constructor for class chemaxon.marvin.alignment.Alignment

Alignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.Alignment

ALIGNMENT - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation

AlignmentAccuracyMode - Enum Class in chemaxon.marvin.alignment

Settings for the representation of a molecular shape.

AlignmentException - Exception in chemaxon.marvin.alignment

AlignmentException() - Constructor for exception chemaxon.marvin.alignment.AlignmentException

AlignmentException(String) - Constructor for exception chemaxon.marvin.alignment.AlignmentException

AlignmentException(Throwable) - Constructor for exception chemaxon.marvin.alignment.AlignmentException

AlignmentMolecule - Class in chemaxon.marvin.alignment

AlignmentMoleculeFactory - Class in chemaxon.marvin.alignment

Creates an AlignmentMolecule form a Molecule based on the settings.

AlignmentMoleculeFactory() - Constructor for class chemaxon.marvin.alignment.AlignmentMoleculeFactory

AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.marvin.alignment

AlignmentPlugin - Class in chemaxon.marvin.calculations

Plugin layer for the AlignmentAPI

AlignmentPlugin() - Constructor for class chemaxon.marvin.calculations.AlignmentPlugin

AlignmentProperties - Enum Class in chemaxon.marvin.alignment

AlignmentProperties.ColoringScheme - Enum Class in chemaxon.marvin.alignment

AlignmentProperties.ColorNotSpecifiedCase - Enum Class in chemaxon.marvin.alignment

AlignmentProperties.DegreeOfFreedomType - Enum Class in chemaxon.marvin.alignment

AlignmentProperties.FlexibilityMode - Enum Class in chemaxon.marvin.alignment

Conformational flexibility treatment during the alignment for a pair of a molecule.

AlignmentProperties.NodeType - Enum Class in chemaxon.marvin.alignment

AlignmentProperties.OrientationType - Enum Class in chemaxon.marvin.alignment

AlignOnPairedAtoms - Class in chemaxon.marvin.alignment

Overlays two molecules using the user defined atom pairs
Example:

AlignOnPairedAtoms() - Constructor for class chemaxon.marvin.alignment.AlignOnPairedAtoms

AlignRigidEasy - Class in chemaxon.marvin.alignment

Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.

AlignRigidEasy() - Constructor for class chemaxon.marvin.alignment.AlignRigidEasy

ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aliphatic query atom.

ALIPHATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

aliphaticAtomCount() - Method in class chemaxon.calculations.Ring

Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.

aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aliphaticAtomCount()

aliphaticBondCount() - Method in class chemaxon.calculations.Ring

Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.

aliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aliphaticBondCount()

aliphaticRingCount() - Method in class chemaxon.calculations.Ring

Calculates the number of aliphatic ring systems of the molecule.

aliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aliphaticRingCount()

aliphaticRingCount(int) - Method in class chemaxon.calculations.Ring

Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.

aliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aliphaticRingCount(int)

aliphaticRings() - Method in class chemaxon.calculations.Ring

Identifies the aliphatic rings in the molecule.

aliphaticRings() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aliphaticRings()

aliphaticRings(int) - Method in class chemaxon.calculations.Ring

Identifies aliphatic rings in the molecule having a given size (number of atoms).

aliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aliphaticRings(int)

ALL - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption

All atoms can have translation.

ALL - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

ALL_H - Static variable in class chemaxon.struc.MolAtom

Include any Hydrogen atom.

ALL_MATCH_AMBIG - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

Ambiguous aromatic parts of the target Markush structure can be matched by aliphatic and aromatic forms as well.

ALL_PERM - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType

allringsystems - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

allStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

All stereo centers of molecule.

allStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

All stereo centers with attached data.

Am - Static variable in class chemaxon.core.ChemConst

AMBIGUOUS - Enum constant in enum class com.chemaxon.search.AromatizationMethod

Aromatization for ambiguous 5-membered rings.

AMBIGUOUS - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer

AMBIGUOUS_AROMATIC_ATOMS_IGNORED - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.DEFAULT.
Usage:

             molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             

AMINOACID - Enum constant in enum class chemaxon.struc.SgroupType

AMINOACID_BOND_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "aminoAcidBondColoringEnabled".

ANCHOR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

AND - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

Stereogenic centers belonging to an ANDn group (e.g.

AND - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

AND_OR - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter

Set of enhanced stereo flags.

ANGLE_STEP - Static variable in class chemaxon.struc.MolAtom

angle2D(double, double) - Method in class chemaxon.struc.DPoint3

Calculates the absolute angle in the XY plane of the vector pointing from this point to the other point.

angle3D(DPoint3) - Method in class chemaxon.struc.DPoint3

Calculate the angle of two vectors (this and p) in the range 0.0 through pi.

ANIMATE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "animate".

ANIMATION_DELAY - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "animDelay".

ANIMATION_FPS - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "animFPS".

ANIMATION_SYNCHRONIZATION - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "animSync".

ANTI - Static variable in interface chemaxon.struc.StereoConstants

Non-CIP stereodescriptor, anti (relative configuration).

ANY - Enum constant in enum class chemaxon.struc.BondType

Any bond type.

ANY - Enum constant in enum class chemaxon.struc.SgroupType

ANY - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the any atom A.

ANY - Static variable in class chemaxon.struc.MolBond

Any bond type.

ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants

anyBooleanPropertyTrue(Map<String, String>, String...) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Check the given map, whether there is a String 'true' (case in-sensitive) value for any of the given keys

append(Changes) - Method in class chemaxon.standardizer.Changes

Appends a set of changes to the already existing changes.

append(String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument

Append text to end of document.

appendChars(int, char) - Method in class chemaxon.marvin.io.MolExportModule

Append a character n times to the string buffer.

appendLeft(String, int) - Method in class chemaxon.marvin.io.MolExportModule

Append a string to the buffer in %-ns format.

appendLine(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Appends line to string buffer with closing '\n' character.

appendLines(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Appends lines to string buffer with closing '\n' character if it is not yet present.

appendMEnd() - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Appends the "M END" line to the string buffer.

appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.MDParameters

Extends internal data with a new parametrized metric.

appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.PFParameters

appendpHText(String) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Appends the pH text.

appendRight(int, int, char) - Method in class chemaxon.marvin.io.MolExportModule

Append an integer to the buffer in the right hand side of an n-characters wide field.

appendRight(String, int, char) - Method in class chemaxon.marvin.io.MolExportModule

Append a string to the buffer in the right hand side of an n-characters wide field.

apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker

apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculator.TaggedCalculatorInputChecker

Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.

apply(Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker

Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.

applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane

Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.

applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane

Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.

Ar - Static variable in class chemaxon.core.ChemConst

ARC_BRACES - Static variable in class chemaxon.struc.graphics.MBracket

The default arc angle of the Braces Rectangle in degrees.

ARC_ROUND - Static variable in class chemaxon.struc.graphics.MBracket

The default arc angle of the Rounded Rectangle in degrees.

areAttachmentPointsVisible() - Method in class chemaxon.marvin.MolPrinter

Gets the attachment points visibility.

areChildSgroupsVisible() - Method in class chemaxon.struc.Sgroup

Checks whether the child S-groups are visible.

areChildSgroupsVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Checks whether the child S-groups are visible.

areMonomersTransformed() - Method in class chemaxon.sss.search.SearchOptions

Obtain monomer transformation information.

areNeighbors(int, int) - Method in interface chemaxon.struc.Smolecule

Tests whether two atoms are connected.

arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane

Are popup menus enabled?

ArgumentException - Exception in chemaxon.common.util

Checked exception to indicate that a tool has been passed an illegal argument, typically used for CLI.

ArgumentException() - Constructor for exception chemaxon.common.util.ArgumentException

Creates a new instance of ArgumentException without detail message.

ArgumentException(String) - Constructor for exception chemaxon.common.util.ArgumentException

Constructs an instance of ArgumentException with the specified detail message.

ARGUMENTS - Static variable in class chemaxon.marvin.services.ServiceDescriptor

Property key for Arguments as an Unmodifiable List

ARO_R - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction

Number of aromatic rings.

AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph

Aromatization type for ambiguous 5-membered rings.

AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph

Basic aromatization.

AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph

Huckel aromatization.

AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph

General (Daylight conform) aromatization.

AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph

Loose aromatization.

AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph

Substructure aromatization.

AROMATIC - Enum constant in enum class chemaxon.struc.BondType

Aromatic bond type.

AROMATIC - Static variable in class chemaxon.struc.MolAtom

Aromatic query atom.

AROMATIC - Static variable in class chemaxon.struc.MolBond

Aromatic bond type.

AROMATIC_ATOM - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aromatic or aliphatic query atom.

AROMATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

aromaticAtomCount() - Method in class chemaxon.calculations.Ring

Calculates the number of all aromatic atoms in the molecule.

aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aromaticAtomCount()

aromaticBondCount() - Method in class chemaxon.calculations.Ring

Calculates the number of all aromatic bonds in the molecule.

aromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aromaticBondCount()

AROMATICITY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that aromaticity problem had found in the molecule

AromaticityCheckerResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult for identifying aromaticity problems, thus errorType property is StructureCheckerErrorType.AROMATICITY

AromaticityCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AromaticityCheckerResult

Constructor which initialize all the properties.

AromaticityErrorChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting aromatization problems.

AromaticityErrorChecker() - Constructor for class chemaxon.checkers.AromaticityErrorChecker

Default constructor.

AromaticityErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AromaticityErrorChecker

Parameterized constructor.

aromaticRingCount() - Method in class chemaxon.calculations.Ring

Calculates the number of all aromatic ring systems in the molecule (SSSR).

aromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aromaticRingCount()

aromaticRingCount(int) - Method in class chemaxon.calculations.Ring

Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.

aromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aromaticRingCount(int)

aromaticRings() - Method in class chemaxon.calculations.Ring

Identifies the aromatic rings in the molecule.

aromaticRings() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aromaticRings()

aromaticRings(int) - Method in class chemaxon.calculations.Ring

Indentifies aromatic rings in the molecule having a given size (number of rings).

aromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.aromaticRings(int)

aromatization(GeneralExportOptions.AromatizationMethod) - Method in class chemaxon.formats.GeneralExportOptions.Builder

Sets the aromatization method.

AROMATIZATION_AMBIG - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Ambiguous aromatizatization.

AROMATIZATION_BASIC - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Aromatization using the basic method.

AROMATIZATION_GENERAL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Aromatization using the general method.

AROMATIZATION_LOOSE - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Aromatization using the loose method.

AromatizationMethod - Enum Class in com.chemaxon.search

Enum for aromatization methods used during the search process.

aromatize - Variable in class chemaxon.marvin.io.MolExportModule

Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, etc, dearomatize if -1, do nothing if 0.

aromatize() - Method in class chemaxon.struc.MoleculeGraph

Aromatize molecule using the default general aromatization method.

aromatize(boolean) - Method in class chemaxon.struc.MoleculeGraph

Aromatize (using the default general aromatization method) or dearomatize molecule.

aromatize(int) - Method in class chemaxon.struc.Molecule

Aromatizes molecule.

aromatize(int) - Method in class chemaxon.struc.MoleculeGraph

Aromatizes molecule.

aromatize(int) - Method in class chemaxon.struc.RgMolecule

Aromatizes molecule.

aromatize(int, boolean) - Method in class chemaxon.struc.Molecule

Aromatizes molecule.

aromatize(int, boolean) - Method in class chemaxon.struc.MoleculeGraph

Aromatizes molecule.

aromatize(int, boolean) - Method in class chemaxon.struc.RgMolecule

Aromatizes molecule.

aromatize(int, String, boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Aromatize or dearomatize molecule in the specified cell.

AromatizeAction - Class in chemaxon.standardizer.actions

Aromatization standardizer action

AromatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AromatizeAction

Initializes the action with parameters

AromatizeAction.Type - Enum Class in chemaxon.standardizer.actions

Type of aromatization

aromatizeAll(boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Aromatize or dearomatize molecules in all cells.

Aromatizer - Enum Class in com.chemaxon.search.transformation.transformers

Aromatizer transformer.

arrangeComponents() - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean).
Usage:

             CleanUtil.arrangeComponents(molecule, true, true);
             

arrangeComponents(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Arranges molecule components (reactants, agents, products, R-group definitions) nicely.

arrangeComponents(MoleculeGraph, boolean) - Static method in class chemaxon.marvin.util.CleanUtil

Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.

arrangeComponents(MoleculeGraph, boolean, boolean) - Static method in class chemaxon.marvin.util.CleanUtil

Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.

arrangeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Arrange data attached to DataSgroup.

arrangeHydrogenIncerments(Molecule, int, String, double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

arrangeMolecules(MoleculeGraph[], int, int) - Static method in class chemaxon.marvin.util.CleanUtil

Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice.

arrangeReaction(RxnMolecule) - Static method in class chemaxon.marvin.util.CleanUtil

Arranges reaction components nicely

arrangeRelativeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Arrange data attached to DataSgroup.

arrangeSgBrackets(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Arrange sgroup brackets in the molecule.

ArrayMDocSource - Class in chemaxon.marvin.io

MDocSource implementation for an array of documents or molecules.

ArrayMDocSource(MDocument[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource

Creates a document source for an array of documents.

ArrayMDocSource(Molecule[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource

Creates a document source for an array of molecules.

ArrayMDocSource(List<?>) - Constructor for class chemaxon.marvin.io.ArrayMDocSource

Creates a document source for a list of documents or molecules.

ARROW_BACK_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Arrow points back.

ARROW_CROSSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Crossed arrow flag.

ARROW_CURVED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Curved arrow flag.

ARROW_DASHED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Dashed arrow flag.

ARROW_EQUILIBRIUM_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Equilibrium arrow flag.

ARROW_GROUP1_MASK - Static variable in class chemaxon.struc.graphics.MPolyline

Mask for the equilibrium and retrosynthetic arrow flags.

ARROW_GROUP2_MASK - Static variable in class chemaxon.struc.graphics.MPolyline

Mask for the curved, dashed and crosed arrow flags.

ARROW_HALF_LEFT - Static variable in class chemaxon.struc.graphics.MPolyline

Only the left half of the arrow head is drawn.

ARROW_HALF_MASK - Static variable in class chemaxon.struc.graphics.MPolyline

Unshifted mask of the half arrow option bits in flags.

ARROW_HALF_RIGHT - Static variable in class chemaxon.struc.graphics.MPolyline

Only the right half of the arrow head is drawn.

ARROW_RETROSYNTHETIC_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Retrosynthetic arrow flag.

arrowFlags - Variable in class chemaxon.struc.graphics.MPolyline

Arrow flags.

As - Static variable in class chemaxon.core.ChemConst

ASK - Enum constant in enum class chemaxon.checkers.FixMode

on problem requests user interaction

asProperties(String) - Method in class chemaxon.marvin.common.UserSettings

asSet() - Method in enum class chemaxon.calculator.CalculatorTag

Returns a cached set that contains this element only.

asymmetricAtomCount() - Method in class chemaxon.calculations.stereo.Stereochemistry

Calculates the number of atoms having four different ligands.

asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.asymmetricAtomCount()

asymmetricAtoms() - Method in class chemaxon.calculations.stereo.Stereochemistry

Retrieves the indexes of atom having four different ligands.

asymmetricAtoms() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.asymmetricAtoms()

asymmetricEuclidean(float[], float[], double) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric Euclidean distance.

asymmetricEuclidean(int[], int[], double) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric Euclidean distance.

asymmetricNormalizedEuclidean(float[], float[], double) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric normalized Euclidean distance.

asymmetricNormalizedEuclidean(int[], int[], double) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric normalized Euclidean distance.

asymmetricTanimoto(float[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric Tanimoto dissimilarity for floating point values.

asymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric Tanimoto dissimilarity for floating point values.

asymmetricXYZSum - Variable in class chemaxon.descriptors.PFParameters

Stores last calculatred asymmetric Tanimoto sum.

asymmetryFactors - Variable in class chemaxon.descriptors.MDParameters

asymmetry ratio of parametrized asymmetric metrics

AsyncCallback<T> - Interface in chemaxon.marvin.services

Callback interface for asynchronous service calls

At - Static variable in class chemaxon.core.ChemConst

atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

The atom whose the neighbours are processed.

ATOM - Static variable in class chemaxon.jep.context.AtomContext

ATOM - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Calculation domain type: calculation refers to atoms.

ATOM_ATOM_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants

This String represents the key of cloned atom, original atom map

ATOM_COUNT - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "atomcount".

ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomFont".

ATOM_FONT_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomFontSize".

ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom maps had found in the molecule

ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomMappingVisible".

ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomNumberingType".

ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Deprecated.

in 6.2.0 use atomNumberingType parameter instead.

ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomPropertiesVisible".

ATOM_QUERY_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing that an atom has a query property set.

ATOM_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "atomSet".

ATOM_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomSetColor".

ATOM_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomsize".

ATOM_STRINGS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "atomStrings".

ATOM_SYMBOL_VISIBLE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants

ATOM_SYMBOLS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "atomSymbolsVisible".

ATOM_TYPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom with the specified symbol had found in the molecule

ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom

Number of atom types in the elements array

ATOM_TYPE_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom number.

ATOM_TYPES - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme

ATOM_VALUE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom values had found in the molecule

atomChanged(MolAtom) - Method in interface chemaxon.calculations.clean.AtomChangeEventListener

AtomChangeEventListener - Interface in chemaxon.calculations.clean

AtomChecker - Class in chemaxon.checkers

Descendants of the abstract AtomChecker class check every atom for a specific error or property.

AtomChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomChecker

Constructor to create a Structure checker instance with the given errorType.

AtomContext - Class in chemaxon.jep.context

Expression evaluation context containing an input molecule and an input atom.

AtomContext() - Constructor for class chemaxon.jep.context.AtomContext

Constructor.

atomCount - Variable in class chemaxon.struc.MoleculeGraph

The number of atoms.

atomCount() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the number of atoms in the molecule.

atomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of atoms in the molecule including implicit hydrogens.

atomCount() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the number of atoms in the molecule.

atomCount(int) - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the number of atoms of a given element in the molecule (including its isotopes).

atomCount(int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the number of atoms of a given element in the molecule (including its isotopes).

atomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the number of atoms of a given element in the molecule.

atomCount(int, int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the number of atoms of a given element in the molecule.

ATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

Atom count of the molecule

AtomIndexMapper - Interface in com.chemaxon.search.transformation

Atom index mapper.

AtomIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomIterator

Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.

AtomLabels - Class in chemaxon.checkers.util

The atom labels storage class.

AtomLabels() - Constructor for class chemaxon.checkers.util.AtomLabels

Initializes the atom labels

ATOMLIST - Static variable in class chemaxon.sss.search.MarkushFeature

Deprecated.

Expansion type: atom list.

AtomMapChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atom maps.

AtomMapChecker() - Constructor for class chemaxon.checkers.AtomMapChecker

Default constructor

atomMapMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether atom map numbers should be considered in search.

atomMapping() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult

Array of atom - atom mapping.

AtomNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator

Constructs an iterator to process the atoms connecting to the specified atom according to the atom and bond related behavior of this factory.

AtomProperty - Class in chemaxon.struc

Class for storing atom property enumerations.

AtomProperty() - Constructor for class chemaxon.struc.AtomProperty

AtomProperty.Radical - Enum Class in chemaxon.struc

Enumeration of the supported radicals.

AtomQueryPropertyChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atoms having an query property set.

AtomQueryPropertyChecker() - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker

Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.

AtomQueryPropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker

Creates a new AtomQueryPropertyChecker instance to detect the given query properties.

AtomQueryPropertyCheckerResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult for identifying atom query properties, thus errorType property is StructureCheckerErrorType.ATOM_QUERY_PROPERTY by default.

AtomQueryPropertyCheckerResult(StructureChecker, List<MolAtom>, Molecule, String, List<String>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AtomQueryPropertyCheckerResult

Constructor which initialize all the properties.

atoms() - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence

Returns list for the atom references in the molecule.

atoms() - Method in class chemaxon.struc.MoleculeGraph

Provides an unmodifiable list view of the atoms in the molecule.

AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters

Selection which contains atom indexes.

AtomSelection(List<Integer>, List<Integer>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Constructs an AtomSelection from lists.

atomSet - Variable in class chemaxon.struc.Sgroup

Set for storing the atoms of the s-group's graph.

ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants

Either stereo atom type.

ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants

Stereo atom type mask.

ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants

No stereo atom type specified.

ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants

Specific stereo atom type.

AtomTypeChecker - Class in chemaxon.checkers

A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.

AtomTypeChecker() - Constructor for class chemaxon.checkers.AtomTypeChecker

Default constructor.

AtomTypeChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomTypeChecker

Parameterized constructor providing the possibility for descendants to initialize with their own error type.

AtomTypeChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomTypeChecker

Parameterized constructor.

atomTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether atom types should be considered in search.

AtomValueChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atoms with atom value.

AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker

Default constructor.

ATROP - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType

ATROP - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type

Atrop stereo center.

AtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop

Filter for atrop stereo centers.

AtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter

ATROPISOMER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atropisomers are found in the molecule

AtropisomerChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting atropisomers in the molecule.

AtropisomerChecker() - Constructor for class chemaxon.checkers.AtropisomerChecker

Initializes the atropisomer structure checker

AtropIsomerDetector - Class in chemaxon.marvin.alignment

Molecular mechanics based atropisomer detection.

AtropIsomerDetector() - Constructor for class chemaxon.marvin.alignment.AtropIsomerDetector

AtropIsomerDetector.Accuracy - Enum Class in chemaxon.marvin.alignment

AtropStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters

Atrop stereo center implementation.

AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter

Constructs a new instance of axial stereo center.

AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter

Constructs a new instance of axial stereo center with attached data.

AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by AtropStereoCenter(AtomSelection, AtropStereoIUPACValue).

AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by AtropStereoCenter(AtomSelection, AtropStereoIUPACValue, List).

atropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the atrop stereocenters.

atropStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the atrop stereocenters with attached data.

AtropStereoDescriptor - Class in chemaxon.struc

Descriptor representing atrop stereo information, the rotation of two aromatic rings connected by a single bond (axis), and at least 3 of the ligands in the ring connected to the axis has a non-ring ligand. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.ODD means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.EVEN means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is counter-clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.UNKNOWN means that it can not be decided if it is clockwise or counter-clockwise, but there is no wiggly bond - like a 2D structure without wedge information.. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.WIGGLY means that there is a wiggly bond on either ligand in the ring connected to the axis, or the axis is wiggly.

AtropStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AtropStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AtropStereoDescriptor

ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom

S-group attachment point on first and second site.

ATTACH_NONE - Static variable in class chemaxon.struc.MolAtom

There is no S-group attachment point setting on this atom.

ATTACH_UNKNOWN - Static variable in class chemaxon.struc.MolAtom

S-group attachment point information

ATTACH1 - Static variable in class chemaxon.struc.MolAtom

S-group attachment point on first site.

ATTACH2 - Static variable in class chemaxon.struc.MolAtom

S-group attachment point on second site.

ATTACHED_DATA - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that attached data had found in the molecule

ATTACHED_DATA_MATCH_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for exact match of attached data.

ATTACHED_DATA_MATCH_GENERAL - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for general match of attached data.

ATTACHED_DATA_MATCH_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for ignoring attached data.

AttachedData - Class in com.chemaxon.calculations.stereoanal.stereocenters

Data object which contains a name and a data (String).

AttachedData(String, String) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData

Creates an AttachedData class.

AttachedDataChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting attached data in the molecule.

AttachedDataChecker() - Constructor for class chemaxon.checkers.AttachedDataChecker

Default constructor.

AttachedDataChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AttachedDataChecker

Parameterized constructor.

ATTACHMENT_ATOM - Static variable in interface chemaxon.sss.SearchConstants

Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.

ATTACHMENT_LABEL - Static variable in interface chemaxon.sss.SearchConstants

Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...

ATTACHMENT_MAP - Static variable in interface chemaxon.sss.SearchConstants

Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int).

ATTACHMENT_NONE - Static variable in interface chemaxon.sss.SearchConstants

Constant for attachment point representation in ligands: none (no attachment point data).

ATTACHMENT_POINT - Static variable in interface chemaxon.sss.SearchConstants

Constant for attachment point representation in ligands: R-group attachment.

ATTACHMENT_RLABEL - Static variable in interface chemaxon.sss.SearchConstants

Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String).

AttachmentPoint - Class in chemaxon.struc.sgroup

Attachment Point class for the Superatom S-group.

AttachmentPoint(MolAtom, int, MolBond) - Constructor for class chemaxon.struc.sgroup.AttachmentPoint

Constructs an AttachmentPoint object

Au - Static variable in class chemaxon.core.ChemConst

AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Automatic check for structures.

AUTO_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "autoscale".

AUTO_TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "autoTabScale".

AUTO_UNGROUP - Static variable in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

AutoMapper - Class in com.chemaxon.mapper

AutoMapper is a tool that performs automated chemical reaction mapping.

AutoMapper() - Constructor for class com.chemaxon.mapper.AutoMapper

Initializes an AutoMapper object

AutoMapper.Options - Class in com.chemaxon.mapper

Option object for set common options when mapping called by static way.

AUTOMATIC_FOG_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "automaticFogEnabled".

AUTOMATIC_REACTION_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "automaticReactionEnabled".

AUTORM - Static variable in class chemaxon.marvin.swing.MAction

Remove menu items automatically when the menu becomes invisible.

AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat

Image object (java.awt.Image).

AXIAL - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType

AXIAL - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type

Axial stereo center (eg.

AxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial

Filter for axial stereo centers.

AxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter

AxialStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters

Axial stereo center implementation.

AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter

Constructs a new instance of axial stereo center.

AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter

Constructs a new instance of axial stereo center with attached data.

AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by AxialStereoCenter(AtomSelection, AxialStereoIUPACValue).

AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by AxialStereoCenter(AtomSelection, AxialStereoIUPACValue, List).

axialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the axial stereocenters.

axialStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the axial stereocenters with attached data.

AxialStereoDescriptor - Class in chemaxon.struc

AxialStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AxialStereoValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AxialStereoDescriptor

B

B - Static variable in class chemaxon.core.ChemConst

Ba - Static variable in class chemaxon.core.ChemConst

BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "background".

BACKGROUNDLOAD_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "bgloadEnabled".

BACKGROUNDLOAD_PRIORITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "bgload".

backgroundThread - Variable in class chemaxon.standardizer.runner.BasicStandardizerRunner

balabanIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.

BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "ballRadius".

BASE64 - Static variable in class chemaxon.formats.MFileFormat

BASE64 encoded file.

BASIC - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type

Basic aromatization

BASIC - Enum constant in enum class com.chemaxon.search.AromatizationMethod

Basic aromatization.

BASIC - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer

BASIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin

Constant denoting basic pKa.

BasicStandardizerRunner - Class in chemaxon.standardizer.runner

This is the default implementation of StandardizerActionRunner interface.

BasicStandardizerRunner(StandardizerConfigurationReader) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner

Initialize a BasicStandardizerRunner instance with the StandardizerConfiguration read from the provided configuration reader.

BasicStandardizerRunner(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner

Initialize a BasicStandardizerRunner instance with specified StandardizerConfiguration.

BBB - Class in chemaxon.calculations.bbb

BBB score calculator.

BBB.Property - Class in chemaxon.calculations.bbb

Simple DTO that contains the predicted value, its BBB score and the BBB score multiplied with the corresponding BBB multiplier.

BBBFunction - Enum Class in chemaxon.calculations.bbb

Base phys-chem property calculators and its score functions for BBB score calculation.

BCUT - Class in chemaxon.descriptors

Implements BCUT descriptors.

BCUT() - Constructor for class chemaxon.descriptors.BCUT

Creates a new, empty BCUT descriptor.

BCUT(BCUT) - Constructor for class chemaxon.descriptors.BCUT

Copy constructor.

BCUT(BCUTParameters) - Constructor for class chemaxon.descriptors.BCUT

Creates a new instance according to the parameters.

BCUT(String) - Constructor for class chemaxon.descriptors.BCUT

Creates a new instance according to the parameters.

BCUTGenerator - Class in chemaxon.descriptors

Descriptor generator class for the BCUT descriptor.

BCUTGenerator() - Constructor for class chemaxon.descriptors.BCUTGenerator

Creates and initializes a BCUT descriptor generator object.

BCUTParameters - Class in chemaxon.descriptors

Manages parameters for the BCUT descriptor class.

BCUTParameters() - Constructor for class chemaxon.descriptors.BCUTParameters

Creates an empty object.

BCUTParameters(File) - Constructor for class chemaxon.descriptors.BCUTParameters

Creates a new object based on a given configuration file.

BCUTParameters(String) - Constructor for class chemaxon.descriptors.BCUTParameters

Creates a new object based on a given configuration string.

Be - Static variable in class chemaxon.core.ChemConst

beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane

Changes the cursor to hourglass at the beginning of a long operation.

bemismurcko - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

bemismurckoloose - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

Beta - Annotation Interface in com.chemaxon.common.annotations

Indicates that a public API entity (public class, method, or field) is subject to incompatible changes, or even removal, in a future release.

Bh - Static variable in class chemaxon.core.ChemConst

Bi - Static variable in class chemaxon.core.ChemConst

BicycloStereoDescriptor - Class in chemaxon.struc

This class is the atom index based representation which can be assigned to 'endo', 'exo', 'syn', 'anti' ligands of bicyclo[x.y.z]alkanes in case of 0 dimension molecules.

BicycloStereoDescriptor(MolAtom, int, MolAtom[], MolAtom[]) - Constructor for class chemaxon.struc.BicycloStereoDescriptor

Creates a new stereo descriptor for bicyclo stereo.

BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters

descriptor type constants

binaryAsymmetricEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric Euclidean distance of binary descriptors.

binaryAsymmetricNormalizedEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric normalized Euclidean distance of binary descriptors.

binaryAsymmetricNormalizedEuclidean(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics

Calculates the asymmetric normalized Euclidean distance of binary descriptors.

binaryAsymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates asymmetric Tanimoto dissimilarity for binary descriptors.

binaryAsymmetricTanimoto(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics

Calculates asymmetricTanimoto dissimilarity for binary descriptors.

binaryEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the Euclidean distance of two binary descriptors.

binaryNormalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the normalized Euclidean distance of two binary descriptors.

binaryNormalizedEuclidean(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics

Calculates the normalized Euclidean distance of two binary descriptors.

binaryTanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates Tanimoto dissimilarity for binary descriptors.

binaryTanimoto(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics

Calculates Tanimoto dissimilarity for binary descriptors.

binaryTversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates Tversky dissimilarity for binary descriptors.

binaryWeightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric Euclidean distance of binary descriptors.

binaryWeightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.

binaryWeightedAsymmetricNormalizedEuclidean(int[], int, int[], int, float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.

binaryWeightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted Euclidean distance of binary descriptors.

binaryWeightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted normalized Euclidean distance of binary descriptors.

binaryWeightedNormalizedEuclidean(int[], int, int[], int, int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted normalized Euclidean distance of binary descriptors.

Bk - Static variable in class chemaxon.core.ChemConst

BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Constant storing the blue rgb value (the basic pKa result color).

BOLD - Static variable in class chemaxon.struc.graphics.MFont

Bold font style.

BOLD - Static variable in class chemaxon.struc.MolBond

"Bold" attribute of the bond.

BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "boldBondWidth".

BOND_ANGLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that bond angle problem had found in the molecule

BOND_BOND_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants

This String represents the key of cloned bond, original bond map

BOND_DRAGGED_ALONG - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "bondDraggedAlong".

BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "bondHashSpacing".

BOND_LENGTH - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that bond length problem had found in the molecule

BOND_LENGTH - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "bondLength".

BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "bondLengthVisible".

BOND_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "bondSet".

BOND_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "bondSetColor".

BOND_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "bondSpacing".

BOND_TOPOLOGY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule contains bond(s) with topology.

BondAngleChecker - Class in chemaxon.checkers

Bond Angle Checker detects wrong bond angles in 2D structures.

BondAngleChecker() - Constructor for class chemaxon.checkers.BondAngleChecker

Default constructor

BondAngleChecker(double) - Constructor for class chemaxon.checkers.BondAngleChecker

Deprecated.

Not used.

BondAngleCheckerResult - Class in chemaxon.checkers.result

Bond angle checker result.

BondAngleCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongAngleBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondAngleCheckerResult

Constructor which initialize all the properties.

BondAngleFixer - Class in chemaxon.fixers

Bond Angle Fixer fixes wrong bond angles in 2D structures.

BondAngleFixer() - Constructor for class chemaxon.fixers.BondAngleFixer

BondChecker - Class in chemaxon.checkers

Descentants of the abstract BondChecker class detect bond related problems.

BondChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.BondChecker

Constructor to create a Structure checker instance with the given errorType.

bondCount - Variable in class chemaxon.struc.MolAtom

Number of bonds.

bondCount - Variable in class chemaxon.struc.MoleculeGraph

The number of bonds.

bondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of bonds in the molecule including bonds of implicit hydrogens.

BondInfo - Class in chemaxon.marvin.alignment.atrop

Encapsulates bond info.

BondInfo(int, int, int) - Constructor for class chemaxon.marvin.alignment.atrop.BondInfo

Construct.

BondIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.BondIterator

Constructs an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.

bondlength() - Method in class chemaxon.struc.Molecule

Calculate the regular bond length for the unified structure.

bondlength() - Method in class chemaxon.struc.MoleculeGraph

Calculates the regular bond length.

BondLengthChecker - Class in chemaxon.checkers

Bond Length Checker detects bonds with wrong length in 2D structures.

BondLengthChecker() - Constructor for class chemaxon.checkers.BondLengthChecker

Default constructor

BondLengthChecker(Map<String, String>) - Constructor for class chemaxon.checkers.BondLengthChecker

Deprecated.

Checker has no parameters.

BondLengthCheckerResult - Class in chemaxon.checkers.result

Bond angle checker result.

BondLengthCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongLengthBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondLengthCheckerResult

Constructor which initialize all the properties.

BondLengthFixer - Class in chemaxon.fixers

Bond Length Fixer fixes bonds with wrong length in 2D structures.

BondLengthFixer() - Constructor for class chemaxon.fixers.BondLengthFixer

BONDLIST - Static variable in class chemaxon.sss.search.MarkushFeature

Deprecated.

Expansion type: bond list.

BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator

Constructs an iterator to process the bonds connecting to the specified atom.

bonds() - Method in class chemaxon.struc.MolAtom

Provides an unmodifiable list view of the connected bonds of the atom.

bonds() - Method in class chemaxon.struc.MoleculeGraph

Provides an unmodifiable list view of the bonds in the molecule.

bondSkipped(BondInfo, String) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener

Called when visited bond is skipped.

BondTable - Class in chemaxon.core.util

Provides easy lookup of bonds between pair of atoms in a molecule graph.

BondTopologyChecker - Class in chemaxon.checkers

Checker detects bonds with reacting center bond marks.

BondTopologyChecker() - Constructor for class chemaxon.checkers.BondTopologyChecker

Default constructor

bondType(int) - Method in class chemaxon.calculations.TopologyAnalyser

Determines the type of a bond (aromatic bonds are automatically recognized)

BondType - Enum Class in chemaxon.struc

General chemical bond types.

bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether bond types should be considered in search.

bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom

Calculates the average of the bond unit vectors pointing out of this atom.

BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor

Boolean option.

booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp

Gets the boolean value.

BORDER - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "border".

BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Br - Static variable in class chemaxon.core.ChemConst

brackets - Variable in class chemaxon.struc.Sgroup

BRACKETS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing that the molecule contains brackets (S-groups).

BracketsChecker - Class in chemaxon.checkers

Detects brackets (S-groups) in molecules.

BracketsChecker() - Constructor for class chemaxon.checkers.BracketsChecker

Default constructor.

BRIDGEHEAD_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which is connected to a bridgehead atom.

brightness - Variable in class chemaxon.descriptors.ChemicalFingerprint

number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less pausible)

brightness - Variable in class chemaxon.descriptors.ECFP

The number of bits set in the binary vector storage

brightness - Variable in class chemaxon.descriptors.ReactionFingerprint

number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)

btab - Variable in class chemaxon.struc.MoleculeGraph

Bond table.

bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream

Reads a character and writes into the buffer.

build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder

build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

build() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

Builds a ValenceCheckOptions object.

build() - Method in class chemaxon.formats.GeneralExportOptions.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.formats.MolConverter.Builder

Builds the MolConverter.

build() - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

build() - Method in class chemaxon.jep.ConstantTableBuilder

Creates a new constant table based on this builder.

build() - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets sizes, builds split panes.

build() - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

build() - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder

Builds a StandardizerActionFactory based on the previously added InputStream instances

build() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Builds a CheckerFixerFactory based no the previously added InputStream and Properties instances

build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Creates a search options object with the settings specified by this builder instance.

buildButtonBar() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog

buildContentPanel() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog

builder() - Static method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

Creates a new builder.

builder() - Static method in class chemaxon.jep.ConstantTable

Creates a new builder for a constant table.

Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder

Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder

Builder() - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

Builder() - Constructor for class chemaxon.formats.GeneralExportOptions.Builder

Builder() - Constructor for class chemaxon.formats.MolConverter.Builder

Constructs an empty Builder object.

Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder

Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder

Builder() - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder

Creates a Builder object with the default settings.

Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder

Creates a Builder object containing the settings of the given search options object.

BuildupMcs - Class in com.chemaxon.search.mcs.buildup

Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.

BuildupMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.buildup.BuildupMcs

Creates a new BuildupMcs object with the given search options.

BUTTON_MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "buttonmenubar".

BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure

For internal usage only.

C

C - Static variable in class chemaxon.core.ChemConst

C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter

Close the underlying stream.

C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter

Flush the output stream and force any buffered output bytes to be written out.

C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator

Name of the 13C chemical shift atom property.

C13 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus

13C NMR

Ca - Static variable in class chemaxon.core.ChemConst

CACHE_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "cacheMols".

CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for clearing all cached info.

CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in aromatization.

CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for cacheMemory.

CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in graph invariant calculation.

CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in parity calculation.

CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in sssr.

CACHE_REMOVE_TABS - Static variable in class chemaxon.struc.MoleculeGraph

Cache remove option to clear ctab and btab.

cacheMemory - Variable in class chemaxon.struc.MoleculeGraph

calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates a "badness" value for the atomic coordinates.

calcBitCount(int) - Static method in class chemaxon.descriptors.Metrics

Counts the number of bits set (1) in the integer parameter.

calcBitCount(int[]) - Static method in class chemaxon.descriptors.Metrics

Counts the number of bits set (1) in a bit vector.

calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the bracket endpoints from the base line of the bracket.

calcCenter() - Method in class chemaxon.struc.MDocument

Calculates the geometrical center.

calcCenter() - Method in class chemaxon.struc.MoleculeGraph

Calculates the geometrical center.

calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument

Calculates the geometrical center.

calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint

Calculates the geometrical center.

calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph

Calculates the graph invariants with the assumption that hydrogens are removed.

calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the division point of a segment with a given ratio.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator

Calculate and store in freqCount[] absolute frequency counts per cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator

Calculate and store in freqCount[] absolute frequency counts per cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

calcHeight() - Method in class chemaxon.struc.MoleculeGraph

Calculates the molecule height.

calcHybridization() - Method in class chemaxon.struc.MoleculeGraph

Calculates and sets hybridazation state for each atom.

calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the logD value at fixed pH.

calcMaxDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance

calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance

Calculates the minimum distance between two atoms in the molecule.

calcOrderFromLength() - Method in class chemaxon.struc.MolBond

Calculate the bond order from the atomic distances.

calcOrderFromValence() - Method in class chemaxon.struc.MolBond

Calculate bond order from the types and charges of the two atoms.

calcOutRect() - Method in class chemaxon.struc.MoleculeGraph

Calculates the outer rectangle.

calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the outer rectangle.

calcOutRectCenter() - Method in class chemaxon.struc.MoleculeGraph

Calculates the center of the outer rectangle.

calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the center of the outer rectangle.

CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Calculator rgb offset.

calcSimplePolymerBracket(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the points of a simple polymer bracket that belongs to a bond.

calcStereo2() - Method in class chemaxon.struc.MolBond

Computes the stereochemistry of the bond based on the atomic coordinates.

calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond

Computes the stereochemistry of the bond based on the atomic coordinates.

calcStereo2(MolAtom, MolAtom, MolAtom, MolAtom) - Static method in class chemaxon.struc.MolBond

Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates.

calculate() - Method in class chemaxon.marvin.alignment.MMPAlignment

Runs the MCS alignment calculation on the two structures of the constructor.

calculate(int[]) - Method in class chemaxon.marvin.alignment.MolAligner

Calculate best alignment based on the hit map

calculate(Molecule) - Static method in class chemaxon.calculations.bbb.BBB

Calculates the BBB properties and scores of the given Molecule.

calculate(Molecule) - Method in enum class chemaxon.calculations.bbb.BBBFunction

Calculates the BBB property, its score and its multiplied score.

calculate(Molecule) - Static method in class chemaxon.calculations.cnsmpo.CnsMpo

Calculates the CNS MPO properties and scores of the given molecule.

calculate(Molecule) - Method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Calculates the CNS MPO property and its score.

calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator

calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator

Calculates NMR spectrum for the given input molecule.

calculate(Molecule) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Run the atropisomer calculation.

calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator

calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator

calculate(Molecule, Molecule, McsSearchOptions) - Method in interface com.chemaxon.search.mcs.upperbound.UpperBoundCalculator

Returns an upper bound for the number of bonds the Maximum Common Substructure of the given molecules may contain.

calculate(Molecule, ProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Run the atropisomer calculation.

calculate(Molecule, ProgressObserver, DihedralScanListener) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Run the atropisomer calculation.

calculateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.

calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator

calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.

calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator

calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.

calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator

Calculates the stereo descriptors of the given molecule.

calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Calculates the coordinates during expand and contract.

calculateIntrinsicSolubility(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates intrinsic solubility.

calculatePhDependentSolubility(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubility.

calculatePhDependentSolubility(Molecule, double[]) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubilities.

calculatePhDependentSolubility(Molecule, double, double, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubilities.

calculateSimilarityUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.

calculateUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.

CalculatorError - Interface in chemaxon.calculator

An error that might occur when a calculator is initialized.

CalculatorInputChecker - Interface in chemaxon.calculator

Instances of this interface are used by calculators to check if they can process an input molecule.

CalculatorPlugin - Class in chemaxon.marvin.plugin

Common base class for calculator plugins.

CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin

Constructor.

CalculatorPlugin(Consumer<Molecule>, Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin

Constructor.

CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin

CalculatorPluginCachedResults - Class in com.chemaxon.calculations.cli

Provides plugin cached results.

CalculatorPluginCachedResults(String, String, Molecule[], Molecule, String, String, Throwable, boolean) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Constructor.

CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.gui

Common base class for calculator plugin displays.

CalculatorPluginDisplay() - Constructor for class com.chemaxon.calculations.gui.CalculatorPluginDisplay

CalculatorPluginOutput<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.cli

Class providing plugin output in table form.

CalculatorPluginOutput() - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput

Default constructor.

CalculatorPluginOutput(CalculatorPlugin) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput

Constructor that sets plugin.

CalculatorPluginService<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin

Base class for types that implement a functionality related to a specific CalculatorPlugin.

CalculatorPluginService() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginService

CalculatorResultAccess - Interface in com.chemaxon.calculations.cli

Interface providing plugin result access.

CalculatorTag - Enum Class in chemaxon.calculator

List of optional tags that can be reported by a TaggedCalculator.

calcWidth() - Method in class chemaxon.struc.MoleculeGraph

Calculates the molecule width.

calcWidth(Graphics2D) - Method in class chemaxon.struc.graphics.MNameTextBox

Calculates the width of the string in the name text box.

call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Performs the calculation and returns the result returned by PluginWorkUnit.getResult().

call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit

Performs the calculation and returns the result returned by ReusablePluginWorkUnit.getResult().

callback(String, Object) - Method in interface chemaxon.jep.ChemContext

Deprecated, for removal: This API element is subject to removal in a future version.

Use ChemContext.callContextFunction(String, List) instead.

callback(String, Object) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used for accessing the context, will be removed without replacement.

callContextFunction(String, List<Object>) - Method in interface chemaxon.jep.ChemContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.AtomContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.MolContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.ReactionContext

Executes the specified context function with the given parameters.

callService(HTTPServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.httpservice.HTTPServiceHandler

callService(JsonServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.json.JsonServiceHandler

callService(LocalServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.localservice.LocalServiceHandler

callService(SoapServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.soap.SoapServiceHandler

callService(XMLRPCServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceHandler

callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.marvin.services.ServiceHandler

Performs thread-safe asynchronous service call.

callService(DT, Object...) - Method in class chemaxon.marvin.services.ServiceHandler

Performs a service call.

CAN_BE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

canBeCT(int, int) - Method in class chemaxon.struc.MoleculeGraph

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

canBeCT(int, int, boolean) - Method in class chemaxon.struc.MoleculeGraph

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

canBeCT(int, int, boolean) - Method in class chemaxon.struc.RgMolecule

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

canBeCT(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Determines whether the given bond can be a CIS/TRANS or not.

canBeReactionComponent() - Method in class chemaxon.struc.Molecule

Tests whether an object of this class can be a reaction component.

canBeReactionComponent() - Method in class chemaxon.struc.RgMolecule

Tests whether an object of this class can be a reaction component.

canBeReactionComponent() - Method in class chemaxon.struc.RxnMolecule

Tests whether an object of this class can be a reaction component.

canBeSMARTS(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner

Stops the background thread

cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment

Cancel the ongoing calculation

cancel() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

cancel() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Stops the background thread

CANCELLED - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult

CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

canonicalName(String) - Static method in class chemaxon.marvin.io.Encoding

Standardize a Java encoding.

canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.

carboaliphaticRingCount() - Method in class chemaxon.calculations.Ring

Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).

carboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.carboaliphaticRingCount()

carboaromaticRingCount() - Method in class chemaxon.calculations.Ring

Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).

carboaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.carboaromaticRingCount()

carboRingCount() - Method in class chemaxon.calculations.Ring

Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).

carboRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.carboRingCount()

carboRingCount(int) - Method in class chemaxon.calculations.Ring

Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).

carboRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.carboRingCount(int)

carboRings() - Method in class chemaxon.calculations.Ring

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).

carboRings() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.carboRings()

carboRings(int) - Method in class chemaxon.calculations.Ring

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.

carboRings(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.carboRings(int)

caretUpdate(CaretEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

CBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

CCLENGTH - Static variable in class chemaxon.struc.MolBond

Default bond length.

Cd - Static variable in class chemaxon.core.ChemConst

CDParameters - Class in chemaxon.descriptors

Manages parameters the CustomDescriptor class.

CDParameters() - Constructor for class chemaxon.descriptors.CDParameters

Creates an empty object.

CDParameters(int) - Constructor for class chemaxon.descriptors.CDParameters

Creates an empty object of the given type.

CDParameters(File) - Constructor for class chemaxon.descriptors.CDParameters

Creates a new descriptor configured from the given file.

CDParameters(String) - Constructor for class chemaxon.descriptors.CDParameters

Creates a new object based on a given configuration string.

CDX - Static variable in class chemaxon.formats.MFileFormat

ChemDraw CDX file.

CDXML - Static variable in class chemaxon.formats.MFileFormat

ChemDraw CDXML file.

Ce - Static variable in class chemaxon.core.ChemConst

CELL - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "cell".

cellSize - Variable in class chemaxon.descriptors.MDParameters

size - number of bits - of one descriptor cell

CELLSIZE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The default viewer cell size.

cellwiseWeights - Variable in class chemaxon.descriptors.MDParameters

is cell weights for parametrized metrics

centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane

Puts the molecule into the center of the display.

Cf - Static variable in class chemaxon.core.ChemConst

CFGenerator - Class in chemaxon.descriptors

The CFGenerator class generates topological fingerprints of molecular graphs.

CFGenerator() - Constructor for class chemaxon.descriptors.CFGenerator

Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.

CFNS - Static variable in class chemaxon.jep.context.AtomContext

The context function names.

CFNS - Static variable in class chemaxon.jep.context.ReactionContext

The context function names.

CFParameters - Class in chemaxon.descriptors

Manages fingerprint parameters.

CFParameters() - Constructor for class chemaxon.descriptors.CFParameters

Creates an empty object.

CFParameters(File) - Constructor for class chemaxon.descriptors.CFParameters

Creates a new object based on a given configuration file.

CFParameters(String) - Constructor for class chemaxon.descriptors.CFParameters

Creates a new object based on a given configuration string.

CHAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

chainAtomCount() - Method in class chemaxon.calculations.Ring

Calculates the number of chain atoms in the molecule excluding hydrogens.

chainAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.chainAtomCount()

chainBondCount() - Method in class chemaxon.calculations.Ring

Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.

chainBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.chainBondCount()

chainTransformers(Transformer...) - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns a chain transformer.

chainTransformers(List<Transformer>) - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns a chain transformer.

changes - Variable in class chemaxon.standardizer.actions.AbstractSgroupAction

Changes - Class in chemaxon.standardizer

The change set of the standardization procedure.

Changes(Molecule) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

Changes(Molecule, StandardizerAction) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

Changes(Molecule, Molecule) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

CHANGING - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle

Only reaction center will be mapped

CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).

characters(char[], int, int) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter

charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets a character of the document.

CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).

CHARGE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).

CHARGE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for ignore charge searching (charge information is ignored during searching).

CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup

Charge is located on atoms and displayed on atoms.

CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup

Charge is located on atoms but displayed on the whole group (bracket).

CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "chargeWithCircle".

CHARGED_H - Static variable in class chemaxon.struc.MolAtom

Include charged Hydrogen atom(s).

chargeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether formal charges of atoms should be considered in search.

ChargePlugin - Class in chemaxon.marvin.calculations

Plugin class for partial charge calculation.

ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin

Constructor.

check() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

check() - Method in interface chemaxon.checkers.runner.CheckerRunner

Invokes a background thread which will run all checkers on the given molecule

check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator

check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator

check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker

check(Molecule) - Method in class chemaxon.checkers.InvalidChecker

check(Molecule) - Method in interface chemaxon.checkers.StructureChecker

Detects a specific error in the molecule.

check(Molecule) - Method in interface chemaxon.jep.MolCondition

Deprecated.

Returns true if molecule should be processed, false otherwise.

check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AliasChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker

Detects atom of the molecule has atom map.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker

Detects if the current atom of the molecule has atom value.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker

Check the atom of the molecule with index i has no atom map.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker

Detects atom of the molecule is a query atom.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker

Detects if the current atom has free electrons.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.BondTopologyChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker

Examines if the bond is a crossed double bond.

check(Molecule, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker

Detects bond of the molecule is crossing another bond or closer than the limit distance.

check(Molecule, MolBond) - Method in class chemaxon.checkers.QueryBondChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker

check(Molecule, E) - Method in class chemaxon.checkers.ComponentChecker

Checks if the component with index i has problem

check(Stack<Object>) - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

Checks the stack.

Check - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Mode

Indicates, that the structurechecker does not automatically fixes.

check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker

Determines if a non chiral molecule contains a chiral flag.

check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker

Determines if all asymmetric centers have absolute stereo configuration

check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker

This method contains the current checking mechanism.

check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker

check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker

Detects attached data in the molecule

check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker

check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker

check1(Molecule) - Method in class chemaxon.checkers.BracketsChecker

check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker

check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker

Determines if a non chiral molecule contains a chiral flag.

check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker

check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker

Iterates through the components and checks every component.

check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker

check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker

check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Detects implicitizable hydrogen atoms.

check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker

check1(Molecule) - Method in class chemaxon.checkers.IncorrectTetrahedralStereoChecker

check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker

check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker

Detects if molecule has charge

check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker

check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker

check1(Molecule) - Method in class chemaxon.checkers.NonStandardWedgeSchemeChecker

check1(Molecule) - Method in class chemaxon.checkers.NonStereoWedgeBondChecker

check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker

check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker

check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker

check1(Molecule) - Method in class chemaxon.checkers.RatomChecker

check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker

check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker

check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.RgroupBridgeRatomChecker

check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.SolventChecker

check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker

check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker

check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker

check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker

check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker

Deprecated.

In version 15.8.3 the checker logic was replaced with the logic implemented in Molecule's stereoClean() method.

check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker

check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker

checkAndWait() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

checkAndWait() - Method in interface chemaxon.checkers.runner.CheckerRunner

Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems

checkAtno(int) - Static method in class chemaxon.struc.MolAtom

Check if the given atomic number is positive and less then atomic type maximum value.

checkBondConsistency() - Method in class chemaxon.struc.MoleculeGraph

checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule

Empty implementation, bond consistency is not checked in case of selections.

checkBondConsistency() - Method in class chemaxon.struc.Sgroup

checkBonds(MolAtom) - Method in class chemaxon.struc.Sgroup

Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.

checkBonds(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.

checkConsistency() - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

checkConsistency() - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

checkConsistency() - Method in class chemaxon.struc.RgMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

checkConsistencyInEmbeddings() - Method in class chemaxon.struc.Sgroup

Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.

checkDocumentVersion(String, String) - Method in class chemaxon.descriptors.MDParameters

Checks if the document is the right version

CheckerClassDescriptor() - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor

Initializes an empty checker class descriptor

CheckerClassDescriptor(String, String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor

Initializes a checker class descriptor

CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Chemaxon's default checker configuration file name

CheckerFixerFactory - Class in chemaxon.structurechecker.factory

Factory for structure checkers and structure fixers.

CheckerFixerFactory.Builder - Class in chemaxon.structurechecker.factory

Builder class for CheckerFixerFactory.

CheckerFixerFactory.CheckerClassDescriptor - Class in chemaxon.structurechecker.factory

Descriptor of a checker class

CheckerFixerFactory.ClassDescriptor - Class in chemaxon.structurechecker.factory

Descriptor of a class

CheckerFixerFactory.FixerClassDescriptor - Class in chemaxon.structurechecker.factory

Descriptor of a fixer class

CheckerInfo - Annotation Interface in chemaxon.checkers

This annotation is responsible for adding GUI based meta data for StructureChecker implementations

CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark

CheckerRunner - Interface in chemaxon.checkers.runner

The descendant of CheckerRunner interface has to provide the functionality to run StructureChecker instances automatically
on the given molecule and fix the problems with the associated StructureFixer instances.

Example:

CheckerRunner can be used directly with the checkAndWait method.

CheckerSeverity - Enum Class in chemaxon.checkers

This enum defines the constants which represent the severity of the StructureChecker implementations

checkFilter(String) - Static method in class chemaxon.sss.search.MolSearch

Checks the syntax of the filtering expression.

checkFilter(String, File) - Static method in class chemaxon.sss.search.MolSearch

Checks the syntax of the filtering expression.

checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Checks the input molecule.

checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule

Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.

checkSgroupConsistency() - Method in class chemaxon.struc.Molecule

Checks the internal consisitency of S-groups.

checkSgroupConsistency() - Method in class chemaxon.struc.RgMolecule

Checks the consistency of S-groups.

checkSgroupConsistency() - Method in class chemaxon.struc.RxnMolecule

Checks the consistency of S-groups.

checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.Sgroup

Checks whether the parameter s-group contains the atoms of this s-group.

checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup.

checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Checks result types.

checkValence(MolAtom) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

checkValence(MoleculeGraph) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MElectronContainer

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject

Is it a valid object in the document?

CHEMAXON - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod

Chemaxon logP calculation method.

chemaxon.calculations - package chemaxon.calculations

Contains chemical computation modules.

chemaxon.calculations.bbb - package chemaxon.calculations.bbb

BBB score calculator.

chemaxon.calculations.cip - package chemaxon.calculations.cip

chemaxon.calculations.clean - package chemaxon.calculations.clean

chemaxon.calculations.cnsmpo - package chemaxon.calculations.cnsmpo

CNS MPO score calculator.

chemaxon.calculations.dipole - package chemaxon.calculations.dipole

chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize

chemaxon.calculations.nmr - package chemaxon.calculations.nmr

chemaxon.calculations.nmr.io - package chemaxon.calculations.nmr.io

chemaxon.calculations.pka - package chemaxon.calculations.pka

chemaxon.calculations.stereo - package chemaxon.calculations.stereo

chemaxon.calculator - package chemaxon.calculator

chemaxon.checkers - package chemaxon.checkers

Structure checkers can be used to filter drawing mistakes or special structural elements.

chemaxon.checkers.result - package chemaxon.checkers.result

This package is used to identify problems found in molecules.

chemaxon.checkers.runner - package chemaxon.checkers.runner

This package supports the automatic running of structure checkers.

chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader

Extension package of the automatic runner functionality.

chemaxon.checkers.util - package chemaxon.checkers.util

chemaxon.common.swing.io.output - package chemaxon.common.swing.io.output

chemaxon.common.util - package chemaxon.common.util

Provides general utility classes.

chemaxon.core - package chemaxon.core

chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo

chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck

chemaxon.core.util - package chemaxon.core.util

chemaxon.descriptors - package chemaxon.descriptors

chemaxon.descriptors.scalars - package chemaxon.descriptors.scalars

chemaxon.fixers - package chemaxon.fixers

Structure fixers can be used to fix problems identified by structure checker instances.

chemaxon.formats - package chemaxon.formats

Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.

chemaxon.formats.factory - package chemaxon.formats.factory

chemaxon.formats.recognizer - package chemaxon.formats.recognizer

Provides classes to recognize files of various file formats.

chemaxon.jep - package chemaxon.jep

Chemical Terms Evaluator classes.

chemaxon.jep.context - package chemaxon.jep.context

Specific chemical terms evaluation contexts.

chemaxon.license - package chemaxon.license

Classes related licenses, license handling, validating, GUI and documentation.

chemaxon.marvin - package chemaxon.marvin

Contains utility classes for rendering molecules.

chemaxon.marvin.alignment - package chemaxon.marvin.alignment

The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.

chemaxon.marvin.alignment.atrop - package chemaxon.marvin.alignment.atrop

Utilities for AtropIsomerDetector.

chemaxon.marvin.beans - package chemaxon.marvin.beans

Provides bean classes for creating Marvin based user interface.

chemaxon.marvin.calculations - package chemaxon.marvin.calculations

Provides specific plugin, plugin loader and table form output implementations.

chemaxon.marvin.collecting - package chemaxon.marvin.collecting

chemaxon.marvin.common - package chemaxon.marvin.common

Contains a class for handling user settings.

chemaxon.marvin.io - package chemaxon.marvin.io

Provides classes for molecule import and export through data streams.

chemaxon.marvin.io.fieldaccess - package chemaxon.marvin.io.fieldaccess

chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats

Core package of any import/export module.

chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl

Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.

chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles

chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer

Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.

chemaxon.marvin.plugin - package chemaxon.marvin.plugin

Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.

chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent

Classes to achieve concurrent processing of calculator plugins.

chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui

Calculator plugin common GUI classes.

chemaxon.marvin.services - package chemaxon.marvin.services

Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.

chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice

chemaxon.marvin.services.json - package chemaxon.marvin.services.json

chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice

chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap

chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice

chemaxon.marvin.sketch - package chemaxon.marvin.sketch

Contains the sketcher's core classes and various sketching modes.

chemaxon.marvin.sketch.swing.modules.documentstyle - package chemaxon.marvin.sketch.swing.modules.documentstyle

chemaxon.marvin.swing - package chemaxon.marvin.swing

chemaxon.marvin.uif.dialog - package chemaxon.marvin.uif.dialog

chemaxon.marvin.util - package chemaxon.marvin.util

Contains some utilities for example for molecule cleaning and Swing.

chemaxon.marvin.view - package chemaxon.marvin.view

Control records in MarvinView.

chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing

Swing support for MarvinView tables.

chemaxon.naming - package chemaxon.naming

Name to Structure conversion.

chemaxon.naming.document - package chemaxon.naming.document

Document to Structure (D2S) conversion.

chemaxon.naming.document.annotate - package chemaxon.naming.document.annotate

chemaxon.nfunk.jep.function - package chemaxon.nfunk.jep.function

chemaxon.sss - package chemaxon.sss

chemaxon.sss.formula - package chemaxon.sss.formula

chemaxon.sss.screen - package chemaxon.sss.screen

Classes for screeening.

chemaxon.sss.search - package chemaxon.sss.search

chemaxon.sss.search.options - package chemaxon.sss.search.options

chemaxon.standardizer - package chemaxon.standardizer

Contains packages for structure standardization.

chemaxon.standardizer.actions - package chemaxon.standardizer.actions

Contains basic standardizer actions.

chemaxon.standardizer.advancedactions - package chemaxon.standardizer.advancedactions

Contains advanced standardizer actions.

chemaxon.standardizer.concurrent - package chemaxon.standardizer.concurrent

Contains classes for concurrent execution of standardization.

chemaxon.standardizer.configuration - package chemaxon.standardizer.configuration

Contains classes for handling configurations of standardizer.

chemaxon.standardizer.configuration.reader - package chemaxon.standardizer.configuration.reader

Contains classes for handling configuration deserialization.

chemaxon.standardizer.runner - package chemaxon.standardizer.runner

Contains classes for executing standardization based on a configuration.

chemaxon.struc - package chemaxon.struc

Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.

chemaxon.struc.graphics - package chemaxon.struc.graphics

Contains graphics MDocument elements.

chemaxon.struc.prop - package chemaxon.struc.prop

Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.

chemaxon.struc.sgroup - package chemaxon.struc.sgroup

S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.

chemaxon.struc.stereo - package chemaxon.struc.stereo

chemaxon.structurechecker.factory - package chemaxon.structurechecker.factory

chemaxon.util - package chemaxon.util

chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin

chemaxon.util.iterator - package chemaxon.util.iterator

Provides iterator classes for molecules and their components.

chemaxon.util.progress - package chemaxon.util.progress

Common components of Calculator APIs.

ChemConst - Class in chemaxon.core

ChemConst() - Constructor for class chemaxon.core.ChemConst

ChemContext - Interface in chemaxon.jep

Interface of expression evaluation contexts.

ChemContext.ProvidesFunction - Annotation Interface in chemaxon.jep

Repeatable annotation used on ChemContext implementations to declare the context functions supported by the ChemContext.callContextFunction(String, List) method.

ChemContext.ProvidesFunctionContainer - Annotation Interface in chemaxon.jep

Container for the repeatable ChemContext.ProvidesFunction annotation.

ChemicalFingerprint - Class in chemaxon.descriptors

The ChemicalFingerprint class implements topological fingerprints as a type of MolecularDescriptors.

ChemicalFingerprint() - Constructor for class chemaxon.descriptors.ChemicalFingerprint

Creates a new, empty instance of ChemicalFingerprint without allocating internal storage.

ChemicalFingerprint(CFParameters) - Constructor for class chemaxon.descriptors.ChemicalFingerprint

Creates a new instance of ChemicalFingerprint according to the parameters given.

ChemicalFingerprint(ChemicalFingerprint) - Constructor for class chemaxon.descriptors.ChemicalFingerprint

Copy constructor.

ChemicalFingerprint(String) - Constructor for class chemaxon.descriptors.ChemicalFingerprint

Creates a new instance of ChemicalFingerprint according to the parameters given.

ChemJEP<C extends ChemContext> - Class in chemaxon.jep

Expression parser and evaluator for chemical expressions.

ChemJEP() - Constructor for class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Direct creation of a ChemJEP object will no longer be supported, use the Evaluator.compile(java.lang.String) methods instead.

ChemJEP(Class<? extends C>) - Constructor for class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Direct creation of a ChemJEP object will no longer be supported, use the Evaluator.compile(java.lang.String) methods instead.

CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents molecules marked with "absolute stereo" flag.

chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry

Calculates the number of chiral centers.

chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.chiralCenterCount()

chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry

Determines the chiral center atoms.

chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.chiralCenters()

ChiralFlagChecker - Class in chemaxon.checkers

Implementation of AbstractStructureChecker detecting "absolute stereo flag" on molecule.

ChiralFlagChecker() - Constructor for class chemaxon.checkers.ChiralFlagChecker

Constructs ChiralFlagChecker instance

ChiralFlagErrorChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).

ChiralFlagErrorChecker() - Constructor for class chemaxon.checkers.ChiralFlagErrorChecker

Default constructor

CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants

Axially chiral atom with M configuration.

CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants

Chirality mask in flags.

CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants

Axially chiral atom with P configuration.

CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants

Pseudo-asymmetric chiral atom of r configuration.

CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of R configuration.

CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants

Pseudo-asymmetric chiral atom of s configuration.

CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of S configuration.

CHIRALITY_SUPPORT - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "chiralitySupport".

CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants

R/S shown always.

CHIRALITYSUPPORT_ALL_POSSIBLE - Static variable in interface chemaxon.struc.StereoConstants

R/S shown always and highlight possible chiral centers as well.

CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants

R/S not shown for any molecule.

CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants

R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.

CIPStereoCalculator - Class in chemaxon.calculations.cip

Stereo calculator with the Cahn, Ingold, Prelog priority rules.

CIPStereoDescriptorIface - Interface in chemaxon.struc

Cahn-Ingold-Prelog (CIP) stereodescriptor interface.

CIPStereoDescriptorIface.CIPType - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue - Interface in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AtropStereoValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AxialStereoValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.CisTransStereoValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue - Enum Class in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue - Enum Class in chemaxon.struc

CIPStereoRecognizer - Class in chemaxon.core.calculations.stereo

Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial, cis/trans and atrop stereo features.

CIPStereoRecognizer() - Constructor for class chemaxon.core.calculations.stereo.CIPStereoRecognizer

CIRCULAR_RGROUP_REFERENCE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule with circular R-group definition found

CircularRGroupReferenceChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting circular R-group references.

CircularRGroupReferenceChecker() - Constructor for class chemaxon.checkers.CircularRGroupReferenceChecker

Initializes the checker

CIS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue

2 dimension: The rigid part's maximal indexed ligands placed in the same half-plane according to the rigid part.
0 dimension: CIS stereo value was set on the double bond for it's maximal indexed ligands.

CIS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue.Z.

CIS - Static variable in interface chemaxon.struc.StereoConstants

Cis double bond.

CIS_TRANS - Static variable in interface chemaxon.struc.StereoConstants

Cis and trans double bond mask.

CisDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans

Filter for CIS double bonds.

CisDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter

cisDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the CIS double bonds.

CISTRANS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType

CISTRANS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type

Cis-trans stereo center.

CISTRANS - Enum constant in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType

Double bond stereoisomers.

CisTransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans

Filter for cis-trans stereo centers.

CisTransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter

cisTransDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the CIS-TRANS double bonds.

cisTransDoubleBondsWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the CIS-TRANS double bonds with attached data.

CisTransStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters

Cis-trans stereo center implementation.

CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter

Constructs a new instance of cis-trans stereo center.

CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter

Constructs a new instance of cis-trans stereo center with attached data.

CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CisTransStereoCenter(AtomSelection, CisTransStereoIUPACValue).

CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CisTransStereoCenter(AtomSelection, CisTransStereoIUPACValue, List).

CisTransStereoDescriptor - Class in chemaxon.struc

CisTransStereoDescriptor(CIPStereoDescriptorIface.CIPValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.CisTransStereoDescriptor

Cl - Static variable in class chemaxon.core.ChemConst

CLASS - Static variable in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

Property key for Service class name as String

ClassDescriptor(String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

className - Variable in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

clean(int) - Method in class chemaxon.formats.MolConverter.Builder

Enables cleaning.

clean(int) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder

Enables cleaning.

clean(int, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

clean(int, String) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).

clean(int, String, int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Clean the specified cell.

clean(int, String, MProgressMonitor) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor).

clean(MoleculeGraph, int) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates.

clean(MoleculeGraph, int, String) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates.

clean(MoleculeGraph, int, String, MProgressMonitor) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates.

Clean2DAction - Class in chemaxon.standardizer.advancedactions

Clean molecule graph in 2D standardizer action

Clean2DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean2DAction

Initializes the action with parameters

Clean2DAction.Type - Enum Class in chemaxon.standardizer.advancedactions

Type of clean action (partial, full, template based or convert 3D to 2D)

clean3d(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

clean3d(Molecule, int) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

Clean3DAction - Class in chemaxon.standardizer.advancedactions

Clean molecule graph in 3D standardizer action

Clean3DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean3DAction

Initializes the action with parameters

cleanAll(int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Clean all cells.

Cleaner - Class in chemaxon.calculations.clean

Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.

Cleaner() - Constructor for class chemaxon.calculations.clean.Cleaner

CleanFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which cleans the molecule in 2d

CleanFixer() - Constructor for class chemaxon.fixers.CleanFixer

CLEANING_2D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "clean2dOpts".

CLEANING_3D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "clean3dOpts".

CLEANING_DIMENSION - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "cleanDim".

CLEANING_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "cleanOpts".

cleanupRemovedRgroupMember(MoleculeGraph, int) - Method in class chemaxon.struc.RgMolecule

Clean-up after R-group removal.

CleanUtil - Class in chemaxon.marvin.util

Utility methods for cleaning.

CleanUtil() - Constructor for class chemaxon.marvin.util.CleanUtil

clear() - Method in class chemaxon.descriptors.BCUT

Clears the descriptor, all values are set to zero.

clear() - Method in class chemaxon.descriptors.ChemicalFingerprint

Clears the fingerprint: sets all bins to store zero value.

clear() - Method in class chemaxon.descriptors.CustomDescriptor

Clears the descriptor: sets all cells to store zero value.

clear() - Method in class chemaxon.descriptors.ECFP

Clears the fingerprint, all values are set to zero.

clear() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Clears the fingerprint: sets all bins to store zero value.

clear() - Method in class chemaxon.descriptors.ReactionFingerprint

Clears the fingerprint: sets all bins to store zero value.

clear() - Method in class chemaxon.descriptors.ScalarDescriptor

Clears the descritor: sets its value to zero value.

clear() - Method in class chemaxon.descriptors.ShapeDescriptor

Clears the fingerprint, all values are set to zero.

clear() - Method in class chemaxon.formats.MolConverter.Builder

Clears all settings.

clear() - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

clear() - Method in interface chemaxon.jep.ChemContext

Clears the context.

clear() - Method in class chemaxon.jep.context.AtomContext

Clears the context.

clear() - Method in class chemaxon.jep.context.MolContext

Clears the context.

clear() - Method in class chemaxon.jep.context.ReactionContext

Clears the context.

clear() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Clears the configuration of action

clear() - Method in class chemaxon.struc.MDocument

Clears the document.

clear() - Method in class chemaxon.struc.MolAtom

Clear query properties, charge, and hcount.

clear() - Method in class chemaxon.struc.Molecule

Clears the molecule.

clear() - Method in class chemaxon.struc.MoleculeGraph

Clears the molecule.

clear() - Method in class chemaxon.struc.MPropertyContainer

Clears properties.

clear() - Method in class chemaxon.struc.MSelectionDocument

Clears the document.

clear() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Clears the display.

CLEAR - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Remove absolute stereo

clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

clearCachedInfo(int) - Method in class chemaxon.struc.MoleculeGraph

Deletes the cached information depending on the given options.

clearChangesInUserComparators() - Method in class chemaxon.sss.search.SearchOptions

Used in initializing searches.

clearCheckerMarks() - Method in class chemaxon.struc.MDocument

Clears the checker marks

clearComparators() - Method in class chemaxon.sss.search.MolSearch

Delete all comparator from the search object.

clearExtraLabel() - Method in class chemaxon.struc.MolAtom

Clears the extra label.

clearExtraLabels() - Method in class chemaxon.struc.Molecule

Clears extra atom labels.

clearForImport(String) - Method in class chemaxon.struc.Molecule

Initializes molecule for import.

clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph

Clears the bonds vector, the properties, the flags, and sets the origin coordinates to 0.

clearForImport(String) - Method in class chemaxon.struc.RgMolecule

Clear the edges vector and the properties.

clearForImport(String) - Method in class chemaxon.struc.RxnMolecule

Clear the edges vector and the properties.

clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane

Reset undo queue.

clearInactiveTasks(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil

Clears the inactive tasks list.

ClearIsotopesAction - Class in chemaxon.standardizer.actions

Clear isotopes standardizer action

ClearIsotopesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearIsotopesAction

Initializes the action

clearLines() - Method in class chemaxon.struc.graphics.MTextBox

Clears all lines.

clearMark() - Method in class chemaxon.marvin.io.PositionedInputStream

Disables the mark (if any) on this stream.

clearMatch() - Method in class chemaxon.sss.search.MolSearch

clearMatch() - Method in class chemaxon.sss.search.Search

Clears the extra prerequisites of the structure search specified using addMatch calls.

clearObjects() - Method in class chemaxon.struc.Molecule

clearObjects() - Method in class chemaxon.struc.RgMolecule

clearObjects() - Method in class chemaxon.struc.RxnMolecule

Deletes the graphical objects from this.

clearObjects() - Method in class chemaxon.struc.Sgroup

Clears all MObject-s that belong to this S-groups.

clearProperties() - Method in class chemaxon.struc.MolAtom

Removes all properties from this atom.

clearProperties() - Method in class chemaxon.struc.MolBond

Removes all properties from this bond.

clearProperties() - Method in class chemaxon.struc.Molecule

Clears RDfile/SDfile properties.

clearQProps() - Method in class chemaxon.struc.MolAtom

Clears query props.

clearSavedAtomIndices() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

clearSets() - Method in class chemaxon.struc.MDocument

Clears the atomSets and the bondSets.

ClearStereoAction - Class in chemaxon.standardizer.actions

Clear stereo standardizer action

ClearStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearStereoAction

Initializes the action with parameters

ClearWedgeFixer - Class in chemaxon.fixers

Clears wedges.

ClearWedgeFixer() - Constructor for class chemaxon.fixers.ClearWedgeFixer

CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Flag that indicates an import operation

CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Flag that indicates an export operation

CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Undefined clipboard operation state identifier

CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Temporary property name to mark the molecule if it comes from a file via the clipboard

clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Clipboard operation type.

clone() - Method in class chemaxon.checkers.AbstractStructureChecker

clone() - Method in class chemaxon.checkers.StructureCheckerDescriptor

clone() - Method in class chemaxon.checkers.SubstructureChecker

clone() - Method in class chemaxon.core.util.BondTable

clone() - Method in class chemaxon.descriptors.BCUT

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.ChemicalFingerprint

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.CustomDescriptor

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.ECFP

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.MolecularDescriptor

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.ReactionFingerprint

Creates a copy with identical internal state.

clone() - Method in class chemaxon.descriptors.ScalarDescriptor

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.HAcc

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.HDon

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.Heavy

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.LogD

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.LogP

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.Mass

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.TPSA

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.ShapeDescriptor

clone() - Method in class chemaxon.fixers.StructureFixerDescriptor

clone() - Method in class chemaxon.formats.MolConverter.Builder

Clones the object.

clone() - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

clone() - Method in class chemaxon.sss.search.MolSearchOptions

clone() - Method in class chemaxon.sss.search.SearchOptions

Makes an identical copy of this SearchObject.

clone() - Method in class chemaxon.standardizer.AbstractStandardizerAction

clone() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

clone() - Method in class chemaxon.standardizer.actions.AbstractSgroupAction

clone() - Method in class chemaxon.standardizer.actions.AliasToGroupAction

clone() - Method in class chemaxon.standardizer.actions.AromatizeAction

clone() - Method in class chemaxon.standardizer.actions.ClearStereoAction

clone() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

clone() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

clone() - Method in class chemaxon.standardizer.actions.ExpandAction

clone() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

clone() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

clone() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

clone() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

clone() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

clone() - Method in class chemaxon.standardizer.actions.TautomerizeAction

clone() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

clone() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

clone() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

clone() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

clone() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

clone() - Method in class chemaxon.standardizer.advancedactions.TransformAction

clone() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

clone() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

clone() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

clone() - Method in class chemaxon.struc.CTransform3D

clone() - Method in class chemaxon.struc.DPoint3

Make an identical copy.

clone() - Method in class chemaxon.struc.graphics.MAnalysisBox

clone() - Method in class chemaxon.struc.graphics.MAssigner

clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint

clone() - Method in class chemaxon.struc.graphics.MBracket

clone() - Method in class chemaxon.struc.graphics.MChemicalStruct

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MEFlow

clone() - Method in class chemaxon.struc.graphics.MEFlowBasePoint

clone() - Method in class chemaxon.struc.graphics.MElectron

clone() - Method in class chemaxon.struc.graphics.MElectronContainer

clone() - Method in class chemaxon.struc.graphics.MEllipse

clone() - Method in class chemaxon.struc.graphics.MFont

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MMidPoint

clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky

clone() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MNameTextBox

clone() - Method in class chemaxon.struc.graphics.MPolyline

clone() - Method in class chemaxon.struc.graphics.MRArrow

clone() - Method in class chemaxon.struc.graphics.MRectangle

clone() - Method in class chemaxon.struc.graphics.MRectanglePoint

clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky

clone() - Method in class chemaxon.struc.graphics.MRoundedRectangle

clone() - Method in class chemaxon.struc.graphics.MTextBox

clone() - Method in class chemaxon.struc.MDocument

Creates a clone.

clone() - Method in class chemaxon.struc.MObject

Creates a clone.

clone() - Method in class chemaxon.struc.MolAtom

Clones the atom.

clone() - Method in class chemaxon.struc.MolBond

Make a copy of this object.

clone() - Method in class chemaxon.struc.Molecule

Makes an identical copy of the molecule.

clone() - Method in class chemaxon.struc.MoleculeGraph

Make an identical copy of the molecule.

clone() - Method in class chemaxon.struc.MPoint

clone() - Method in class chemaxon.struc.MPropertyContainer

Clones this object.

clone() - Method in class chemaxon.struc.PageSettings

Clones this object.

clone() - Method in class chemaxon.struc.prop.MBooleanProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MDoubleProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MHCoords3DProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MIntegerProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MMoleculeProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MObjectProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MStringProp

Clones the object.

clone() - Method in class chemaxon.struc.QueryBond

Make a copy of this object.

clone() - Method in class chemaxon.struc.RgMolecule

Clone the markush structure.

clone() - Method in class chemaxon.struc.RxnMolecule

Make an identical copy of the reaction structure.

clone() - Method in class chemaxon.struc.SelectionMolecule

Create a clone of this SelectionMolecule.

clone() - Method in class chemaxon.struc.sgroup.SgroupAtom

Clones the S-group superatom and it's SuperatomSgroup as well.

clone() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Clones the SuperatomSgroup (and not the Molecule).

cloneAsMTextBox() - Method in class chemaxon.struc.graphics.MAnalysisBox

cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule

Copies the specified atoms.

cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Copies the specified atoms.

cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond

Clones this bond.

cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.QueryBond

Clones this bond.

cloneBondTable(BondTable) - Static method in class chemaxon.core.util.BondTable

Clones the bond table.

cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MHashProp

Clones the object.

cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MListProp

Clones the object.

cloneConfiguration() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Clones the configuration

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule

Copies the specified atoms and bonds of this molecule to another one.

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Copies the specified atoms of this molecule graph to another one.

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Copies the specified atoms of this graph to another one.

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Copies the specified nodes and edges of this graph to another one.

clonecopy(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions

Copies parameters to other.

clonecopy(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions

Copies all search options to other.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule

Makes another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Make another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Make another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Make another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule

Copies the clones of atoms and bonds of this graph to another one.

clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Copies the specified atoms and bonds of this molecule graph to another one.

clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule

Copies the specified atoms and bonds of this graph to another one.

clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions

clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions

Copies all search options except search type to other.

clonecopyWithoutSgroups(Molecule) - Method in class chemaxon.struc.Molecule

Copies the all the contents except the S-groups into another molecule object.

cloneDocument() - Method in class chemaxon.struc.MDocument

Creates a clone.

cloneDocument() - Method in class chemaxon.struc.MSelectionDocument

Creates a clone.

cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom

Clones the S-group superatom partially.

cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker

cloneItem() - Method in class chemaxon.checkers.InvalidChecker

cloneItem() - Method in interface chemaxon.checkers.StructureChecker

Returns a clone of this StructureChecker instance

cloneItem() - Method in class chemaxon.standardizer.AbstractStandardizerAction

cloneItem() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

cloneItem() - Method in interface chemaxon.standardizer.StandardizerAction

Returns a clone of this StandardizerAction instance

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

cloneMainMolecule() - Method in class chemaxon.struc.MDocument

Creates a clone.

cloneMainMoleculeGraph() - Method in class chemaxon.struc.MDocument

Creates a clone.

cloneMFont() - Method in class chemaxon.struc.graphics.MFont

Creates a clone.

cloneMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

cloneMolecule() - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 2014.09.01.0 use Molecule.clone() instead

cloneMoleculeWithDocument() - Method in class chemaxon.struc.Molecule

Makes an identical copy of the molecule and its document.

cloneMoleculeWithDocument() - Method in class chemaxon.struc.RgMolecule

cloneMoleculeWithDocument() - Method in class chemaxon.struc.RxnMolecule

cloneProp() - Method in class chemaxon.struc.MDocument.Prop

Creates a clone.

cloneProp() - Method in class chemaxon.struc.MProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MFontProp

cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MMoleculeStringProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MObjectProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MStringProp

Clones the object.

cloneSets(MDocument) - Method in class chemaxon.struc.MDocument

Clones the atom/bond sets from doc.

cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.Sgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.Sgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.DataSgroup

Gets a new DataSgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Gets a new Sgroup instance.

cloneStructure() - Method in class chemaxon.struc.Sgroup

Gets the clone of the structure stored.

cloneTemporraryObjects(MDocument) - Method in class chemaxon.struc.MDocument

close() - Method in class chemaxon.formats.MolConverter

Closes the exporter and the output stream.

close() - Method in class chemaxon.formats.MolExporter

Closes the MolExportModule and the underlying stream.

close() - Method in class chemaxon.formats.MolImporter

Close the underlying input stream.

close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Interrupts parsing.

close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter

close() - Method in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Close the underlying input stream.

close() - Method in class chemaxon.marvin.io.MDocSource

Closes the underlying input stream(s).

close() - Method in class chemaxon.marvin.io.MolExportModule

Close the stream.

close() - Method in class chemaxon.marvin.io.MRecordImporter

Closes the input stream.

close() - Method in interface chemaxon.marvin.io.MRecordReader

Closes the input stream.

close() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer

Closes the importers.

close() - Method in interface chemaxon.util.progress.ProgressObserver

Notifies that the represented task has completed (either successfully or because of a failure), and no further work will be done.

close() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Closes the output.

close() - Method in interface com.chemaxon.util.concurrent.CloseableIterator

close(int) - Method in class chemaxon.formats.MolConverter

Closes the exporter.

close(int) - Method in class chemaxon.formats.MolExporter

Closes the MolExportModule and, optionally, the underlying stream.

close(int) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Closes the output.

closeableIterator(Iterator<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper

Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator.
NOTE: the returned iterator provides the same molecule instances with maps added

closeableIterator(Iterator<Molecule>, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.

closeableIterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper

Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator using the specified number of threads for mapping.
NOTE: the returned iterator provides the same molecule instances with maps added

closeableIterator(Iterator<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper

Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator using the specified mappers for mapping.

CloseableIterator<T> - Interface in com.chemaxon.util.concurrent

An auto-closeable wrapper for the Iterator class, so you should use this class with try-with-resources statements!

closeableResultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.

closeableResultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String, boolean) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.

CLOSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Closed flag.

closeSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane

Closes the sketcher window that belongs the the specified cell.

closeWindow(int) - Method in class chemaxon.marvin.beans.MViewPane

Closes the detached viewer window of the specified cell.

closeWindows() - Method in class chemaxon.marvin.beans.MarvinPane

Closes all windows opened by this MarvinPane.

Cm - Static variable in class chemaxon.core.ChemConst

CML - Static variable in class chemaxon.formats.MFileFormat

Chemical Markup Language.

Cn - Static variable in class chemaxon.core.ChemConst

CnsMpo - Class in chemaxon.calculations.cnsmpo

CNS MPO score calculator.

CnsMpo.Property - Class in chemaxon.calculations.cnsmpo

Simple DTO that contains the predicted value and its CNS MPO score.

CnsMpoFunction - Enum Class in chemaxon.calculations.cnsmpo

Base phys-chem property calculators and its score functions for CNS MPO calculation.

Co - Static variable in class chemaxon.core.ChemConst

codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Add mass number information to the given code.

COL_MOLECULE - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for adding query-target column to ligand table.

COL_SCAFFOLD - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for adding scaffold column to ligand table.

colDec - Variable in class chemaxon.descriptors.PFParameters

atom set colors

collectLonePairContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

collectLonePairsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

collectMElectronContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

Collects all MElectronContainers of an atom, if the atom is part of a Molecule, which has an MDocument.

collectMElectronsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectron

Deprecated, for removal: This API element is subject to removal in a future version.

collectRadicalContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

collectRadicalsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

color() - Method in class chemaxon.sss.search.Decomposition

Colors ligands, scaffold, query and target by setting color data in atoms by calling MolAtom.setSetSeq(int).

color(Molecule) - Static method in class chemaxon.sss.search.Decomposition

Colors a molecule by setting color data in atoms by calling MolAtom.setSetSeq(int).

color(Molecule, String) - Static method in class chemaxon.sss.search.Decomposition

Colors a molecule by setting color data in the specified molecule property (SDF tag).

color(String) - Method in class chemaxon.sss.search.Decomposition

Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag).

COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "colorScheme".

ColorGenerator - Class in chemaxon.marvin.util

A final class which provides a static access to a color distant color creator class.

ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator

COLORING_ALL - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Constant for setting all coloring options, currently scaffold and R-groups.

COLORING_NONE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Constant for no hit coloring.

COLORING_RGROUPS - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Constant for R-group coloring.

COLORING_SCAFFOLD - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Constant for scaffold coloring.

COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "cols".

com.chemaxon.calculations.admet - package com.chemaxon.calculations.admet

com.chemaxon.calculations.cli - package com.chemaxon.calculations.cli

com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal

API of the elemental analysis functionality.

com.chemaxon.calculations.elemanal.factory - package com.chemaxon.calculations.elemanal.factory

com.chemaxon.calculations.gui - package com.chemaxon.calculations.gui

com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility

com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal

API of the Stereo Analysis Plugin.

com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters

Core filter classes.

com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop

Atrop stereo filter implementations.

com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial

Axial stereo filter implementations.

com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans

Cis-trans stereo filter implementations.

com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral

Tetrahedral stereo filter implementations.

com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters

Stereocenter implementations of Stereo Analysis API.

com.chemaxon.calculations.stereoisomers - package com.chemaxon.calculations.stereoisomers

com.chemaxon.common.annotations - package com.chemaxon.common.annotations

Provides annotations for Chemaxon classes.

com.chemaxon.mapper - package com.chemaxon.mapper

com.chemaxon.search - package com.chemaxon.search

Tools for chemical search.

com.chemaxon.search.mcs - package com.chemaxon.search.mcs

Contains classes for finding the maximum common substructure (MCS) of molecular structures.

com.chemaxon.search.mcs.buildup - package com.chemaxon.search.mcs.buildup

Contains MCS algorithm implementation based on the "build up" method.

com.chemaxon.search.mcs.maxclique - package com.chemaxon.search.mcs.maxclique

Contains MCS algorithm implementation based on the "maximum clique" method.

com.chemaxon.search.mcs.upperbound - package com.chemaxon.search.mcs.upperbound

Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.

com.chemaxon.search.transformation - package com.chemaxon.search.transformation

com.chemaxon.search.transformation.transformers - package com.chemaxon.search.transformation.transformers

com.chemaxon.search.transformation.util - package com.chemaxon.search.transformation.util

com.chemaxon.util.concurrent - package com.chemaxon.util.concurrent

This package contains an Iterator wrapper that can be used to perform calculations simultaneously on multiple elements provided by the wrapped iterator, and returns the calculation results while preserving the original order of elements.

com.chemaxon.version - package com.chemaxon.version

combine(Collection<? extends CalculatorInputChecker>) - Static method in interface chemaxon.calculator.CalculatorInputChecker

Combines the given checkers into a single one that reports all errors reported by the given checkers.

compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator

compareAtoms(int, int) - Method in class chemaxon.sss.search.MolComparator

Compares atoms of indices a1 and a2.

compareBonds(int, int) - Method in class chemaxon.sss.search.MolComparator

Compares bonds of indices b1 and b2.

compareHit(int[], int) - Method in class chemaxon.sss.search.MolComparator

Checks a partial hit during the search algorithm.

compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Comparison method which uses the priority field for ordering.

compareTo(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

compareTo(BicycloStereoDescriptor) - Method in class chemaxon.struc.BicycloStereoDescriptor

Compares two bicyclostereo descriptors.

compareTo(RgroupBridgeId) - Method in class chemaxon.struc.RgroupBridgeId

compareTo(AttachmentPoint) - Method in class chemaxon.struc.sgroup.AttachmentPoint

Compares two attachment points by their order.

compareTo(Object) - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

compile(String) - Method in class chemaxon.jep.ChemJEP

Compiles the expression string to an inner structure.

compile(String) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, C) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, C, ConstantTable) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, Class<? extends C>) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, Class<? extends C>, ConstantTable) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, Class<? extends C>, SymbolTable) - Method in class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

Use Evaluator.compile(String, Class, ConstantTable) instead.

COMPILE_ERROR - Static variable in class chemaxon.jep.ChemJEP

The compilation error message.

COMPLETE - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle

All atoms will be mapped

COMPONENT - Enum constant in enum class chemaxon.struc.SgroupType

ComponentChecker<E> - Class in chemaxon.checkers

Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).

ComponentChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.ComponentChecker

Constructor to create a Structure checker instance with the given errorType.

componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Hides windows if the parent frame is hidden.

componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Does nothing.

componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Does nothing.

componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MViewPane

componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Shows windows if the parent frame is hidden.

composition() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

composition(int) - Method in class chemaxon.calculations.ElementalAnalyser

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

COMPOSITION - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "composition".

COMPRESS - Static variable in class chemaxon.formats.MdlCompressor

Compression flag.

compressedData - Variable in class chemaxon.descriptors.PFParameters

Buffer for compressed data, used in MolecularDescriptor.toData( final int[] ).

computeFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Computes the scaling factor for the unscaled NMR spectrum function.

computeFunctionScale(double, double[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

ConcurrentStandardizerProcessor - Class in chemaxon.standardizer

Performs standardization of molecules in concurrent mode.

ConcurrentStandardizerProcessor() - Constructor for class chemaxon.standardizer.ConcurrentStandardizerProcessor

ConcurrentStandardizerProcessor.MolTransformer - Interface in chemaxon.standardizer

Molecule transformer.

CONFIDENCE - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the confidence that the structure is correct.

config - Variable in class chemaxon.checkers.StructureCheckOptions

The configuration of the structure check.

CONFIG_DIR - Static variable in class chemaxon.jep.Evaluator

Default directory for storing configuration files.

CONFIG_PATH_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction

The key of configuration path parameter of the abstract action.

configFilePath - Variable in class chemaxon.descriptors.MDParameters

location of the configuration file

ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader

This interface is provided for classes which can read the configuration of CheckerRunner.

ConfigurationUtility - Class in chemaxon.standardizer.configuration

Utility to manage standardizer configuration

ConfigurationUtility() - Constructor for class chemaxon.standardizer.configuration.ConfigurationUtility

CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "confirmTransfer".

CONFORMATION - Enum constant in enum class chemaxon.calculator.CalculatorTag

CONFORMER_CONFORMERS - Enum constant in enum class chemaxon.calculator.CalculatorTag

CONFORMER_HASVALIDCONFORMER - Enum constant in enum class chemaxon.calculator.CalculatorTag

CONFORMER_LECONFORMER - Enum constant in enum class chemaxon.calculator.CalculatorTag

ConformerPlugin - Class in chemaxon.marvin.calculations

Plugin class for conformer calculation.

ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin

CONJUGATED - Enum constant in enum class chemaxon.struc.BondType

Conjugation state of the bond.

CONJUGATED - Static variable in class chemaxon.struc.MolBond

Conjugation state of the bond.

connectedMode(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether the common substructures should be connected or they can consist of multiple fragments.

connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule

connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Sets the original connections to the new atom.

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject

CONSENSUS - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod

Consensus model using Chemaxon and Klopman's models and the PhysProp database.

Consent - Enum Class in chemaxon.marvin.collecting

constant - Variable in class chemaxon.marvin.services.ServiceArgument

field indicates constant argument

constants() - Method in class chemaxon.jep.ConstantTable

Returns an immutable set containing the names of the constants in this table.

constantTable() - Method in class chemaxon.jep.ChemJEP

Returns the constant table used by this parser.

constantTable() - Method in class chemaxon.jep.Evaluator

Returns the table of predefined constants (molecules, molecule sets and other constants defined in the built-in and the user-defined jep.script).

ConstantTable - Class in chemaxon.jep

Immutable table of constants used in a Chemical Terms evaluator.

ConstantTableBuilder - Class in chemaxon.jep

A builder for a ConstantTable.

contains(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

contains(MDocument) - Method in class chemaxon.struc.MDocument

Tests whether the document contains all objects of another document.

contains(MObject) - Method in class chemaxon.struc.MDocument

Searches an object in the document.

contains(MolAtom) - Method in class chemaxon.struc.MolBond

contains(MolAtom) - Method in class chemaxon.struc.Molecule

Checks if the molecule graph contains the specified atom.

contains(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Checks if the molecule graph contains the specified atom.

contains(MolAtom) - Method in class chemaxon.struc.RgMolecule

Checks if the root structure or an R-group contains the specified node.

contains(MolAtom) - Method in class chemaxon.struc.RxnMolecule

Checks if a reactant, agent or product structure contains the specified node.

contains(MolAtom) - Method in class chemaxon.struc.Sgroup

Is this atom contained by the s-group?

contains(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.

contains(MolBond) - Method in class chemaxon.struc.RgMolecule

Checks if the root structure or an R-group contains the specified edge.

contains(MolBond) - Method in class chemaxon.struc.RxnMolecule

Checks if a reactant, agent or product structure contains the specified edge.

contains(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Does the molecule graph contain the specified fragment?

contains(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether the container contains the specified property object.

contains(MProp) - Method in class chemaxon.struc.prop.MCollectionProp

Tests whether the collection contains the specified property.

contains(String) - Method in class chemaxon.checkers.util.AtomLabels

Gets whether the atom labels contain the specified atom label

contains(String) - Method in class chemaxon.checkers.util.DataExclusionList

containsAllAtomsOf(Sgroup) - Method in class chemaxon.struc.Sgroup

Checks if the S-group contains the atoms of another S-group.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MElectronContainer

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.MObject

Checks if the object contains the specified atom reference.

containsConstant(String) - Method in class chemaxon.jep.ConstantTable

Returns true if this table contains the given constant.

containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Decides whether a molecule graph contains coordinate bonds.

containsLadderTypePolymer() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether the structure of this sgroup contains a ladder-type repeating unit.

containsMulticenterSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Decides whether a molecule contains Multicenter S-groups.

containsOnlyOne(Class<?>) - Method in class chemaxon.struc.MDocument

Deprecated, for removal: This API element is subject to removal in a future version.

containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle

containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject

containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom

Returns true if this atom has a mapping for the specified property key.

containsPropertyKey(String) - Method in class chemaxon.struc.MolBond

Returns true if this bond has a mapping for the specified property key.

containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if molecule contains pseudo atom.

containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Decides whether a molecule contains SRU S-groups.

CONTEXT - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the context of the structure recognized in the text.

CONTEXT_INDEX - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: index of the hit inside the context.

contract(int) - Method in class chemaxon.struc.Sgroup

Sets the state to Sgroup.XSTATE_C.

contract(int) - Method in interface chemaxon.struc.sgroup.Expandable

Contracts the S-group.

contract(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Contracts this S-group.

contract(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Contracts this S-group.

ContractGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule

ContractGroupFixer() - Constructor for class chemaxon.fixers.ContractGroupFixer

contractOrExpandSgroups(int, String, boolean) - Method in class chemaxon.marvin.view.MDocStorage

Contract or expand S-groups in the specified cell.

contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.view.MDocStorage

Contract or expand S-groups in all molecules.

contractSgroups() - Method in class chemaxon.struc.Molecule

Contracts all S-groups.

contractSgroups(int) - Method in class chemaxon.struc.Molecule

Contracts all S-groups.

ContractSgroupsAction - Class in chemaxon.standardizer.actions

Standardizer action contracting s-groups of the target molecule

ContractSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ContractSgroupsAction

Initializes the action

convert() - Method in class chemaxon.formats.MdlCompressor

Compression/decompression

convert() - Method in class chemaxon.formats.MolConverter

Convert the next molecule.

convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor

(Un)compress the specified molfile or SDfile.

convert(byte[], int, int) - Method in class chemaxon.marvin.io.Encoding

Converts a byte array to a string.

convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy

convert(double, double) - Method in class chemaxon.calculations.nmr.Multiplet

Multiplies the parameters of this multiplet (unit conversion).

convert(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Creates an MDL mol or compressed mol representation of the molecule.

convert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule

Convert a molecule to a string or byte array.

convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult

convert(Molecule, Map<String, Map<?, ?>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method converts the entities contained in this result according to the convertData.

convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.ModeConverter

convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.TypeConverter

convert(String, boolean) - Method in interface chemaxon.naming.NameConverter

Convert a name into the corresponding structure.

convert(String, int) - Static method in class chemaxon.formats.MdlCompressor

(Un)compress the specified molfile or SDfile.

ConvertAliasToGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the aliases to contracted abbreviated groups in the molecule

ConvertAliasToGroupFixer() - Constructor for class chemaxon.fixers.ConvertAliasToGroupFixer

ConvertConstants - Class in chemaxon.checkers.result

This class contains convert relevant constants

ConvertConstants() - Constructor for class chemaxon.checkers.result.ConvertConstants

convertCoordinateBondsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Converts coordinate bonds to data sgroups (attached data) with field name MRV_COORDINATE_BOND.

ConvertDoubleBondsAction - Class in chemaxon.standardizer.actions

Convert double bonds standardizer action

ConvertDoubleBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertDoubleBondsAction

Initializes the action with parameters

ConvertDoubleBondsAction.Type - Enum Class in chemaxon.standardizer.actions

Type of conversion

convertExplicitHToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts explicit Hydrogen atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts explicit Hydrogen atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.

convertExplicitLonePairsToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts explicit lone pairs from a molecule to implicit.

convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts implicit Hydrogen atoms of the molecule to explicit.

convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Convert implicit lone pairs of the atoms of a molecule to explicit.

convertPageSettingsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX.

ConvertPiMetalBondsAction - Class in chemaxon.standardizer.actions

Convert Pi-Metal coordinate bond to coordinate bond action.

ConvertPiMetalBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertPiMetalBondsAction

Initializes a convert pi-metal bond action

ConvertPseudoToGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the pseudo informations to contracted abbreviated groups in the molecule

ConvertPseudoToGroupFixer() - Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer

convertResult(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner

Deprecated.

This method converts the result by changing the atoms and bonds back to the original instead of the cloned ones

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker

Handles the mapping of a cloned and expanded molecule result to the original molecule.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker

This implementation does nothing.

ConvertToAtomFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information

ConvertToAtomFixer() - Constructor for class chemaxon.fixers.ConvertToAtomFixer

convertToBondType(int) - Static method in enum class chemaxon.struc.BondType

Creates BondType from the given number.

ConvertToCarbonFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms

ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer

ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond

ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer

ConvertToElementalFormFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms

ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer

ConvertToEnhancedStereoAction - Class in chemaxon.standardizer.actions

Convert to enhanced stereo standardizer action

ConvertToEnhancedStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Initializes the action with parameters

convertToFrags() - Method in class chemaxon.struc.Molecule

Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.

ConvertToIonicFormFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.

ConvertToIonicFormFixer() - Constructor for class chemaxon.fixers.ConvertToIonicFormFixer

ConvertToPlainDoubleBondFixer - Class in chemaxon.fixers

Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.

ConvertToPlainDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToPlainDoubleBondFixer

ConvertToSingleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the bond to single bond.

ConvertToSingleBondFixer() - Constructor for class chemaxon.fixers.ConvertToSingleBondFixer

convertToSmilingFormat(Molecule) - Static method in class chemaxon.formats.MFileFormatUtil

Tries to convert a molecule to a SMILES related format.

convertToSmilingFormat(MProp) - Static method in class chemaxon.formats.MFileFormatUtil

Try to convert a property to text with a SMILES related format argument.

convertToString(MDocument, String, int) - Static method in class chemaxon.formats.MolExporter

Converts the document to text format.

convertToString(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler

Converts the value associated with the given key in the given MPropertyContainer to string.

convertToString(MProp, String) - Static method in class chemaxon.marvin.io.MPropHandler

Converts the property to text format.

convertToString(String) - Method in class chemaxon.struc.MProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.7, replaced by MolExporter.convertToString(MDocument, String, int)

convertToString(String, int) - Method in class chemaxon.struc.MProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).

convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).

convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MFontProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).

convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts crossed double bond to wiggly

ConvertToWigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToWigglyDoubleBondFixer

convertTransform(CTransform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle

COORDDEP - Static variable in class chemaxon.struc.MProp

Coordinate dependent property.

COORDINATE - Enum constant in enum class chemaxon.struc.BondType

Coordinate bond.

COORDINATE - Static variable in class chemaxon.struc.MolBond

Coordinate bond flag.

COORDINATE_BOND_STYLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "coordinateBondStyle".

COORDINATE_BOND_STYLE_AT_MULTICENTER - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "coordinateBondStyleAtMulticenter".

CoordinationSystemErrorChecker - Class in chemaxon.checkers

Detects errors of multicenter coordination systems.

CoordinationSystemErrorChecker() - Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker

Default constructor

COORDS_UPDATE - Static variable in interface chemaxon.struc.sgroup.Expandable

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, no replacement.
Not supported feature.

COPOLYMER - Enum constant in enum class chemaxon.struc.SgroupType

COPOLYMER_ALT - Enum constant in enum class chemaxon.struc.SgroupType

COPOLYMER_BLK - Enum constant in enum class chemaxon.struc.SgroupType

COPOLYMER_RAN - Enum constant in enum class chemaxon.struc.SgroupType

COPY_AS_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants

Default format to be selected on Copy as dialog.

COPY_AS_IMAGE_BITMAP - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated, for removal: This API element is subject to removal in a future version.

COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated, for removal: This API element is subject to removal in a future version.

COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated, for removal: This API element is subject to removal in a future version.

COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated, for removal: This API element is subject to removal in a future version.

COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Deprecated, for removal: This API element is subject to removal in a future version.

since 5.3.3 has no sense

copyOf(ShapeData) - Static method in class chemaxon.marvin.alignment.ShapeData

CopyOptConstants - Interface in chemaxon.marvin.util

Deprecated, for removal: This API element is subject to removal in a future version.

since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this interface either non exists in the new implementation or its value has changed. See the constants own description for details.

copyProperties(MAssigner) - Method in class chemaxon.struc.graphics.MAssigner

Copies the assigner properties to another assigner object.

copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket

Copies line properties to another line object.

copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow

copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline

Copies line properties to another line object.

copyProperties(MRArrow) - Method in class chemaxon.struc.graphics.MRArrow

Copies arrow properties to another arrow object.

correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

countAllAtoms() - Method in class chemaxon.struc.MolAtom

Counts all atoms represented by this atom.

countAllAtoms() - Method in class chemaxon.struc.Sgroup

Counts the total number of atoms recursively.

countAllAtoms() - Method in class chemaxon.struc.sgroup.SgroupAtom

Counts all atoms represented by this atom.

countEnumerations() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the number of all enumerated structures, no arithmetic overflow because counts in BigInteger.

countEnumerationsMagnitude() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures.

countExpandableContractableSgroups() - Method in class chemaxon.struc.Molecule

Counts the expandable and contractable S-groups.

countOrderedComponentSgroups() - Method in class chemaxon.struc.Molecule

Counts the ordered component S-groups.

countRecords(MProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.view.MDocStorage

Counts the total number of records and sets the size of the document storage.

countRecordsInFraction(double, int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage

Deprecated, for removal: This API element is subject to removal in a future version.

COVALENT_COUNTER_ION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that incorrectly drawn covalent counter ion had found in the molecule

COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Covalent hydration error remark.

CovalentCounterionChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).

CovalentCounterionChecker() - Constructor for class chemaxon.checkers.CovalentCounterionChecker

Default constructor

covalentRadiusOf(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the covalent radius in C-C bond length units.

Cr - Static variable in class chemaxon.core.ChemConst

crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

create() - Static method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Constructs a new StereoisomerSettings object with default settings.

create(byte[]) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

Call AlignmentMolecule.create(byte[], DegreeOfFreedomType) with AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE.

create(byte[], AlignmentProperties.DegreeOfFreedomType) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule

Deserializes an AlignmentMolecule from a byte array.

create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

create(Molecule, Molecule) - Method in interface com.chemaxon.search.mcs.McsCustomMatcherFactory

Creates a custom matcher for atom and bond pairs of the given query and target structures.

create(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

Creates a similarity calculator object according to the user defined parameters.

create(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Loads a plugin from the classpath based on its fully qualified name.

create(String, int, int) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

Creates a similarity calculator object according to the user defined parameters.

create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Loading plugins from plugin-specific jars is no longer supported, use CalculatorPlugin.create(String) instead.

createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas

Constructs an elemental analysis from molecular formula.

createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas

Deprecated.

Constructs an elemental analysis from molecular formula.

createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value

createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value

createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value and type

createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value and type

createAromatizedSearcher(AromatizationMethod) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher that considers aromatization differences of the input molecule.

createAromatizedSearcher(AromatizationMethod, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher which considers aromatization according to the specified rules and initializes it with the specified search options.

createArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler

Creates an array property.

createArrayXSD(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler

Creates an array property from the XSD type.

createAtomIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.

createAtomNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an iterator to get the atom neighbours of the specified atom.

createBondIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.

createBondNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an iterator to get the bonds connecting to the specified atom.

createBondTable(int, int) - Static method in class chemaxon.core.util.BondTable

Creates a new bond table for a molecule graph with the specified number of atoms and bonds.

createBondType(int) - Static method in enum class chemaxon.struc.BondType

Deprecated, for removal: This API element is subject to removal in a future version.

since 2014.06.04. use BondType.convertToBondType(int) instead.

createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil

createChecker(String, Map<String, String>) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory

This method creates a requested (type represented in checkerId) StructureChecker instance with the give parameters

createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes

createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument

Creates a ServiceArgument constant based on string value and argument type.
Supported types are String, Integer, Long, Double, Float and Boolean

createDefaultParameterPanel(Class, String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory

createDefaultParameterPanel(String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory

Creates default parameter panel based on XML config.

createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph

Creates a dehydrogenized version of the molecule.

createEMF(String, String) - Static method in class chemaxon.util.ImageExportUtil

Creates a .NET based EMF picture.

createErrorMessage(StandardizerConfiguration) - Static method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Creates an error message based on an invalid configuration

createExportModule() - Method in class chemaxon.formats.MFileFormat

Creates the export module.

createExportModule(String) - Method in interface chemaxon.formats.factory.MolExportModuleFactory

Creates the export module.

createExportModule(String) - Method in class chemaxon.formats.MFileFormat

Creates the export module.

createExportModule(String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates an export module for the specified format.

createExportModule(String, String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates an export module for the specified format with the specified encoding.

createFixer(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory

This method creates a StructureFixer instance identified by fixerId parameters

createGearch() - Method in class chemaxon.struc.Molecule

createGearch() - Method in class chemaxon.struc.MoleculeGraph

createGearch() - Method in class chemaxon.struc.RgMolecule

createGearch() - Method in class chemaxon.struc.RxnMolecule

createGearch() - Method in class chemaxon.struc.SelectionMolecule

createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

CreateGroupAction - Class in chemaxon.standardizer.advancedactions

Create Group standardizer action

CreateGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.CreateGroupAction

Initializes a create group standardizes action

createImporter(InputStream) - Method in interface chemaxon.formats.ImportOptions

Creates a MolImporter from the given input stream.

createImportMod(MolInputStream) - Static method in class chemaxon.marvin.io.MRecordImporter

Creates an importer for the specified molecule input stream.

createImportMod(String) - Static method in class chemaxon.marvin.io.MRecordImporter

Creates an importer for the specified molecule format.

createImportModule() - Method in interface chemaxon.formats.factory.MolImportModuleFactory

Creates the molecule import module.

createImportModule() - Method in class chemaxon.formats.MFileFormat

Creates the molecule import module.

createInDocumentAt(DPoint3, MDocument) - Static method in class chemaxon.struc.NoStructure

Creates a NoStructure at the given location.

createInDocumentFrom(Molecule, MDocument) - Static method in class chemaxon.struc.NoStructure

Creates a NoStructure from the given component.

createMElectronContainer(DPoint3[], MolAtom, boolean) - Static method in class chemaxon.struc.graphics.MElectronContainer

createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.3.1, replaced by SwingUtil.createMenu

createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil

Utility method to create a menu with a label specified as a resource.

createMenu(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu with a label specified as a resource.

createMenuItem(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu with a label specified as a resource.

createMenuItem(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu with a label specified as a resource.

createMenuItem(ResourceBundle, String, Class<?>, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu item with a label specified as a resource.

createMessagePane(String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a message pane with HTML text content.

createMMoleculeProp(String) - Static method in class chemaxon.marvin.io.MPropHandler

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Returns the molecule form with largest distribution.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the canonical tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the modified input molecule (e.g.

createMol() - Method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

As of 23.15, no replacement

createMol() - Method in class chemaxon.marvin.io.formats.mdl.MolImport

Creates a new target molecule object.

createMol() - Method in class chemaxon.marvin.io.MolImportModule

Creates a new target molecule object for the import.

createMol() - Method in class chemaxon.marvin.io.MRecordImporter

Creates an empty target molecule for import.

createMolConverter(InputStream, OutputStream, String[], int[]) - Static method in class chemaxon.formats.MolConverter

Creates a MolConverter instance with the attributes specified in the parameters.

createMolecule() - Method in class chemaxon.struc.Sgroup

Creates a molecule object that contains only this group.

createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Creates a molecule object that contains only one SuperatomSgroup identical to this one.

createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup

Creates a cloned sgroup instance and a molecule object that contains only this sgroup.

createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.

createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory

Creates a MoleculeIterator object for iterating through a molecule array (Molecule[]).

createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory

Creates a MoleculeIterator object for iterating through collection of molecules (Molecule objects).

createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter

Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.

createNew() - Static method in class chemaxon.marvin.calculations.HlbPlugin.Builder

Constructs a new HlbPlugin instance.

createNew(Molecule) - Static method in class chemaxon.marvin.alignment.MCSAlignment.Factory

Constructs a new instance of ConformationAlignment class.

createNext() - Method in class chemaxon.struc.graphics.MTextAttributes

Creates identical attributes for the next section.

createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates the parameter panel.

createPreConcatenatedAffineTransform(Graphics2D) - Method in class chemaxon.struc.graphics.MTextBoxTransformation

createReaction(MoleculeGraph, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

createRecognizer() - Method in interface chemaxon.formats.factory.RecognizerFactory

Creates a recognizer module.

createRecognizer() - Method in class chemaxon.formats.MFileFormat

Creates a recognizer module.

createRecognizer(String) - Method in class chemaxon.formats.MFileFormat

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead

createRecordReader(MolInputStream, String) - Method in interface chemaxon.formats.factory.MRecordReaderFactory

Creates the record reader.

createRecordReader(MolInputStream, String) - Method in class chemaxon.formats.MFileFormat

Creates the record reader.

createRecordReader(InputStream, String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates a record reader for an input stream.

createRecordReader(InputStream, String, String, String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates a record reader for an input stream.

createResult(Molecule, List<StructureCheckerResult>) - Method in class chemaxon.checkers.ReactionChecker

This method a merged StructureCheckerResult from the List of StructureCheckerResult which contains the problems of the components in the reaction

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AliasChecker

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomChecker

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.PseudoAtomChecker

createResult(Molecule, List<MolBond>) - Method in class chemaxon.checkers.BondChecker

createResult(Molecule, List<E>) - Method in class chemaxon.checkers.ComponentChecker

Creates a StructureCheckerResult from a List containing the components.

createResultView(String, MolPanel) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

createRgComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.

createRotationAboutBond(MolBond, double) - Static method in class chemaxon.marvin.util.CleanUtil

Creates a rotation transformation about a bond.

createRxnComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.

createSavedCoordsArray(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Creates an empty array for the atomic coordinates of a structure.

createScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler

Creates a scalar property.

createScalar(String, String, MProgressMonitor) - Static method in class chemaxon.marvin.io.MPropHandler

Creates a scalar property.

createScalarXSD(String, String) - Static method in class chemaxon.marvin.io.MPropHandler

Creates a scalar property from the XSD type.

createSearcher(Transformer, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Constructs a searcher with the specified parameters.

createSearcherWithoutAromatization() - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher that does not handle aromatization.

createSearcherWithoutAromatization(MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher that doesn't consider aromatization.

createSearcherWithoutAromatization(SimpleSearcher, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher with the specified search options, other parameters (query, target, etc.) are copied from the specified searcher if possible (in case of BaseMolSearch).

createServiceHandler() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor

createServiceHandler() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor

createServiceHandler() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

createServiceHandler() - Method in class chemaxon.marvin.services.ServiceDescriptor

Creates a new service handler for this descriptor.

createServiceHandler() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

createServiceHandler() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor

createSgroupIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an s-group iterator for the specified molecule of the factory.

createSmolecule() - Method in class chemaxon.struc.MoleculeGraph

Creates a Smolecule represenation of this molecule.

createSpacePanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates space panel with given molecules, creates colored surface to each molecule.

createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.

createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.

createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Creates standardized molecule, the original input molecule is cloned.

createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use ResonancePlugin.createStandardizedMolecule(Molecule) instead

createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use TautomerizationPlugin.createStandardizedMolecule(Molecule) instead

createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use CalculatorPlugin.createStandardizedMolecule(Molecule) instead

createStatistics - Variable in class chemaxon.descriptors.MDGenerator

indicates if statistical data has to be gathered during generation

createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a sub-panel with a title.

createTautomerMoleculeBasedOnDecoration(Molecule, boolean) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

createTopLeftConstraints() - Static method in class chemaxon.marvin.util.SwingUtil

Creates GridBagConstraints for the top left component.

createUserDefined(String, String, String, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, String, long) - Static method in class chemaxon.formats.MFileFormat

Creates a user-defined format descriptor.

createUserDefined(String, List<String>, List<String>, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, Map<String, Integer>, long) - Static method in class chemaxon.formats.MFileFormat

Creates a user-defined format descriptor.

createViewPanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates view panel with given molecules, places molecule properties in formatted texts.

createViewPanel(Molecule[], int, int, int, int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates view panel with given molecules, places molecule properties in formatted texts.

createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter

createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter

Constructs the specified visitor implementation.

createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter

createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter

createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter

createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter

createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter

createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter

createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter

createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter

createVisitor(Consumer<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter

createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter

createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter

createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter

createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter

createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter

createVisitor(Consumer<T>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter

Constructs the specified visitor implementation.

CRITICAL_ERROR_MSG - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Critical error message.

cross(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3

Calculates the cross product of the two vectors

CROSSED - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Crossed double bond type

CROSSED_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that crossed double bond had found in the molecule

CrossedDoubleBondChecker - Class in chemaxon.checkers

A descendant of BondChecker for the detection of unspecified double bonds represented by crossed bond type.

CrossedDoubleBondChecker() - Constructor for class chemaxon.checkers.CrossedDoubleBondChecker

Default constructor

CrossedDoubleBondFixer - Class in chemaxon.fixers

Deprecated, for removal: This API element is subject to removal in a future version.

use ConvertToWigglyDoubleBondFixer

CrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.CrossedDoubleBondFixer

Deprecated.

CROSSLINK - Enum constant in enum class chemaxon.struc.SgroupType

Cs - Static variable in class chemaxon.core.ChemConst

CSMDL_IN - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.

CSMOL_OUT - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed Molfiles and Rgfiles.

CSRDF - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed RDfiles.

CSRXN_OUT - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed Rxnfiles.

CSSDF_OUT - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed SDfiles.

cssr - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

CSSR - Enum constant in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption

Complete set of smallest rings.

CSV - Static variable in class chemaxon.formats.MFileFormat

ctab - Variable in class chemaxon.struc.MoleculeGraph

Connection table.

CTransform3D - Class in chemaxon.struc

3D transformation matrix.

CTransform3D() - Constructor for class chemaxon.struc.CTransform3D

Constructs an identity transformation.

CTransform3D(CTransform3D) - Constructor for class chemaxon.struc.CTransform3D

Copy constructor.

CTSPECIFIC_H - Static variable in class chemaxon.struc.MolAtom

Deprecated.

As of Marvin 5.11
Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.

CTUMASK - Static variable in interface chemaxon.struc.StereoConstants

Double bond stereo mask.

CTUNKNOWN - Static variable in interface chemaxon.struc.StereoConstants

Deprecated.

As of Marvin 6.1,
Usage:

 In the specified methods the CIS|TRANS or
 CIS|TRANS|CTUNSPEC values are used instead.
 

CTUNSPEC - Static variable in interface chemaxon.struc.StereoConstants

Unspecified double bond.

Cu - Static variable in class chemaxon.core.ChemConst

CubeRecognizer - Class in chemaxon.formats.recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

CubeRecognizer() - Constructor for class chemaxon.formats.recognizer.CubeRecognizer

Deprecated.

currentBond - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Current bond pointer of the iterator.

currentMetricIndex - Variable in class chemaxon.descriptors.MDParameters

index of the parametrized metric currently in use

cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Move the cursor down.

cursorLeft(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorRight(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorToRowEnd(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorToRowStart(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorUp(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Moves the cursor up.

CUSTOM_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

custom name property

CustomDescriptor - Class in chemaxon.descriptors

The CustomDescriptor class implements a generic molecular descriptor class which supports third party or use defined descriptors.

CustomDescriptor() - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.

CustomDescriptor(int, int) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.

CustomDescriptor(CDParameters) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new instance of CustomDescriptor according to the parameters given.

CustomDescriptor(CustomDescriptor) - Constructor for class chemaxon.descriptors.CustomDescriptor

Copy constructor.

CustomDescriptor(String) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new instance of CustomDescriptor according to the parameters given.

CustomFunction - Interface in chemaxon.jep

Base interface for custom Chemical Terms functions.

CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "customizationEnabled".

customMatching(McsCustomMatcherFactory) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets the factory to be used to create a custom matcher.

CXON - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Object Notation.

CXSMARTS - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Extended SMARTS.

CXSMILES - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Extended SMILES.

cyclomaticNumber() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the smallest number of graph edges which must be removed such that no circuit remains.

D

D2S - Static variable in class chemaxon.formats.MFileFormat

Any document format recognized by Document to Structure (doc, odt, ...).

data - Variable in class chemaxon.descriptors.MDParameters

buffer for external data format generation, used in MolecularDescriptor.toData()

DATA - Enum constant in enum class chemaxon.struc.SgroupType

DATA_COLLECTION_CONSENT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

DATA_COLLECTION_SERVER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

DataExclusionList - Class in chemaxon.checkers.util

A list of Strings to be excluded by AttachedDataChecker.

DataExclusionList(String) - Constructor for class chemaxon.checkers.util.DataExclusionList

DataSgroup - Class in chemaxon.struc.sgroup

Data Sgroup.

DataSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.DataSgroup

Creates a Data S-group with the specified parent.

DataSgroup(DataSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.DataSgroup

Copy constructor.

DataSgroup(DataSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.DataSgroup

Copy constructor.

DataSgroupCheckerResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.

DataSgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DataSgroupCheckerResult

Constructor which initialize all the properties.

date() - Element in annotation interface com.chemaxon.common.annotations.SubjectToRemoval

Db - Static variable in class chemaxon.core.ChemConst

DBS_ALL - Static variable in interface chemaxon.struc.StereoConstants

Double bond stereo checking for all double bonds.

DBS_MARKED - Static variable in interface chemaxon.struc.StereoConstants

Double bond stereo checking for marked double bonds only.

DBS_NONE - Static variable in interface chemaxon.struc.StereoConstants

No double bond stereo checking.

DEAROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph

General dearomatization.

DEAROM_HUCKELCHECK - Static variable in class chemaxon.struc.MoleculeGraph

Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.

DEAROM_HUCKELCHECK_EX - Static variable in class chemaxon.struc.MoleculeGraph

Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.

DEAROMATIZATION_GENERAL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

General dearomatization method.

DEAROMATIZATION_HUCKEL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Dearomatization method with Hückel rule checking.

DEAROMATIZATION_HUCKEL_EX - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Dearomatization method with Hückel rule checking.

dearomatize() - Method in class chemaxon.struc.Molecule

Dearomatize molecule.

dearomatize() - Method in class chemaxon.struc.MoleculeGraph

Dearomatize molecule.

dearomatize(int) - Method in class chemaxon.struc.MoleculeGraph

Dearomatize molecule.

DearomatizeAction - Class in chemaxon.standardizer.actions

Dearomatization standardizer action

DearomatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DearomatizeAction

Initializes the action

DearomatizeFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the aromatic rings in the molecule into Kekule representation.

DearomatizeFixer() - Constructor for class chemaxon.fixers.DearomatizeFixer

DEBUG - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "debug".

Debye - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit

Debye unit.

DEBYE_TO_EA - Static variable in class chemaxon.calculations.dipole.DipoleResult

Debye to eA conversion upon multiplication.

decForm - Variable in class chemaxon.descriptors.MDParameters

to format floating point output

DECLINE - Enum constant in enum class chemaxon.marvin.collecting.Consent

decode(String, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes

Reads attributes of the next section from a string.

decode(String, MFont, MTextAttributes.MFontCreator, double) - Method in class chemaxon.struc.graphics.MTextAttributes

Reads attributes of the next section from a string.

decodeHIsotopeMass(int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Extract H isotope information from the given Chemaxon compressed mol format code of the atom.

Decomposition - Class in chemaxon.sss.search

Class storing RGroupDecomposition results.

Decomposition(Molecule, Molecule, int[][], Molecule[], Molecule) - Constructor for class chemaxon.sss.search.Decomposition

Constructor.

decompress(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Uncompresses input byte array and stores the uncompressed array in params.data.

DECOMPRESS - Static variable in class chemaxon.formats.MdlCompressor

Decompression.

decorateSubPanel(JPanel, String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates border and title for a panel.

decorateTautomerRegions(Molecule, int, OptionalInt) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

decQProp(String) - Method in class chemaxon.struc.MolAtom

Decrements the value of a query property.

decValenceProp() - Method in class chemaxon.struc.MolAtom

Decrements the value of the valence property.

DEF_IONICSTRENGTH - Static variable in class chemaxon.marvin.calculations.pKaPlugin

The default ionic strength of the pKa calculation models (small and large).

DEF_MAXIONS - Static variable in class chemaxon.marvin.calculations.pKaPlugin

The default value of the number of ionizable atoms to consider.

DEF_TEMPERATURE - Static variable in class chemaxon.marvin.calculations.pKaPlugin

The default temperature in Kelvins.

Default - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView

DEFAULT - Enum constant in enum class chemaxon.descriptors.MetricsType

DEFAULT - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

No aromatization.

DEFAULT - Enum constant in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption

No change in hydrogens.

DEFAULT - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption

Default error handling.

DEFAULT - Static variable in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

default factory id

DEFAULT - Static variable in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

The default options: both ValenceCheckOptions.isLocalAromatic() and ValenceCheckOptions.isTraditionalNitrogensAllowed() return true.

DEFAULT - Static variable in class chemaxon.marvin.io.Encoding

The system's default encoding.

DEFAULT - Static variable in class chemaxon.standardizer.StandardizerActionFactory

default factory id

DEFAULT - Static variable in class chemaxon.struc.graphics.MTextAttributes

Default attributes object.

DEFAULT - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory

default factory id

DEFAULT_ARROW_HEAD_LENGTH - Static variable in class chemaxon.struc.graphics.MPolyline

Default arrow head length.

DEFAULT_ARROW_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline

Default arrow head width.

DEFAULT_ASYMMETRY_FACTOR - Static variable in class chemaxon.descriptors.MDParameters

DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.CFParameters

DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.RFParameters

DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.CFParameters

DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.RFParameters

DEFAULT_CACHE_SIZE - Static variable in class com.chemaxon.mapper.AutoMapper

default cache size

DEFAULT_CACHE_SIZE_PROPERTY - Static variable in class com.chemaxon.mapper.AutoMapper

cache size property key

DEFAULT_CHECKERS_CONFIG_PATH - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader

path to default checker configuration list

DEFAULT_CONFIG_FILE - Static variable in class com.chemaxon.calculations.gui.PluginFactory

The default config file name.

DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Chemaxon's default checker configuration path

DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.standardizer.StandardizerActionFactory

Chemaxon's default standardizer action configuration path

DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory

Chemaxon's default checker configuration path

DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader

The default location of Chemaxon standard checker runner configuration

DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Chemaxon's default checker configuration file schema path

DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.standardizer.StandardizerActionFactory

Chemaxon's default standardizer action configuration file schema path

DEFAULT_DIAMETER - Static variable in class chemaxon.descriptors.ECFPParameters

DEFAULT_DISSIMILARITY_THRESHOLD - Static variable in interface chemaxon.sss.SearchConstants

Default threshold value for similarity search.

DEFAULT_EQUILIBRIUM_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline

Default equilibrium head width.

DEFAULT_FUZZINESS_FACTOR - Static variable in class chemaxon.descriptors.PFParameters

DEFAULT_FUZZY_CUTOFF - Static variable in class chemaxon.descriptors.PFParameters

DEFAULT_FUZZY_LOWER_BOUND - Static variable in class chemaxon.descriptors.PFParameters

DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.CFParameters

default values for parameters

DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.ECFPParameters

default values for parameters

DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.RFParameters

default values for parameters

DEFAULT_LOWER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters

default values for parameters

DEFAULT_MAX_CONSIDERED_RING_SIZE - Static variable in class com.chemaxon.search.mcs.McsSearchOptions

Default value for McsSearchOptions.Builder.maxConsideredRingSize(int).

DEFAULT_MAX_CROSS_SIZE - Static variable in class chemaxon.struc.graphics.MPolyline

Default maximum cross size.

DEFAULT_OPTIONS - Static variable in interface chemaxon.struc.sgroup.Expandable

Default expansion/contraction options.

DEFAULT_OUTPUT_PRECISION - Static variable in class chemaxon.descriptors.MDParameters

DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.HBParameters

default values for parameters

DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.LDParameters

DEFAULT_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor

the default priority value

DEFAULT_RANDOM_SEED - Static variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Default random seed.

DEFAULT_RECURSION_LEVEL - Static variable in class chemaxon.sss.screen.HashCode

DEFAULT_RESOLUTION - Static variable in class chemaxon.descriptors.PFParameters

default values

DEFAULT_RETROSYNTHETIC_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline

Default retrosynthetic head width.

DEFAULT_RLOGIC_RANGE - Static variable in class chemaxon.struc.RgMolecule

Default R-logic range.

DEFAULT_SALT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction

Default salt dictionary file path.

DEFAULT_SAMPLING_ACCURACY - Static variable in class chemaxon.marvin.alignment.AtropIsomerDetector

Default for parameter AtropIsomerDetector.setSamplingAccuracy(int).

DEFAULT_SAVE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "defaultSaveFormat".

DEFAULT_SCALE_FACTOR - Static variable in class chemaxon.descriptors.MDParameters

constants, default parameter values

DEFAULT_SEARCHTYPE - Static variable in interface chemaxon.sss.SearchConstants

Default search type equals SUBSTRUCTURE.

DEFAULT_SOLVENT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Default solvent dictionary file path.

DEFAULT_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader

path to default standardizer action configuration list

DEFAULT_STEP_SIZE - Static variable in class chemaxon.descriptors.scalars.LDParameters

DEFAULT_SUPERSCRIPT_DELTAY - Static variable in class chemaxon.struc.graphics.MTextAttributes

Default value of the y shift attribute in superscripts

DEFAULT_SUPERSCRIPT_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes

Default value of the font scale attribute in superscripts

DEFAULT_SUPERSCRIPT_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes

Default value of the superscript level attribute in superscripts

DEFAULT_TAG_NAME - Static variable in class chemaxon.jep.Evaluator

Default SDFile tag to store the evaluation result.

DEFAULT_THICKNESS - Static variable in class chemaxon.struc.graphics.MPolyline

Default line thickness.

DEFAULT_TIMEOUT_LIMIT - Static variable in class chemaxon.sss.search.SearchOptions

DEFAULT_TOOL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "defaultTool".

DEFAULT_UNGROUP - Static variable in class chemaxon.struc.Molecule

Do not ungroup and do not expand S-group's children.

DEFAULT_UPPER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters

DEFAULT_USER_CHECKER_FILENAME - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader

Default user defined checker file name for fallback.

DEFAULT_VALUE - Static variable in class chemaxon.core.util.BondTable

The default (null) value in the matrix.

DEFAULT_WEIGHT - Static variable in class chemaxon.descriptors.MDParameters

DEFAULT_XML_CONFIG - Static variable in class chemaxon.descriptors.PFParameters

defaultCategories() - Static method in class com.chemaxon.calculations.solubility.SolubilityCategories

Creates default categories.

DefaultExternalStructureCheckerResult - Class in chemaxon.checkers.result

This descendant of DefaultStructureCheckerResult also implements the ExternalStructureCheckerResult interface thus providing a default implementation base class for external structure checkers' results.

DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult

Constructor which initialize all the properties.

DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult

Deprecated.

use DefaultExternalStructureCheckerResult(StructureChecker, List, List, Molecule, String, String, String, String, String, Icon, int)

DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult

Constructor which initialize all the properties.

DefaultPluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent

Work unit performing plugin calculation and returning the cached results.

DefaultPluginWorkUnit(CalculatorPluginOutput<?>, boolean) - Constructor for class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit

Constructor.

DefaultSolubilityCategory - Enum Class in com.chemaxon.calculations.solubility

Default solubility categories.

DefaultStructureCheckerResult - Class in chemaxon.checkers.result

This class is the default implementation of StructureCheckerResult

DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult

Deprecated.

use DefaultStructureCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead

DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult

Constructor which initialize all the properties.

DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult

Constructor which initialize all the properties.

defaultWeight - Variable in class chemaxon.descriptors.MDParameters

value for all missing weight parameters

dehydrogenize(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int) with parameter MolAtom.ALL_H does the same.

deleteAllUserComparators() - Method in class chemaxon.sss.search.SearchOptions

Deletes all comparator added by the user.

deleteChar() - Method in class chemaxon.struc.graphics.MTextBox

Removes the character under the cursor.

deleteCharBackward() - Method in class chemaxon.struc.graphics.MTextBox

Removes the character before the cursor (backspace).

deleteUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions

Deletes a given user defined comparator if found.

density - Variable in class chemaxon.descriptors.MDGenerator

DENY_IF_NOT_SPECIFIED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase

description() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the description of the checker

description() - Element in annotation interface chemaxon.fixers.FixerInfo

Returns the description of the fixer.

description() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the description of the action

description() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

description() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory

description() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory

Description.

DESCRIPTION - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

description of checker

DESCRIPTION - Static variable in class chemaxon.fixers.StructureFixerDescriptor

description of fixer

DESCRIPTION - Static variable in class chemaxon.marvin.services.ServiceDescriptor

Property key for Service description as String

DESCRIPTION - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

description of action

DESCRIPTOR_URI - Static variable in class chemaxon.marvin.services.json.JsonServiceDescriptor

Property key for Service descriptor as String

DescriptorGenerator - Class in chemaxon.descriptors

Simple class for generating molecular descriptors (fingerprints).

DescriptorGenerator(String) - Constructor for class chemaxon.descriptors.DescriptorGenerator

Creates a new instance using the given descriptor type with its default configuration parameters.

DescriptorGenerator(String, String) - Constructor for class chemaxon.descriptors.DescriptorGenerator

Creates a new instance using the given descriptor type with the given XML configuration.

descrType - Variable in class chemaxon.descriptors.CDParameters

descriptor type

descrValue - Variable in class chemaxon.descriptors.ScalarDescriptor

descriptor value

desiredLength(int, int, int, int) - Static method in class chemaxon.struc.MolBond

Desired length of a bond between two atoms in Angstroms.

destroySketcher() - Method in class chemaxon.marvin.beans.MViewPane

Closes all detached sketcher windows.

DETACH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "detach".

DETACHABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "detachable".

detectRecordPositions(IntVector) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Deprecated.

detectRecordPositions(IntVector) - Method in interface chemaxon.marvin.io.MRecordReader

Deprecated.

determinant() - Method in class chemaxon.struc.CTransform3D

Computes the determinant of the matrix.

determinant2D() - Method in class chemaxon.struc.CTransform3D

Computes the determinant of the 2D matrix.

determineArrowDistance(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule

Project the point (x,y,z) to the line of the reaction arrow 'ar'.

determinePosition(DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox

Deprecated, for removal: This API element is subject to removal in a future version.

use MTextBox.determinePosition(Graphics, DPoint3, boolean) in case you have a special graphics context to be used for font calculations.

determinePosition(Graphics, DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox

Determines the character index based on the passed view coordinate.

determineType(double, double, double) - Method in class chemaxon.struc.RxnMolecule

Determines whether a point should be in a reactant, in a product or in an agent.

determineType(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule

Determines whether a point should be in a reactant, in a product or in an agent.

DICE - Enum constant in enum class chemaxon.descriptors.MetricsType

DihedralRotator - Class in chemaxon.marvin.alignment

Rotates a dihedral in a 3D molecule

DihedralRotator(Molecule) - Constructor for class chemaxon.marvin.alignment.DihedralRotator

creates a rotator object

DihedralScanListener - Interface in chemaxon.marvin.alignment.atrop

Callback to track dihedral scan steps.

DihedralScanResult - Class in chemaxon.marvin.alignment.atrop

Results of a dihedral scan.

DihedralScanResult(BondInfo) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanResult

Construct for a dihedral.

dihedralScanStep(BondInfo, DihedralScanStep, Molecule, Molecule) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener

Called when a dihedral scan step is performed.

DihedralScanStep - Class in chemaxon.marvin.alignment.atrop

One step in a dihedral scan.

DihedralScanStep(double, double) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanStep

Construct.

DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph

Dimension bits in flags.

DIPOLE - Enum constant in enum class chemaxon.calculator.CalculatorTag

DipoleCalculator - Class in chemaxon.calculations.dipole

Calculates the components of the dipole vector.

DipoleCalculator.Builder - Class in chemaxon.calculations.dipole

Builder class for dipole moment calculation.

DipoleResult - Class in chemaxon.calculations.dipole

Dipole moment calculation result.

DipoleResult(double, double, double, DipoleResult.Unit, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult

Constructor.

DipoleResult(double, double, double, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult

Constructor.

DipoleResult.Unit - Enum Class in chemaxon.calculations.dipole

Dipole moment units.

dirty - Variable in class chemaxon.sss.search.SearchOptions

This flag is set to true whenever any of the options change.

DISABLE_ACCELERATOR - Static variable in class chemaxon.marvin.swing.MAction

Disables the keyboard shortcut while still displaying its name in the menu.

DISABLE_SPECIAL_NODES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "disableSpecialNodes".

disableNewEmfGenerator() - Static method in class chemaxon.util.ImageExportUtil

Disables the new .NET based EMF generator.

Discarded - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type

Indicates, that the structure checker puts invalid structures to the discarded file.

discardedPath - Variable in class chemaxon.checkers.StructureCheckOptions

The path of the invalid/unfixable output structures

DisconnectMetalAtomsAction - Class in chemaxon.standardizer.actions

Disconnect metal atoms standardizer action

DisconnectMetalAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DisconnectMetalAtomsAction

Initializes the disconnect metal atoms action

DISPLAY_QUALITY - Static variable in class chemaxon.marvin.common.ParameterConstants

Deprecated, for removal: This API element is subject to removal in a future version.

Deprecated since Marvin 6.4. No settings is used intead of this, only High Quality exists from now on.

displayInMarvinSpace - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Display in MarvinSpace is enabled or not.

DISSIMILARITY_PROPERTY_NAME - Static variable in interface chemaxon.sss.SearchConstants

Name of the mrv/sdf property which stores the dissimilarity values.

distance(DPoint3) - Method in class chemaxon.struc.DPoint3

Calculates the distance between two points.

distance2D(DPoint3) - Method in class chemaxon.struc.DPoint3

Calculates the distance between two points in the XY plane.

DistanceBasedMetalloceneFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts incorrectly drawn metallocenes into multicenter based coordinate bond representation.

DistanceBasedMetalloceneFixer() - Constructor for class chemaxon.fixers.DistanceBasedMetalloceneFixer

distanceCount(int, int) - Method in class chemaxon.calculations.TopologyAnalyser

Counts the given value in a row of the distance matrix.

distanceDegree(int) - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.

distanceFrom(double, double) - Method in class chemaxon.struc.MObject

Gets the 2D distance from the specified point.

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct

Gets the 2D distance from the specified point.

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlow

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets the 2D distance from the specified point.

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Gets the 2D distance from the specified point.

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Gets the 2D distance from the specified point.

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MObject

Gets the 2D distance from the specified point.

distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MPoint

Gets the 2D distance from the specified point.

distanceFrom(MoleculeGraph, double, double, CTransform3D) - Static method in class chemaxon.struc.graphics.MChemicalStruct

Gets the 2D distance from the specified point.

DIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Divalent radical center.

DIVALENT_SINGLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Divalent radical center with singlet electronic configuration.

DIVALENT_TRIPLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Divalent radical center with triplet electronic configuration.

DNA - Static variable in class chemaxon.formats.MFileFormat

DNA sequence.

DO_NOT_FIX - Enum constant in enum class chemaxon.checkers.FixMode

on problem do nothing

doAction(ActionEvent) - Method in class chemaxon.marvin.swing.MAction

Performs a custom action.

DOC_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: name of the principal author(s) of a document.

DOC_CREATION_DATE - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the date on which the document was created.

DOC_LAST_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: name of the last (most recent) author of a document.

DOC_PATENT_ASSIGNEES - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the assignees of the patent, separated by newline characters.

DOC_PATENT_ID - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the patent identifier.

DOC_PATENT_INVENTORS - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the inventors of the patent, separated by newline characters.

DOC_PATENT_IPC - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the IPC classification(s) for the patent, separated by newline characters.

DOC_PATENT_IPCR - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the IPCR classification(s) for the patent, separated by newline characters.

DOC_TITLE - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the title of the document.

docProduced(MDocStorage, MDocument, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener

Document retrieved from source.

document - Variable in class chemaxon.descriptors.MDParameters

contains the XML document

DOCUMENT - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the file name of the source document.

DocumentAnnotator - Class in chemaxon.naming.document.annotate

Generate a chemically annotated HTML view of a document.

DocumentAnnotator(File) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator

Constructs a DocumentAnnotator to annotate the given document file.

DocumentAnnotator(InputStream) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator

Constructs a DocumentAnnotator to annotate the given document.

DocumentAnnotator(InputStream, DocumentAnnotator.DocumentType) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator

Constructs a DocumentAnnotator to annotate the given document.

DocumentAnnotator.DocumentType - Enum Class in chemaxon.naming.document.annotate

Document type enum for DocumentAnnotator.

DocumentAnnotator.Listener - Interface in chemaxon.naming.document.annotate

The interface for a DocumentAnnotator progress event listener.

DocumentAnnotator.ProgressInfo - Class in chemaxon.naming.document.annotate

Represents the state of progress during a document annotation process.

DocumentAnnotatorOptions - Class in chemaxon.naming.document.annotate

Represents various options regarding how a document should be annotated, both in terms of input and output.

DocumentAnnotatorOptions.Builder - Class in chemaxon.naming.document.annotate

A builder for DocumentAnnotatorOptions, allowing for options to be built using a fluent interface.

DocumentAnnotatorOptions.ImageFormat - Enum Class in chemaxon.naming.document.annotate

A list of supported image formats for popups in the annotated document.

DocumentStyleAPI - Class in chemaxon.marvin.sketch.swing.modules.documentstyle

API for DocumentStyle management.

DocumentStyleAPI() - Constructor for class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI

DocumentToStructure - Class in chemaxon.naming.document

A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files.

DocumentToStructure() - Constructor for class chemaxon.naming.document.DocumentToStructure

done() - Method in interface chemaxon.util.progress.ProgressObserver

Deprecated, for removal: This API element is subject to removal in a future version.

Implement ProgressObserver.close() instead, and create instances of this interface in a try-with-resources block.

DONOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin

Donor sign displayed in GUI.

DONR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

DONT_REMOVE_LAST_COMPONENT_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction

Property key for "Don't Remove Last Component" option

DOODLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule with serious scanning or drawing issue had found

doPaste() - Method in class chemaxon.marvin.beans.MarvinPane

Invokes Paste actions.

doPaste() - Method in class chemaxon.marvin.beans.MSketchPane

Invokes Paste action.

doPaste() - Method in class chemaxon.marvin.beans.MViewPane

Invokes Paste action.

doSetSetSeqs(Molecule[], int, String) - Method in class chemaxon.marvin.view.MDocStorage

DOT_DISCONNECTED_FRAGMENTS - Enum constant in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Dot-disconnected molecular formula of a multifragment molecule.
For example: C7H5O2.Na for sodium benzoate.

DOTDISCONNECTED_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "dotdisconnectedformalchargeformula".

DOTDISCONNECTED_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "dotdisconnectedformula".

DOTDISCONNECTED_ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "dotdisconnectedisotopeformalchargeformula".

DOTDISCONNECTED_ISOTOPE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "dotdisconnectedisotopeformula".

dotDisconnectedFormula() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the dot-disconnected molecular formula of a multifragment molecule.

dotDisconnectedIsotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the dot-disconnected isotope formula of a multifragment molecule.

dotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the dot-disconnected isotope formula of a multifragment molecule.

DOUBLE - Enum constant in enum class chemaxon.struc.BondType

Double bond type.

DOUBLE - Static variable in class chemaxon.struc.MolBond

Double bond type.

DOUBLE_BOND - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

DOUBLE_BOND_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule contains either double bonds which are not valid

DOUBLE_OR_AROMATIC - Enum constant in enum class chemaxon.struc.BondType

Double or aromatic query bond type.

DOUBLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond

Double or aromatic query bond type.

doubleStringWidth(String, MFont, FontMetrics, Graphics) - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets the width of a string as a floating point number.

doubleValue() - Method in class chemaxon.struc.prop.MDoubleProp

Gets the double floating point value.

DOWN - Static variable in class chemaxon.struc.MolBond

Single bond down flag.

DOWN_WEDGE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "downWedge".

DPoint3 - Class in chemaxon.struc

Point in three dimensional space.

DPoint3() - Constructor for class chemaxon.struc.DPoint3

Construct a zero point.

DPoint3(double, double, double) - Constructor for class chemaxon.struc.DPoint3

Construct a point from the specified coordinates.

DPoint3(DPoint3) - Constructor for class chemaxon.struc.DPoint3

Copy constructor.

DRAGGABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "draggable".

dropBinaryVector() - Method in class chemaxon.descriptors.ECFP

Drops the binary vector storage.

Ds - Static variable in class chemaxon.core.ChemConst

DT_FORMATTED - Static variable in class chemaxon.struc.sgroup.DataSgroup

Field type: formatted.

DT_NUMERIC - Static variable in class chemaxon.struc.sgroup.DataSgroup

Field type: numeric.

DT_TEXT - Static variable in class chemaxon.struc.sgroup.DataSgroup

Field type: text.

DT_UNSPEC - Static variable in class chemaxon.struc.sgroup.DataSgroup

Field type: unspecified.

DT_URL - Static variable in class chemaxon.struc.sgroup.DataSgroup

Field type: url.

DUPLICATE - Static variable in interface chemaxon.sss.SearchConstants

Duplicate search (formerly called perfect).

Dy - Static variable in class chemaxon.core.ChemConst

DynamicArgument<CT,RT> - Class in chemaxon.marvin.services

ServiceArguments implementing this interface should support automatic evaluation of arguments before service call based on context.
NOTE: subclasses MUST HAVE default constructor to use from Marvin Sketch

DynamicArgument() - Constructor for class chemaxon.marvin.services.DynamicArgument

DynamicArgument(String) - Constructor for class chemaxon.marvin.services.DynamicArgument

DYNAMICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin

pKa's prefix (acidic/basic) does depend on the submitted micro state

E

E - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

E - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration

E_OR_UNSPEC - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration

E_OR_Z - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration

E_SINK - Static variable in class chemaxon.struc.graphics.MEFlow

Electron sink.

E_SOURCE - Static variable in class chemaxon.struc.graphics.MEFlow

Electron source.

eA - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit

Atomic charge unit * Angstrom.

eccentricity(int) - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.

ECFP - Class in chemaxon.descriptors

The ECFP class implements Extended-Connectivity Fingerprints (ECFPs) as a type of MolecularDescriptors.

ECFP() - Constructor for class chemaxon.descriptors.ECFP

Creates a new, empty instance of ECFP without allocating internal storage.

ECFP(ECFP) - Constructor for class chemaxon.descriptors.ECFP

Copy constructor.

ECFP(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFP

Creates a new instance of ECFP according to the parameters given.

ECFP(String) - Constructor for class chemaxon.descriptors.ECFP

Creates a new instance of ECFP according to the parameters given.

ECFPFeature - Class in chemaxon.descriptors

Class for representing the substructural features of ECFP fingerprints.

ECFPFeatureLookup - Class in chemaxon.descriptors

Class for retrieving the substructural features of ECFP fingerprints.

ECFPFeatureLookup() - Constructor for class chemaxon.descriptors.ECFPFeatureLookup

Creates a new ECFPFeatureLookup instance with the default ECFP configuration parameters.

ECFPFeatureLookup(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup

Creates a new ECFPFeatureLookup instance with the given ECFP configuration parameters.

ECFPFeatureLookup(String) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup

Creates a new ECFPFeatureLookup instance with the given ECFP configuration parameters.

ECFPGenerator - Class in chemaxon.descriptors

The ECFPGenerator class generates ECFP fingerprints of molecular graphs.

ECFPGenerator() - Constructor for class chemaxon.descriptors.ECFPGenerator

Creates a new instance of ECFPGenerator, which can be used to generate ECFP fingerprints for an arbitrary number of molecules.

ECFPParameters - Class in chemaxon.descriptors

Manages ECFP fingerprint parameters.

ECFPParameters() - Constructor for class chemaxon.descriptors.ECFPParameters

Creates an empty object.

ECFPParameters(File) - Constructor for class chemaxon.descriptors.ECFPParameters

Creates a new object based on a given configuration file.

ECFPParameters(String) - Constructor for class chemaxon.descriptors.ECFPParameters

Creates a new object based on a given configuration string.

EDITABLE - Static variable in class chemaxon.marvin.beans.MViewPane

Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinView in a new window.

EDITABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "editable".

EDITOR_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

editor class name property of checker

EDITOR_CLASS_NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

editor class name property of standardizer action

editorClassName() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the name of the checker's editor

editorClassName() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the editor class name of the action

electronegOf(int) - Static method in class chemaxon.struc.MolAtom

Gets 10 times the electronegativity value for the specified element.

electronRadious - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint

ELEMENT_COUNT - Static variable in class chemaxon.core.ChemConst

Number of elements in the periodic system

ELEMENT_COUNT - Static variable in class chemaxon.struc.MolAtom

Number of elements in the periodic system

ElementalAnalyser - Class in chemaxon.calculations

Calculates molecular formula, mass, MS mass and composition.

ElementalAnalyser() - Constructor for class chemaxon.calculations.ElementalAnalyser

ElementalAnalyserPlugin - Class in chemaxon.marvin.calculations

Calculates molecular formula, mass, MS mass and composition.

ElementalAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.ElementalAnalyserPlugin

ElementalAnalyserPlugin.ResultType - Enum Class in chemaxon.marvin.calculations

Represents the different result types of the elemental analyser plugin.

ElementalAnalysis - Interface in com.chemaxon.calculations.elemanal

Calculates molecular formula, mass, MS mass and composition.

ELEMENTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "elements".

EMF - Static variable in class chemaxon.formats.MFileFormat

Windows Enhanced Metafiles.

EMPTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule structure was empty

EMPTY - Static variable in class chemaxon.jep.ConstantTable

An empty constant table.

EMPTY - Static variable in class chemaxon.struc.MolAtom

Empty atom type.

EMPTY_MOLECULE - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy

In case of standardization error an empty molecule is provided on the output

EmptyStructureChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting structures having no atoms.

EmptyStructureChecker() - Constructor for class chemaxon.checkers.EmptyStructureChecker

Default constructore

ENABLED_2D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "2dviewerEnabled".

ENABLED_3D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "3dviewerEnabled".

enableDefaultHeavyAtomLimits() - Static method in interface chemaxon.calculator.TaggedCalculator

Sets the global input checker to one that uses the default heavy atom limits.

enclosesPoint(double, double) - Method in class chemaxon.struc.graphics.MBracket

Checks if a specified point is enclosed by this bracket.

encode(MFont, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes

Returns the string representation of the attributes.

encoding - Variable in class chemaxon.marvin.io.PositionedInputStream

The encoding.

Encoding - Class in chemaxon.marvin.io

File encoding information.

Encoding(String, int, ByteOrder) - Constructor for class chemaxon.marvin.io.Encoding

Creates an Encoding for the specified name, word length and byte order.

END_CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: key of the molecule property which contains the ending character offset since the beginning of the document, for text formats (html, xml, txt).

endElement(String, String, String) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter

endGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream

Deprecated, for removal: This API element is subject to removal in a future version.

endHourglass() - Method in class chemaxon.marvin.beans.MarvinPane

Changes the hourglass cursor back to normal at the end of a long operation.

ENDO - Static variable in interface chemaxon.struc.StereoConstants

Non-CIP stereodescriptor, endo (relative configuration).

endRecord(boolean) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

It must be called at the end of record.

endReuse(int) - Method in class chemaxon.struc.Molecule

End reusing atoms.

endReuse(int) - Method in class chemaxon.struc.RgMolecule

End reusing atoms.

endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument

Tests whether the document ends with the specified character.

endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Tests whether this text portion ends with the specified character.

EnhancedStereo - Class in com.chemaxon.calculations.stereoanal.stereocenters

Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

EnhancedStereo(StereoConstants.EnhancedStereoType) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo

Creates enhanced stereo representation.

EnhancedStereo(StereoConstants.EnhancedStereoType, int) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo

Creates enhanced stereo representation.

EnhancedStereoGroup - Class in com.chemaxon.calculations.stereoanal.stereocenters

Enhanced stereo descriptor class.

EnhancedStereoGroup(EnhancedStereo, List<TetrahedralStereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup

Creates enhanced stereo group.

enqueueUpdate() - Method in class chemaxon.marvin.view.swing.TableSupport

Enqueues an update task.

ensureValidity() - Method in class chemaxon.struc.graphics.MElectronContainer

ENTRY_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Configuration entry separator token of the action string

EPS - Static variable in class chemaxon.formats.MFileFormat

Encapsulated PostScript vector image format.

EPSILON - Static variable in class chemaxon.marvin.calculations.HBDAPlugin

EPSILON - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

The microspecies is ignored if its distribution is less than EPSILON for all pH values.

equals(Encoding) - Method in class chemaxon.marvin.io.Encoding

Tests whether two encodings are equal.

equals(CTransform3D, double) - Method in class chemaxon.struc.CTransform3D

equals(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether two attributes objects equal or not.

equals(Object) - Method in class chemaxon.calculations.pka.PKaTrainingResult

equals(Object) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

equals(Object) - Method in class chemaxon.checkers.AbstractStructureChecker

equals(Object) - Method in class chemaxon.checkers.AromaticityErrorChecker

equals(Object) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

equals(Object) - Method in class chemaxon.checkers.AttachedDataChecker

equals(Object) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

equals(Object) - Method in class chemaxon.checkers.result.AromaticityCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.BondAngleCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.BondLengthCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.ExplicitHydrogenResult

equals(Object) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.ReactionCheckerResult

Deprecated.

equals(Object) - Method in class chemaxon.checkers.result.RgroupCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.SgroupCheckerResult

equals(Object) - Method in class chemaxon.checkers.result.SubstructureCheckerResult

equals(Object) - Method in class chemaxon.checkers.StructureCheckerDescriptor

equals(Object) - Method in class chemaxon.checkers.util.AtomLabels

equals(Object) - Method in class chemaxon.checkers.util.DataExclusionList

equals(Object) - Method in class chemaxon.checkers.ValencePropertyChecker

equals(Object) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

equals(Object) - Method in class chemaxon.fixers.StructureFixerDescriptor

equals(Object) - Method in class chemaxon.marvin.io.Encoding

Tests whether two encodings are equal.

equals(Object) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

equals(Object) - Method in class chemaxon.sss.search.Decomposition

Returns true if this decomposition is equivalent to the specified decomposition.

equals(Object) - Method in class chemaxon.sss.search.MarkushFeature

Deprecated.

equals(Object) - Method in class chemaxon.sss.search.SearchHit

equals(Object) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

equals(Object) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

equals(Object) - Method in class chemaxon.struc.AtropStereoDescriptor

equals(Object) - Method in class chemaxon.struc.AxialStereoDescriptor

equals(Object) - Method in class chemaxon.struc.CisTransStereoDescriptor

equals(Object) - Method in class chemaxon.struc.CTransform3D

equals(Object) - Method in class chemaxon.struc.DPoint3

Two points equal if their coordinates equal.

equals(Object) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Two points equal if their atoms equal.

equals(Object) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Two points equal if their atoms equal.

equals(Object) - Method in class chemaxon.struc.graphics.MElectron

equals(Object) - Method in class chemaxon.struc.graphics.MElectronContainer

equals(Object) - Method in class chemaxon.struc.graphics.MFont

Tests whether two font objects equal.

equals(Object) - Method in class chemaxon.struc.graphics.MMidPoint

Two midpoints equal if their parent lines are the same and the polyline point indices also equal.

equals(Object) - Method in class chemaxon.struc.graphics.MRectanglePoint

Two rectangle points equal if their parent rectangles are the same and they are on the same corner or edge.

equals(Object) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether two attributes objects equal or not.

equals(Object) - Method in class chemaxon.struc.MPoint

Two points equal if their location equals.

equals(Object) - Method in class chemaxon.struc.prop.MBooleanProp

equals(Object) - Method in class chemaxon.struc.prop.MCollectionProp

equals(Object) - Method in class chemaxon.struc.prop.MDoubleArrayProp

equals(Object) - Method in class chemaxon.struc.prop.MDoubleProp

equals(Object) - Method in class chemaxon.struc.prop.MFontProp

equals(Object) - Method in class chemaxon.struc.prop.MHashProp

equals(Object) - Method in class chemaxon.struc.prop.MHCoords3DProp

equals(Object) - Method in class chemaxon.struc.prop.MIntegerArrayProp

equals(Object) - Method in class chemaxon.struc.prop.MIntegerProp

equals(Object) - Method in class chemaxon.struc.prop.MListProp

equals(Object) - Method in class chemaxon.struc.prop.MMoleculeProp

equals(Object) - Method in class chemaxon.struc.prop.MMoleculeStringProp

equals(Object) - Method in class chemaxon.struc.prop.MObjectProp

equals(Object) - Method in class chemaxon.struc.prop.MStringProp

equals(Object) - Method in class chemaxon.struc.RgroupBridgeId

equals(Object) - Method in class chemaxon.struc.StereoActivePart

equals(Object) - Method in class chemaxon.struc.TetrahedralStereoDescriptor

equalsHead(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether the head bonds equal the given bonds.

equalsNext(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether the attributes of two neighboring sections equal or not.

equalsTail(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether the tail bonds equal the given bonds.

equalsTo(Object, int[]) - Method in class chemaxon.struc.AtropStereoDescriptor

equalsTo(Object, int[]) - Method in class chemaxon.struc.AxialStereoDescriptor

equalsTo(Object, int[]) - Method in interface chemaxon.struc.CIPStereoDescriptorIface

equalsTo(Object, int[]) - Method in class chemaxon.struc.CisTransStereoDescriptor

equalsTo(Object, int[]) - Method in class chemaxon.struc.StereoActivePart

equalsTo(Object, int[]) - Method in class chemaxon.struc.TetrahedralStereoDescriptor

EQUILIBRIUM - Static variable in class chemaxon.struc.RxnMolecule

Resonance arrow, the same as the two-headed double reaction arrow.

Er - Static variable in class chemaxon.core.ChemConst

ERROR - Enum constant in enum class chemaxon.checkers.CheckerSeverity

This severity level should used for StructureChecker implementations which search for serious problems in a Molecule

errorList - Variable in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.

ErrorProcessor - Interface in chemaxon.util

Error processing interface.

ErrorReport - Class in com.chemaxon.calculations.stereoanal

Error reporting class.

ErrorReport(AtomSelection, String) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport

Constructs new error report.

ErrorReport(AtomSelection, String, Optional<? extends StereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport

Constructs new error report.

errors() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Error reports.

errorType - Variable in class chemaxon.checkers.AbstractStructureChecker

The error type of the current checker.

Es - Static variable in class chemaxon.core.ChemConst

ESCAPE_CHAR - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "escapeChar".

estimateNumRecords() - Method in class chemaxon.formats.MolImporter

Estimates the total number of records.

estimateNumRecords() - Method in class chemaxon.marvin.io.ArrayMDocSource

Estimates the total number of records.

estimateNumRecords() - Method in class chemaxon.marvin.io.MDocSource

Estimates the total number of records.

estimateNumRecords() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Estimates the total number of records.

estimateProgress() - Method in interface chemaxon.util.iterator.MoleculeIterator

Estimates the iteration progress.

Eu - Static variable in class chemaxon.core.ChemConst

euclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the Euclidean distance.

euclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the Euclidean distance.

EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType

evaluate(C) - Method in class chemaxon.jep.ChemJEP

Evaluates the expression.

evaluate(StandardizerRunner.ErrorHandlingPolicy, StandardizerResult) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

evaluate(CT) - Method in class chemaxon.marvin.services.DynamicArgument

Evaluates the dynamic argument based on context

evaluate(Map<String, String>, List<Object>, ChemContext) - Method in interface chemaxon.jep.CustomFunction

Evaluates this function.

evaluate_boolean(C) - Method in class chemaxon.jep.ChemJEP

Evaluates the expression and converts the result boolean.

evaluate_booleans(C) - Method in class chemaxon.jep.ChemJEP

Evaluates the expression and converts the result to boolean[].

evaluate_double(C) - Method in class chemaxon.jep.ChemJEP

Evaluates the expression and converts the result to double.

evaluate_doubles(C) - Method in class chemaxon.jep.ChemJEP

Evaluates the expression and converts the result to double[].

EVALUATION_ERROR - Static variable in class chemaxon.jep.ChemJEP

The evaluation error message.

Evaluator - Class in chemaxon.jep

Evaluates Chemical Terms expressions.

Evaluator() - Constructor for class chemaxon.jep.Evaluator

Default constructor.

Evaluator(Standardizer) - Constructor for class chemaxon.jep.Evaluator

Constructor for internal use only.

Evaluator(File) - Constructor for class chemaxon.jep.Evaluator

Constructor.

Evaluator(File, Standardizer) - Constructor for class chemaxon.jep.Evaluator

Constructor for internal use only.

Evaluator(File, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

Evaluator(String) - Constructor for class chemaxon.jep.Evaluator

Constructor.

Evaluator(String, Standardizer) - Constructor for class chemaxon.jep.Evaluator

Constructor for internal use only.

Evaluator(String, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

EVALUATOR_DEFAULTS_FILE - Static variable in class chemaxon.jep.Evaluator

Default Function/Plugin settings filename.

EVALUATOR_NAMED_MOLS_FILE - Static variable in class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

EVALUATOR_SCRIPT_FILE - Static variable in class chemaxon.jep.Evaluator

Initial script filename.

EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue

EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue

EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue

EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue.M.

EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue.M.

EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue.S.

EVEN - Static variable in class chemaxon.calculations.stereo.Stereochemistry

EVERY_WEIGHT_IS_ONE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase

EXACT - Static variable in class chemaxon.sss.formula.FormulaSearch

Constant value specifying the exact search type.

EXACT_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction

Key of exact for parsing and property change

EXACT_MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "exactmass".

EXACT_SUBFORMULA - Static variable in class chemaxon.sss.formula.FormulaSearch

Constant value specifying the exact sub formula search type.

exactMass() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.

exactMass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.

exactMassPrecision() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the precision of the monoisitopic weight (number of significant decimal digits).

exactQueryAtomMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether generic query atoms should be matched only to atoms of exactly the same type.

exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether generic query bonds should be matched only to bonds of exactly the same type.

EXCLUDE_KEY - Static variable in class chemaxon.standardizer.actions.AbstractSgroupAction

Key of exclude for parsing and property change

EXCLUDE_XX - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

excludeString - Variable in class chemaxon.standardizer.actions.ContractSgroupsAction

excludeString - Variable in class chemaxon.standardizer.actions.ExpandSgroupsAction

excludeString - Variable in class chemaxon.standardizer.actions.UngroupSgroupsAction

exit() - Method in class chemaxon.marvin.beans.MarvinPane

Closes all windows opened by this MarvinPane and saves user initialization file.

EXO - Static variable in interface chemaxon.struc.StereoConstants

Non-CIP stereodescriptor, exo (relative configuration).

expand(int) - Method in class chemaxon.struc.Sgroup

Sets the state to Sgroup.XSTATE_X or Sgroup.XSTATE_XC.

expand(int) - Method in interface chemaxon.struc.sgroup.Expandable

Expands the S-group.

expand(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Expands this S-group unless it has expandable child s-group because in that case our calculations' behaviour can not be predicted.

expand(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Expands this S-group.

Expandable - Interface in chemaxon.struc.sgroup

Expandable interface for S-groups.

ExpandAction - Class in chemaxon.standardizer.actions

Expand stoichiometry standardizer action

ExpandAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ExpandAction

Initializes the action with parameters

ExpandGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which expands all abbreviated groups in the molecule

ExpandGroupFixer() - Constructor for class chemaxon.fixers.ExpandGroupFixer

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

This implementation does nothing.

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureC