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.AbstractStructureChecker

Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BondAngleChecker

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker

This implementation does nothing.

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker

This implementation does nothing.

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker

This implementation does nothing.

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.OverlappingAtomsChecker

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.OverlappingBondsChecker

expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker

This implementation does nothing.

expandOther(int, Molecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated.

as of Marvin 6.2. use SuperatomSgroup.expand(int) instead on the s-groups desired to be expanded

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

Expands all S-groups.

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

Expands all S-groups.

ExpandSgroupsAction - Class in chemaxon.standardizer.actions

Standardizer action expanding s-groups of the target molecule

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

Initializes the action

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

Error type represents that explicit hydrogen had found in the molecule

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

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

since 5.3

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

Error type represents that explicit lone pair had found in the molecule

ExplicitHydrogenChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting explicit hydrogens.

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

Default constructor All types of explicit hydrogens will be searched.

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

Parameterized constructor If map contains lonely/charged/mapped/isotopic/radical/wedged keys with value false then hydrogens with these types won't be detected.

ExplicitHydrogenFixer - Class in chemaxon.fixers

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

use RemoveExplicitHydrogenFixer

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

Deprecated.

ExplicitHydrogenResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult for identifying explicit hydrogen problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.

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

Constructor which initialize all the properties.

explicitHydrogens - Variable in class chemaxon.marvin.plugin.CalculatorPlugin

explicit hydrogens of the input molecule stored here key: index of the "parent" atom on the input molecule value: the hydrogen atom

EXPLICITIZE - Enum constant in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption

Add explicit hydrogen atoms.

ExplicitLonePairChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting lone pair type atoms.

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

Default constructor

export(NMRSpectrum, double, double, double) - Static method in class chemaxon.calculations.nmr.io.NMRExporter

Returns the x-y point pairs of an NMR spectrum.

exportToBinFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter

Creates a binary representation of the document.

exportToBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter

Creates a binary representation of the molecule.

exportToBinFormat(String) - Method in class chemaxon.struc.MDocument

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

As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String).

exportToBinFormat(String) - Method in class chemaxon.struc.Molecule

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

As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).

exportToFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter

Creates a string representation of the document.

exportToFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter

Creates a string representation of the molecule.

exportToFormat(String) - Method in class chemaxon.struc.MDocument

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

As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String)

exportToFormat(String) - Method in class chemaxon.struc.Molecule

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

As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).

exportToJcampDX(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.io.NMRExporter

Exports the NMR spectrum into JCAMP-DX format.

exportToJcampDX(NMRSpectrum, int) - Static method in class chemaxon.calculations.nmr.io.NMRExporter

Exports the NMR spectrum into JCAMP-DX format.

exportToMol(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.io.NMRExporter

Returns a molecule with its NMR spectrum property.

exportToMol(NMRSpectrum, String) - Static method in class chemaxon.calculations.nmr.io.NMRExporter

Returns a molecule with its NMR spectrum property.

exportToObject(MDocument, String) - Static method in class chemaxon.formats.MolExporter

Creates a String, byte[] or Image representation of the document.

exportToObject(Molecule[], String, MolExportModule) - Static method in class chemaxon.formats.MolExporter

Creates a String, byte[] or Image representation of the given molecules.

exportToObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter

Creates a String, byte[] or Image representation of the molecule.

exportToObject(String) - Method in class chemaxon.struc.MDocument

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

As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String)

exportToObject(String) - Method in class chemaxon.struc.Molecule

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

As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).

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

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

Error type for externally developed StructureChecker classes

EXTERNAL_CHECKER_CONFIGURATION_PATH_PROPERTY_KEY - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory

Java System Property key to globally override default configuration path.

ExternalStructureChecker - Class in chemaxon.checkers

ExternalStructureChecker class provides a super class for externally implemented structure checkers.

ExternalStructureChecker(String) - Constructor for class chemaxon.checkers.ExternalStructureChecker

This constructor creates an external structure checker instance with the given error code

ExternalStructureCheckerResult - Interface in chemaxon.checkers.result

This interface is an extension of StructureCheckerResult that supports external StructureChecker development.

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

Identifier of parameter: "extraBonds".

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

Identifier of parameter: "xtmpls".

extraFlavor - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

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

Error type represents that molecule contains double bonds, that can be cis or trans

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

Identifier of parameter: "ezVisible".

EZConfiguration - Enum Class in chemaxon.struc.stereo

Enumeration of possible E/Z stereo values.

EZDoubleBondChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting double bonds, that can be cis or trans.

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

Initializes the EZ double bond checker

F

F - Static variable in class chemaxon.core.ChemConst

F_ARCHIVE - Static variable in class chemaxon.formats.MFileFormat

General archive format that stores a file in another format.

F_BINARY - Static variable in class chemaxon.formats.MFileFormat

Import/export module handles binary (byte array) data.

F_COORDS - Static variable in class chemaxon.formats.MFileFormat

The format can store atom coordinates if this flag is set.

F_EXPORT - Static variable in class chemaxon.formats.MFileFormat

Export is possible if this flag is set.

F_GRAPHICS - Static variable in class chemaxon.formats.MFileFormat

File format readable by a graphics program (image viewer, ray tracer etc.).

F_IMAGE - Static variable in class chemaxon.formats.MFileFormat

2D image file format, readable by image viewers.

F_IMPORT - Static variable in class chemaxon.formats.MFileFormat

Import is possible if this flag is set.

F_MIXED - Static variable in class chemaxon.formats.MFileFormat

Storage of records in different formats is possible if this flag is set.

F_MOL_MISSING - Static variable in class chemaxon.marvin.io.MRecord

Molecule (or reaction) is missing from the record.

F_MOLECULE - Static variable in class chemaxon.formats.MFileFormat

The format can store molecule(s) if this flag is set.

F_MULTIPLE_RECORDS_LEGAL - Static variable in class chemaxon.formats.MFileFormat

The format is designed to store multiple records if this flag is set.

F_MULTIPLE_RECORDS_POSSIBLE - Static variable in class chemaxon.formats.MFileFormat

The import/export modules can handle files with multiple records if this flag is set, but according to the format definition it is not legal.

F_OBJECT - Static variable in class chemaxon.formats.MFileFormat

Import/export module creates or reads a java object.

F_REACTION - Static variable in class chemaxon.formats.MFileFormat

The format can store reaction(s) if this flag is set.

F_RECOGNIZER - Static variable in class chemaxon.formats.MFileFormat

Format recognizer exists if this flag is set.

F_SINGLE_LINE - Static variable in class chemaxon.formats.MFileFormat

Format uses one line per structure.

F_USER_DEFINED - Static variable in class chemaxon.formats.MFileFormat

User defined format.

F_XML - Static variable in class chemaxon.formats.MFileFormat

The format is XML based if this flag is set.

Factory() - Constructor for class chemaxon.marvin.alignment.MCSAlignment.Factory

FALSE - Static variable in class chemaxon.jep.ChemJEP

Logical result value: FALSE.

FALSE - Static variable in interface chemaxon.jep.CustomFunction

FALSE - Static variable in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

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

Atomic contribution, only for some selected atoms and ring centers.

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

FAST - Enum constant in enum class com.chemaxon.search.mcs.SearchMode

Fast search mode.

FAST_COORDS - Static variable in interface chemaxon.struc.sgroup.Expandable

Fast coordinate calculation in expand.

FASTA - Static variable in class chemaxon.formats.MFileFormat

FASTA file format

FASTA_DNA - Static variable in class chemaxon.formats.MFileFormat

FASTA file format with DNA sequence

FASTA_PEPTIDE - Static variable in class chemaxon.formats.MFileFormat

FASTA file format with peptide sequence

FASTA_RNA - Static variable in class chemaxon.formats.MFileFormat

FASTA file format with RNA sequence

FastUpperBoundCalculator - Class in com.chemaxon.search.mcs.upperbound

This class implements a simple upper bound calculator for the MCS problem.

FastUpperBoundCalculator() - Constructor for class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator

Fe - Static variable in class chemaxon.core.ChemConst

FILE_CHOOSE_ERROR - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult

fileEndPosition - Variable in class chemaxon.marvin.io.MRecord

files - Variable in class chemaxon.checkers.StructureCheckOptions

List of the input files

FileSaveResult - Enum Class in chemaxon.common.swing.io.output

fileStartPosition - Variable in class chemaxon.marvin.io.MRecord

fillInStackTrace() - Method in exception chemaxon.naming.NameFormatException

fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.Molecule

Adds all atoms and bonds to the specified molecule.

fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RgMolecule

Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.

fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RxnMolecule

Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.

fillWithNulls() - Method in class chemaxon.marvin.view.MDocStorage

Set all stored document entries to null.

filter(List<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter

Filter stereo centers.

FILTER_DIM0 - Static variable in class chemaxon.formats.MolExporter

Molecule filter for cleaning 0D molecules only.

FILTER_VALENCE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Filter constant: valence filter.

FilteredCase(String) - Constructor for exception chemaxon.naming.NameFormatException.FilteredCase

FilteredCase(String, Throwable) - Constructor for exception chemaxon.naming.NameFormatException.FilteredCase

filterGroups(StandardizerConfiguration, String[]) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility

Filters the action list of a configuration to a configuration containing only the actions that are in the target groups (or in all groups).

FINAL_CLEAN_ID - Static variable in class chemaxon.standardizer.configuration.ConfigurationUtility

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

It's not required anymore.

FINAL_CLEAN_ID - Static variable in class chemaxon.standardizer.Standardizer

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

find() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Performs MCS search according to the specified options.

findAll() - Method in class chemaxon.sss.search.Search

Looks for all matching patterns in the molecule.

findAllGroups() - Method in class chemaxon.sss.search.Search

Returns the group hits corresponding to all hits.

findAllHits() - Method in class chemaxon.sss.search.MolSearch

findAllHits() - Method in class chemaxon.sss.search.Search

Looks for all matching patterns in the molecule.

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

Finds all smallest S-groups containing the specified atom.

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

Finds an atom in the atoms array.

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

Finds the clone of an atom.

findAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem

Returns the atomic number of the element in the periodic system specified by its symbol.

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

Gets the attachment atom of attachment point with the smallest order.

findBasicFrags(Class<C>) - Method in class chemaxon.struc.MoleculeGraph

Determines the disconnected fragments and puts them into an array.

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

Finds a bond in the bonds array.

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

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

As of Marvin 6.0, replaced by MoleculeGraph.getFragIds(int) and MoleculeGraph.FRAG_BASIC.
Usage:

             mol.getFragIds(MoleculeGraph.FRAG_BASIC);
             

findComponentIds(int[]) - Method in class chemaxon.struc.MoleculeGraph

Assigns a component ID to each connected component formed by the specified atom indexes.

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

Gets the containing multicenter S-group of a multicenter atom.

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

Finds an expanded residue.

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

Finds the crossing bonds.

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

Finds the crossing bonds.

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

Finds the crossing bonds.

findDecomposition() - Method in class chemaxon.sss.search.RGroupDecomposition

Finds the first decomposition result.

findDecomposition(boolean) - Method in class chemaxon.sss.search.RGroupDecomposition

Finds a decomposition result.

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

Finds a contracted residue.

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

Overlays the molecule to align on the reference using the predefined atom pairs.

findFirst() - Method in class chemaxon.sss.search.Search

Looks for the first matching pattern in the target molecule.

findFirstDecomposition() - Method in class chemaxon.sss.search.RGroupDecomposition

Finds the first decomposition result.

findFirstGroup() - Method in class chemaxon.sss.search.Search

Returns the group hit corresponding to the first hit.

findFirstHit() - Method in class chemaxon.sss.search.MolSearch

findFirstHit() - Method in class chemaxon.sss.search.Search

Looks for the first matching pattern in the target molecule.

findFormats(String, long, long) - Static method in class chemaxon.formats.MFileFormatUtil

Gets a list of formats.

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

Determines the subgraph connected to the specified atom.

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

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

As of Marvin 5.6, replaced by MoleculeGraph.findFrag(int, int, MoleculeGraph) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:

             mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
             

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

Determines the subgraph corresponding to the specific fragment ID.

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

Determines the disconnected fragments and puts them into an array.

findFrags(Class<C>) - Method in class chemaxon.struc.MoleculeGraph

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

As of Marvin 5.6, replaced by MoleculeGraph.findFrags(Class, int) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:

             mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
             

findFrags(Class<C>, int) - Method in class chemaxon.struc.Molecule

Determines the disconnected fragments and puts them into an array.

findFrags(Class<C>, int) - Method in class chemaxon.struc.MoleculeGraph

Determines the disconnected fragments and puts them into an array.

findInArray(Object[], int[], int, Object) - Static method in class chemaxon.struc.MoleculeGraph

Finds an object in an array.

findLigandTable(int, int) - Method in class chemaxon.sss.search.RGroupDecomposition

Returns the ligand table.

findLigandTable(int, int, String) - Method in class chemaxon.sss.search.RGroupDecomposition

Returns the ligand table.

findLigandTableRow(int) - Method in class chemaxon.sss.search.RGroupDecomposition

Returns a ligand table row with ligands corresponding to a the first search hit.

findLigandTableRow(int, String) - Method in class chemaxon.sss.search.RGroupDecomposition

Returns a ligand table row with ligands corresponding to a the first search hit.

findMcs() - Method in class com.chemaxon.search.mcs.buildup.BuildupMcs

findMcs() - Method in class com.chemaxon.search.mcs.maxclique.MaxCliqueMcs

findMcs() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Finds the MCS and all related data (fragments and mappings).

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

Randomizes dihedral angles of the input conformation for flexible molecules and aligns.

findNext() - Method in class chemaxon.sss.search.Search

Looks for the next matching pattern in the target molecule.

findNextDecomposition() - Method in class chemaxon.sss.search.RGroupDecomposition

Finds the next decomposition result.

findNextGroup() - Method in class chemaxon.sss.search.Search

Returns the group hit corresponding to the next hit.

findNextHit() - Method in class chemaxon.sss.search.MolSearch

findNextHit() - Method in class chemaxon.sss.search.Search

Searches for the next hit.

findNextHit() - Method in interface com.chemaxon.search.SimpleSearcher

Searches for the next hit.

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

Finds the corresponding RgroupBridgeId for an R-group index.

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

Finds the index of an R-group based on the R-group number.

findScriptLastSectionIndex(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Finds the end of a subscript or superscript.

findSelectedSgroup() - Method in class chemaxon.struc.MSelectionDocument

Gets the smallest sgroup that belongs to the selection.

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

Finds the largest S-group that contains the specified atom.

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

Finds the smallest S-group related to the specified atom.

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

Finds the smallest S-group that contains the specified atom.

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

Finds the smallest S-group containing the specified node.

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

Finds the smallest S-group that has the specified node.

FINGERPRINT - Static variable in class chemaxon.jep.context.MolContext

FingerprintGenerator - Interface in chemaxon.jep

Fingerprint generator used in Chemical Terms match functions.

finishCancel() - Method in exception chemaxon.marvin.view.MDocStorage.CancellationException

This method should be called after catching the exception.

finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MAnalysisBox

Finish cloning a document.

finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Finish cloning a document.

finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Finish cloning a document.

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

finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MPolyline

Finish cloning a document.

finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.MObject

Finish cloning a document.

firstPage - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

The first page of the document that should be annotated.

firstPage(Integer) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

fix - Variable in class chemaxon.checkers.StructureCheckOptions

Fix mode - deprecated.

fix() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

Checks the structure, then fixes the problems based on configuration.
NOTE: FixMode and fixerClassName from configuration is used to choose best fixer.

fix() - Method in interface chemaxon.checkers.runner.CheckerRunner

Runs all StructureChecker on the given molecule and after that fixes all identified problems with the first StructureFixer which is associated with the current problem.

fix(StructureCheckerResult) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

Fixes the given result based on the fixer defined for the checker.

fix(StructureCheckerResult) - Method in interface chemaxon.checkers.runner.CheckerRunner

Fixes the problem identified by result with the first StructureFixer which is associated with the StructureCheckerErrorType of the result.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.AbsentChiralFlagFixer

Deprecated.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.AbsoluteStereoFixer

Deprecated.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.AddChiralFlagFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.BondAngleFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.BondLengthFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.CleanFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ClearWedgeFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ContractGroupFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertAliasToGroupFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertPseudoToGroupFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToAtomFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToCarbonFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToCrossedDoubleBondFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToElementalFormFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToIonicFormFixer

Checker results contain atoms from the alkali metal and alkaline earth metal groups and their ionic counterparts of N, O, S atoms.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToPlainDoubleBondFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToSingleBondFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToWigglyDoubleBondFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.CrossedDoubleBondFixer

Deprecated.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.DearomatizeFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.DistanceBasedMetalloceneFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ExpandGroupFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ExplicitHydrogenFixer

Deprecated.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.FlipWedgeBondFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.IsotopeFixer

Deprecated.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.MapMoleculeFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.MapReactionFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.MetalloceneFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.NeutralizeChargeFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.PartialCleanFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RearomatizeFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RearrangeWedgesFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAliasFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomMapFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomQueryPropertyFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomValueFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAttachedDataFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBondFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBondTopologyFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBracketsFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveChiralFlagFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveExplicitHydrogenFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveInvalidChiralFlagFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveRadicalFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveReactingCenterBondMarkFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveStereoCareBoxFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveValencePropertyFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveZCoordinateFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.RgroupAttachmentFixer

fix(StructureCheckerResult) - Method in interface chemaxon.fixers.StructureFixer

Fixes one molecule problem identified by the result

fix(StructureCheckerResult) - Method in class chemaxon.fixers.SubstructureFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.UngroupFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.ValenceFixer

fix(StructureCheckerResult) - Method in class chemaxon.fixers.WedgeCleanFixer

Deprecated.

fix(StructureCheckerResult) - Method in class chemaxon.fixers.WigglyDoubleBondFixer

Deprecated.

fix(StructureChecker, StructureCheckerResult) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

Tries to fix the problem detected by the specified checker, or falls back to result based behavior.

Fix - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Mode

Indicates, that the structurechecker does automatically fix.

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

on problem applies preferred fix if possible

FIX_CHARGE - Static variable in class chemaxon.struc.MolAtom

Valence checking will replace radicals with charges if this flag is set.

FIX_MODE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

fix mode property

fixable(StructureCheckerResult) - Method in class chemaxon.fixers.PartialCleanFixer

Gets whether the result is fixable.

fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.graphics.MPolyline

fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.graphics.MRectangle

fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.MObject

Sets the parent object for this object.

FIXED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType

Do not move this molecule

fixElectronContainers(MDocument, boolean, boolean) - Static method in class chemaxon.struc.MDocument

Removes unnecesarry MElectronContainers from the give MDocument corresponding to lone pair display options, if an electron of a MEFlow arrow has been removed the arrow is removed as well.

FIXER_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

fixer class name property

FixerClassDescriptor() - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.FixerClassDescriptor

Initializes an empty fixer class descriptor

FixerClassDescriptor(String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.FixerClassDescriptor

Initializes a fixer class descriptor

FIXERFACTORYCONFIG_XML - Static variable in class chemaxon.fixers.StructureFixerFactory

Deprecated.

default fixer configuration file name

FixerInfo - Annotation Interface in chemaxon.fixers

This annotation is responsible for adding UI based meta data for StructureFixer implementations

FixerPriorityComparator - Class in chemaxon.fixers

Comparator of structure fixer for priority Default fixer and order of fixers is defined this way.

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

Fixes - Annotation Interface in chemaxon.fixers

This annotation is used to annotate the StructureFixer implementations which StructureCheckerErrorType can be fixed by the current fixer

FixesExternal - Annotation Interface in chemaxon.fixers

This annotation is used to annotate the StructureFixer implementations which error codes (identified by a unqie String) can be fixed by the current fixer

fixMidPointClones(MObject[], MObject[]) - Static method in class chemaxon.struc.graphics.MPolyline

Fixes the parents of the cloned MMidPoints.

FixMode - Enum Class in chemaxon.checkers

fix mode options

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

Delegates to tracker's fixProperties().

fixProperties() - Method in class chemaxon.struc.RxnMolecule

fixRectanglePointClones(MObject[], MObject[]) - Static method in class chemaxon.struc.graphics.MRectangle

Fixes the parents of the cloned MRectanglePoints.

fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.Molecule

Fix a property containing reference to the molecule.

fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.MoleculeGraph

Fix a property containing reference to the molecule.

fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.RgMolecule

Fix a property containing reference to the molecule.

fixSgroups - Variable in class chemaxon.marvin.io.formats.mdl.MolImport

Fl - Static variable in class chemaxon.core.ChemConst

flag() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo

Returns the enhanced stereo flag (eg.

flatten() - Method in class chemaxon.struc.MPropertyContainer

Flattens hierarchically specified RDF properties.

flavor - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

The DataFlavor represented by the implementation.

FlipWedgeBondFixer - Class in chemaxon.fixers

Flips wedge bonds.

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

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

FLOAT_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters

floatDescr - Variable in class chemaxon.descriptors.CustomDescriptor

storage for the floating point descriptors

flush() - Method in class chemaxon.formats.MolExporter

Flushes the output stream and forces any buffered output bytes to be written out.

Fm - Static variable in class chemaxon.core.ChemConst

FMT_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_IMAGE - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_MOL - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_MRV - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_PLAINTEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_RXN - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_SMILES - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_STRING - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

will be deleted, no need to this constant

FMT_STRUCTURE - Static variable in interface chemaxon.marvin.util.CopyOptConstants

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

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

Identifier of parameter: "fogFactor".

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

forIntValue(int) - Static method in enum class chemaxon.struc.AtomProperty.Radical

Gets the AtomProperty.Radical that's int value is the given parameter.

forIntValue(int) - Static method in enum class chemaxon.struc.stereo.EZConfiguration

FORMAL_CHARGE - Enum constant in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Show the formal (total) charge at the end of the molecular formula, instead of showing the charge of each atom separately.
If FormulaGenerationRule.DOT_DISCONNECTED_FRAGMENTS is also applied, then the charge of each fragment will be shown separately.
This rule has no effect if FormulaGenerationRule.IGNORE_CHARGE is also applied.
For example: [O-]NO -> NO2[-]

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

Result type with the string id "formalchargeformula".

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

Calculates the formal (total) charge of the molecule.

format - Variable in class chemaxon.checkers.StructureCheckOptions

The format of the output structures of the structure checker

format - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

The format string.

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

Returns the format of the annotated property

format(double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Converts a double into String, applying the maximum number of fractional digits specified.

format(double[][], int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Converts a double[][] 2xN table to a 2-column tab-separated string representation of the table.

format(double, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Converts a double into String, applying the maximum number of fractional digits specified.

format(double, StringBuffer) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Converts a double into String, applying the maximum number of fractional digits specified.

FORMAT_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction

The key of the molecule format parameter of the abstract action.

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

Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.

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

Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.

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

Calculates a fixed digit sortable molecular formula.

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

Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.

formula(Set<FormulaGenerationRule>) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.

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

Result type with the string id "formula".

FormulaGenerationRule - Enum Class in com.chemaxon.calculations.elemanal

Molecular formula generation settings.

FormulaSearch - Class in chemaxon.sss.formula

Chemical formula based search class.

FormulaSearch() - Constructor for class chemaxon.sss.formula.FormulaSearch

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

forName(String) - Static method in class chemaxon.marvin.io.Encoding

Creates an Encoding for the specified name, with #UNKNOWN endianness.

fp - Variable in class chemaxon.descriptors.ChemicalFingerprint

storage for the fingerprint

fp - Variable in class chemaxon.descriptors.ECFP

Binary vector storage of the fingerprint

fp - Variable in class chemaxon.descriptors.PharmacophoreFingerprint

storage for the fingerprint

fp - Variable in class chemaxon.descriptors.ReactionFingerprint

storage for the fingerprint

Fr - Static variable in class chemaxon.core.ChemConst

FRAG_BASIC - Static variable in class chemaxon.struc.MoleculeGraph

Basic fragmentation, only atom - atom connections (bond) are considered.

FRAG_KEEPING_MULTICENTERS - Static variable in class chemaxon.struc.MoleculeGraph

Fragmentation without breaking multicenter S-groups.

FRAG_KEEPING_SGROUPS - Static variable in class chemaxon.struc.MoleculeGraph

Fragmentation without breaking S-groups.

FRAG_TYPE_COUNT - Static variable in class chemaxon.struc.MoleculeGraph

Number of fragmentation types.

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

Calculates the number of fragments (disconnected parts) of the molecule.

freqCount - Variable in class chemaxon.descriptors.MDGenerator

fromData(byte[]) - Method in class chemaxon.descriptors.BCUT

Builds a BCUT descriptor from an external data format, created by a previous call to toData().

fromData(byte[]) - Method in class chemaxon.descriptors.ChemicalFingerprint

Builds a fingerprint from an external data format, created by a previous call to toData().

fromData(byte[]) - Method in class chemaxon.descriptors.CustomDescriptor

Builds a CustomDescriptor from an external data format, created by a previous call to toData().

fromData(byte[]) - Method in class chemaxon.descriptors.ECFP

Builds an ECFP fingerprint from an external data format created by toData().

fromData(byte[]) - Method in class chemaxon.descriptors.MolecularDescriptor

Builds a MolecularDescriptor object from its external (database) representation.

fromData(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Builds a PharmacophoreFingerprint from an external data format, created by a previous call to toData().

fromData(byte[]) - Method in class chemaxon.descriptors.ReactionFingerprint

Builds a fingerprint from an external data format, created by a previous call to toData().

fromData(byte[]) - Method in class chemaxon.descriptors.ScalarDescriptor

Builds a descriptor from an external data format, created by a previous call to toData().

fromData(byte[]) - Method in class chemaxon.descriptors.ShapeDescriptor

fromFeatureSet(Set<Integer>) - Method in class chemaxon.descriptors.ECFP

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

As of JChem 5.4.1, replaced by fromIdentiferSet().

fromFile(File) - Method in class chemaxon.descriptors.CDParameters

Sets parameters from an XML file.

fromFile(File) - Method in class chemaxon.descriptors.CFParameters

Sets parameters from an XML file.

fromFile(File) - Method in class chemaxon.descriptors.ECFPParameters

Sets parameters from an XML file.

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

Sets parameters from an XML file.

fromFile(File) - Method in class chemaxon.descriptors.PFParameters

Sets parameters from an XML file.

fromFile(File) - Method in class chemaxon.descriptors.RFParameters

Sets parameters from an XML file.

fromFile(File) - Method in class chemaxon.descriptors.SDParameters

Sets parameters from an XML file.

fromFile(File) - Method in class chemaxon.descriptors.ShapeParameters

Sets parameters from an XML file.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.BCUT

Builds a BCUT descriptor from its float array representation (generated by toFloatArray()).

fromFloatArray(float[]) - Method in class chemaxon.descriptors.ChemicalFingerprint

Builds fingerprint from its float array representation.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.CustomDescriptor

Builds a molecular descriptor from its float array representation.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.ECFP

Builds an ECFP fingerprint from its float array representation.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.MolecularDescriptor

Builds a molecular descriptor from its float array representation.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Builds a molecular descriptor from its float array representation.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.ReactionFingerprint

Builds fingerprint from its float array representation.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.ScalarDescriptor

Builds the descriptor from a float array of one element.

fromFloatArray(float[]) - Method in class chemaxon.descriptors.ShapeDescriptor

fromFormula(String) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas

fromFormula(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas

Deprecated.

fromId(int) - Static method in enum class com.chemaxon.calculations.admet.HergClass

Converts the given integer ID to the appropriate hERG class: 0 to HergClass.SAFE and 1 to HergClass.TOXIC.

fromIdentiferSet(Set<Integer>) - Method in class chemaxon.descriptors.ECFP

Builds an ECFP fingerprint from a set of Integer identifers.

fromIntArray(int[]) - Method in class chemaxon.descriptors.ECFP

Builds an ECFP fingerprint from an array of int identifiers.

fromMethod(AromatizationMethod) - Static method in enum class com.chemaxon.search.transformation.transformers.Aromatizer

Gets the aromatizer-transformer corresponding to the specified aromatization method

fromMolecule(Molecule) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas

fromMolecule(Molecule) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas

Deprecated.

fromMolecule(Molecule, boolean) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas

fromMolecule(Molecule, boolean) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas

Deprecated.

fromMolecule(Molecule, Set<Integer>, boolean) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas

fromMolecule(Molecule, Set<Integer>, boolean) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas

Deprecated.

fromPlainText(Reader) - Static method in class chemaxon.naming.document.annotate.DocumentAnnotator

Constructs a DocumentAnnotator to annotate the given text.

fromString(String) - Method in class chemaxon.descriptors.BCUT

Builds a BCUT descriptor from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.BCUTParameters

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.CDParameters

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.CFParameters

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.ChemicalFingerprint

Builds a fingerprint from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.CustomDescriptor

Builds a descriptor from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.ECFP

Builds an ECFP fingerprint from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.ECFPParameters

Sets parameters from a string representation.

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

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Builds a molecular descriptor from its string representation.

fromString(String) - Method in class chemaxon.descriptors.PFParameters

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Builds a fingerprint from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.ReactionFingerprint

Builds a fingerprint from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.RFParameters

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.ScalarDescriptor

Builds a descriptpr from its string representation created by toString().

fromString(String) - Method in class chemaxon.descriptors.SDParameters

Sets parameters from a string representation.

fromString(String) - Method in class chemaxon.descriptors.ShapeDescriptor

fromString(String) - Method in class chemaxon.descriptors.ShapeParameters

fromString(String) - Static method in enum class chemaxon.sss.search.options.HaltOnErrorOption

Gets the halt on error option value for the string representation.

fromString(String) - Static method in enum class chemaxon.sss.search.options.HomologyTranslationOption

FULL - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Full clean

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

Deprecated.

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

 molecule.setValenceCheckOptions(new ValenceCheckOptions(false,true);
             

FULL - Static variable in interface chemaxon.sss.SearchConstants

Full structure search.

FULL_FRAGMENT - Static variable in interface chemaxon.sss.SearchConstants

Full fragment search (formerly called exact fragment).

functionScale - Variable in class chemaxon.calculations.nmr.NMRSpectrum

Scale factor for NMR spectrum function scaling.

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

Adds those atoms and bonds of another molecule to this one that are not already elements.

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

Adds atoms and bonds of another molecule to this one.

fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.RgMolecule

Add the atoms and bonds of another molecule.

fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.RxnMolecule

Add the atoms and bonds of another molecule.

fuse(RxnMolecule) - Method in class chemaxon.struc.RxnMolecule

Fuse and RxnMolecule to this RxnMolecule.

fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.Molecule

Adds those atoms and bonds of a molecule graph to this one that are not already elements.

fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.MoleculeGraph

Adds the atoms and bonds of another molecule to this one.

fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.RgMolecule

Add those nodes and edges of a graph that are not already elements.

fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.RxnMolecule

Add those nodes and edges of a graph that are not already elements.

fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.SelectionMolecule

Adds those atoms and bonds of a graph to this one that are not already elements.

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

Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.

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

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

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

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

Calculates the number of fused aliphatic rings in the molecule (rings s).

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

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

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

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

Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.

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

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

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

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

Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).

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

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

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

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

Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.

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

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

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

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

Calculates the number of fused aromatic rings in the molecule (rings s).

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

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

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

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

Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.

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

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

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

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

Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).

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

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

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

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

Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.

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

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

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

fuzzinessFactors - Variable in class chemaxon.descriptors.PFParameters

fuzziness factors of parametrized metrics

fuzzyExp - Variable in class chemaxon.descriptors.PFParameters

fuzzi exponent for the FBPA metric, calculated from the fuzziness factor

G

Ga - Static variable in class chemaxon.core.ChemConst

gatherBaseColors() - Static method in class chemaxon.marvin.util.ColorGenerator

Creates a Collection of the base colors.
These colors are:

- black
- white
- red
- green
- blue
- cyan
- magenta
- yellow.

gatherBaseColorsAndBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator

Creates a Collection of the base Molecule RGB colors and base colors.
These colors are the atom label RGB colors of:
- H
- C
- N
- O
- S
- F
- P
- Cl
- Br
- I.

gatherBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator

Creates a Collection of the base Molecule RGB colors.
These colors are the atom label RGB colors of:

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


and

- black
- white

gatherBlackAndWhite() - Static method in class chemaxon.marvin.util.ColorGenerator

Creates a Collection of black and white color

GAUSS_44_SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties

GAUSS_FAST_EXTENDED_ATOMTYPE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties

GAUSS_FAST_EXTENDED_ATOMTYPE_MCS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties

Deprecated.

GAUSS_FAST_PHARMACOPHORE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties

GAUSS_FAST_SHAPE_ONLY - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties

GAUSS_VOLUME_SIMPLE_44 - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

GAUSS_VOLUME_SIMPLE_45 - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

GAUSS_VOLUME_SIMPLE_FAST - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

GAUSS_VOLUME_SIMPLE_FULL - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

GAUSSIAN_CUBE - Static variable in class chemaxon.formats.MFileFormat

Gaussian Cube files.

GAUSSIAN_INPUT - Static variable in class chemaxon.formats.MFileFormat

Gaussian Input Format.

GAUSSIAN_INPUTZ - Static variable in class chemaxon.formats.MFileFormat

Gaussian Input Format: Z-matrix.

GAUSSIAN_OUTPUT - Static variable in class chemaxon.formats.MFileFormat

Gaussian output format.

Gd - Static variable in class chemaxon.core.ChemConst

Ge - Static variable in class chemaxon.core.ChemConst

gearch - Variable in class chemaxon.struc.MoleculeGraph

gearch() - Method in interface chemaxon.struc.Smolecule

Gets graph search algorithms.

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

General aromatization

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

General aromatization.

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

GeneralExportOptions - Class in chemaxon.formats

Abstract class to handle common export options.

GeneralExportOptions(GeneralExportOptions.Builder<?>) - Constructor for class chemaxon.formats.GeneralExportOptions

GeneralExportOptions.AromatizationMethod - Enum Class in chemaxon.formats

GeneralExportOptions.Builder<T extends GeneralExportOptions.Builder<T>> - Class in chemaxon.formats

GeneralExportOptions.HydrogenizeOption - Enum Class in chemaxon.formats

generate() - Method in class chemaxon.sss.search.MarkushGenerator

Generates the RgMolecule with the specified scaffold (see MarkushGenerator.setQuery(chemaxon.struc.Molecule)) covering the specified targets (see MarkushGenerator.setTargets(chemaxon.struc.Molecule[])).

generate(int, int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

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

Use AlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.

generate(int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated.

Use AlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.

generate(Molecule) - Method in class chemaxon.descriptors.BCUT

Creates the BCUT descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.ChemicalFingerprint

Creates the ChemicalFingerprint descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.DescriptorGenerator

Generates descriptor for the given molecule.

generate(Molecule) - Method in class chemaxon.descriptors.ECFP

Creates the ECFP fingerprint for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.MolecularDescriptor

Creates the descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Creates the PharmacophoreFingerprint descriptor from the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.ReactionFingerprint

Creates the ReactionFingerprint descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.ScalarDescriptor

Creates the ScalarDescriptor descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.HAcc

Calculates the HAcc descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.HBParameters

Calculates the descriptor value for the given molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.HDon

Creates the HDon descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.Heavy

Creates the HeavyAtomCount descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.LDParameters

generate(Molecule) - Method in class chemaxon.descriptors.scalars.LogD

Creates the LogD descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.LogP

Creates the LogP descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.Mass

Creates the Mass descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.scalars.TPSA

Creates the TPSA descriptor for the given Molecule.

generate(Molecule) - Method in class chemaxon.descriptors.ShapeDescriptor

generate(Molecule, int[]) - Method in class chemaxon.descriptors.DescriptorGenerator

Generates partial descriptor for the given molecule.

generate(Molecule, int[], MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator

Generates the partial chemical fingerprint for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.BCUTGenerator

Generates the BCUT descriptors for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.BCUTParameters

Calls the descriptor generator for the molecule provided and stores result (the descriptor) in the MolecularDescriptor object.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator

Generates the chemical fingerprint for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.CFParameters

Calls CFGenerator and generates the descriptor for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator

Generates the ECFP fingerprint for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPParameters

Calls ECFPGenerator and generates the descriptor for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator

Generates the molecular descriptor for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in interface chemaxon.descriptors.MolecularDescriptorGenerator

Deprecated.

Creates a certain type of MolecularDescriptor (depending on the specific ganerator providing this service) for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator

Generates the pharmacophore fingerprint of the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.PFParameters

Calls the corresponding MolecularDescriptorGenerator and generates the descriptor for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator

Generates the reaction fingerprint for the given reaction molecule object.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.RFParameters

Calls RFGenerator and generates the descriptor for the given molecule.

generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeGenerator

generate(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Creates the descriptor for the given Molecule.

generateBracketCoords(Sgroup, int) - Static method in class chemaxon.marvin.util.CleanUtil

Generates brackets with coordinates for a specified S-group.

generateBracketCoords(Sgroup, int, boolean) - Static method in class chemaxon.marvin.util.CleanUtil

Generates brackets with coordinates for a specified S-group.

generateColors(int) - Static method in class chemaxon.marvin.util.ColorGenerator

Generates the specified number of different Colors, with no forbidden colors.

generateColors(int, Collection<Color>) - Static method in class chemaxon.marvin.util.ColorGenerator

Generates the specified number of different Colors, which are different enough from the specified forbidden colors.

generateData(int, Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

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

use ShapeData.toData instead.

generateEMFToFile(String, String, String) - Static method in class chemaxon.util.ImageExportUtil

Creates a new .NET based EMF picture and saves it to the given file.

generateMultiplet() - Method in class chemaxon.calculations.nmr.Multiplet

Generates the line positions and intensities of this multiplet.

generator - Variable in class chemaxon.descriptors.MDParameters

generates MolecularDescriptors

GENERIC - Enum constant in enum class chemaxon.sss.search.options.TautomerEqualityMode

GENERIC - Enum constant in enum class chemaxon.sss.search.options.TautomerTransformationMode

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

GEOMETRY - Enum constant in enum class chemaxon.calculator.CalculatorTag

GEOMETRY_PROJECTION - Enum constant in enum class chemaxon.calculator.CalculatorTag

GeometryPlugin - Class in chemaxon.marvin.calculations

Plugin class for geometric properties calculations.

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

Constructor.

get(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the content of the specified hitogram bin.

get(int) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Returns the group definition at specified index.

get(int) - Method in class chemaxon.struc.prop.MHashProp

Gets a value.

get(int) - Method in class chemaxon.struc.prop.MListProp

Gets the specified element.

get(int, int, float) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

get(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the histogram bar height of two features ('fa'-'fb') corresponding to the given ditance 'dist'.

get(String) - Method in class chemaxon.struc.MPropertyContainer

Gets a property object.

get(String) - Method in class chemaxon.struc.prop.MHashProp

Gets a value.

GET - Enum constant in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method

mehtod GET

get3DMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the 3D molecule used in 3D surface area calculation.

getAbbreviation() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets the abbreviation of the group.

getAbbreviation(int) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Gets the abbreviation at the provided index

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

Determines the absolute cell index of a visible cell

getAbsoluteCellIndex(JComponent) - Method in class chemaxon.marvin.beans.MViewPane

Determines in which cell the specified component is located.

getAbsoluteLabelVisible() - Method in class chemaxon.marvin.common.UserSettings

Are Absolute labels visible?

getAbsoluteXY() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.

getAbundance(int, int) - Static method in class chemaxon.struc.PeriodicSystem

Natural abundance of the isotope

getAcceptorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the overall acceptor atom count (without multiplicity) in the molecule.

getAcceptorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin

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

Use HBDAPlugin.getAcceptorSiteCount() instead.

getAcceptorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin

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

Use HBDAPlugin.getAcceptorSiteCount() instead!

getAcceptorSiteCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the overall acceptor count (with multiplicity) in the molecule.

getAcceptorSiteCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the atomic acceptor count corresponding to the specified atom index.

getAccuracyMode() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties

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

Gets the base StandardizerAction of the changes

getActionCommand() - Method in class chemaxon.marvin.swing.MAction

Gets the action command string.

getActionCount() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets the action count of the configuration

getActionIndexes(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets the indexes of actions defined by the provided action string

getActionMap() - Method in class chemaxon.struc.graphics.MTextBox

Returns the ActionMap used to determine what Action to fire for particular KeyStroke binding.

getActionName() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

Gets the name of the original action

getActions() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets all actions of the configuration

getActions(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets actions of a group of the configuration

getActions(String...) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets actions of a group of the configuration

getActionString() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

getActionStringTokens() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Gets the action string token of the checker

getActionStringTokens() - Method in class chemaxon.fixers.StructureFixerDescriptor

Gets the action string token of the fixer

getActionStringTokens() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the action string tokens of the action

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

Gets the list of atoms added during the standardization procedure

getAgent(int) - Method in class chemaxon.struc.RxnMolecule

Gets an agent.

getAgentCount() - Method in class chemaxon.struc.RxnMolecule

Gets the number of agents.

getAgents() - Method in class chemaxon.struc.RxnMolecule

Gets all agents in an array.

getAlias() - Method in class chemaxon.marvin.services.ServiceArgument

Returns the argument alias.

getAlias() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the service alias.

getAliasNames() - Method in class chemaxon.descriptors.BCUT

getAliasNames() - Method in class chemaxon.descriptors.ChemicalFingerprint

getAliasNames() - Method in class chemaxon.descriptors.ECFP

getAliasNames() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

getAliasNames() - Method in class chemaxon.descriptors.ReactionFingerprint

getAliasNames() - Method in class chemaxon.descriptors.ShapeDescriptor

getAliasstr() - Method in class chemaxon.struc.MolAtom

Gets the alias string or pseudo atom type string for pseudo atoms.

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

getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.PairwiseAlignment

getAlignedMoleculesAsFragments() - Method in interface chemaxon.marvin.alignment.PairwiseComparison

After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.

getAlignedMoleculesAsFragments() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

getAlignedQuery() - Method in class chemaxon.marvin.alignment.PairwiseAlignment

getAlignedQuery() - Method in interface chemaxon.marvin.alignment.PairwiseComparison

getAlignedQuery() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

getAlignedTarget() - Method in class chemaxon.marvin.alignment.PairwiseAlignment

getAlignedTarget() - Method in interface chemaxon.marvin.alignment.PairwiseComparison

getAlignedTarget() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

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

getAlignScaffold() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Gets the scaffold aligning mode

getAliphaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the aliphatic atom count.

getAliphaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the aliphatic bond count.

getAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the aliphatic ring count.

getAliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getAliphaticRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

Use TopologyAnalyserPlugin.getAliphaticRingCount(int)

getAliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the aliphatic rings in the molecule.

getAliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getAllAtomCount() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the atom count (including implicit hydrogens).

getAllAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the atom count.

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

Gets the attachment atoms (atoms having attachment point).

getAllFragments() - Method in class chemaxon.struc.RxnMolecule

Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.

getAllFromDocument(MDocument) - Static method in class chemaxon.struc.NoStructure

Returns all NoStructure labels from the document.

getAllMolecules() - Method in class chemaxon.struc.MDocument

Gets an array containing all molecule objects.

getAllNonEmptyMolecules() - Method in class chemaxon.struc.MDocument

Gets an array containing all non-empty molecule objects.

getAllObjects() - Method in class chemaxon.struc.MDocument

Gets all objects stored in this document and from the chemical structure of the document.

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

getAllObjects() - Method in class chemaxon.struc.RgMolecule

getAllObjects() - Method in class chemaxon.struc.RxnMolecule

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

Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)

getAllOptionsAsString(String) - Method in class chemaxon.sss.search.SearchOptions

Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)

getAnalysisBoxTerms() - Method in class chemaxon.marvin.common.UserSettings

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

Represented angle.

getAngle(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the angle of 3 atoms.

getAngle(int, int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the angle of 3 atoms.

getAngleCheckerResult() - Method in class chemaxon.checkers.result.BondAngleCheckerResult

Returns the internal representation of the angle checker result, which contains all information required to fix bond angle errors.

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

Gets index of animated cells of the table (or simple viewer).

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

Gets the repeat delay for animations.

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

Gets the frames per second for animations.

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

Gets the any bond style.

getAppliedActions() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Gets the list of applied actions

getAppliedActions() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

getAppliedActions() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Gets the list of actions applied in the configuration at the last execution

getAppliedTaskIDs() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Returns the IDs of tasks applied to the last input molecule.

getAppliedTaskIDs() - Method in class chemaxon.standardizer.Standardizer

Returns the IDs of tasks applied to the last input molecule.

getAppliedTaskIndexes() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Returns the indexes of tasks applied to the last input molecule.

getAppliedTaskIndexes() - Method in class chemaxon.standardizer.Standardizer

Returns the indexes of tasks applied to the last input molecule.

getArcAngle() - Method in class chemaxon.struc.graphics.MPolyline

Gets the central angle of the arc.

getArcCenter(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline

Returns the arc center.

getArcHeight() - Method in class chemaxon.struc.graphics.MRoundedRectangle

getArcRadius(CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Gets the arc radius.

getArcRadius(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline

getArcWidth() - Method in class chemaxon.struc.graphics.MRoundedRectangle

getArgument(int) - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the type of the specified argument

getArgumentCount() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the number of arguments

getArguments() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns an unmodifiable list of the argument types

getAromataType() - Method in class chemaxon.checkers.result.AromaticityCheckerResult

Returns the type of the aromatization

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

Returns the aromatic and or aliphatic ring atom indexes.
Note: This method does not aromatize the already aromatized rings.

getAromaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the aromatic atom count.

getAromaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the aromatic bond count.

getAromaticRingCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the total partial charge of the smallest aromatic ring containing the specified atom.

getAromaticRingCharge(int, int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the partial charge of the smallest aromatic ring containing the specified atom.

getAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the aromatic ring count.

getAromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getAromaticRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

Use TopologyAnalyserPlugin.getAromaticRingCount(int)

getAromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the aromatic rings in the molecule.

getAromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getAromaticSystemCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the total partial charge of the aromatic system containing the specified atom.

getAromaticSystemCharge(int, int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the partial charge of the aromatic system containing the specified atom.

getAromatizationMethod() - Method in class chemaxon.formats.GeneralExportOptions

Gets the aromatization method.

getAromatizationMethod() - Method in enum class com.chemaxon.search.transformation.transformers.Aromatizer

getAromatizedStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the enumerated structures in aromatized form.

getAromatizeMethod() - Method in class chemaxon.marvin.common.UserSettings

Gets the aromatize method.

getAromatizer(AromatizationMethod) - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns an aromatizer transformer.

getAromType() - Method in class chemaxon.checkers.AromaticityErrorChecker

Returns the aromType

getArrayFlags() - Method in interface chemaxon.struc.Smolecule

Gets info about the used arrays.

getArrowAsProperty() - Method in class chemaxon.struc.RxnMolecule

Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.

getArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline

Gets the arrow flags.

getArrowLength(int) - Method in class chemaxon.struc.graphics.MPolyline

Gets the arrow head length.

getArrowWidth(int) - Method in class chemaxon.struc.graphics.MPolyline

Gets the arrow head width.

getASA() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule.

getASAHydrophobic() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns water accessible surface area of all hydrophobic (|qi|<0.125) atoms.

getASANegative() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0).

getASAPlus() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0).

getASAPolar() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns water accessible surface area of all polar (|qi|>=0.125) atoms.

getAsBitSet() - Method in class chemaxon.descriptors.DescriptorGenerator

Returns the generated descriptor in a BitSet representation if it is available.

getAscent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the ascent of this portion.

getAsFloatArray() - Method in class chemaxon.descriptors.DescriptorGenerator

Returns the generated descriptor in a float array representation if it is available.

getAsIntArray() - Method in class chemaxon.descriptors.DescriptorGenerator

Returns the generated descriptor in an int array representation if it is available.

getAsMolecule() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the found common substructure as a Molecule object.

getAssignedAtoms() - Method in class chemaxon.struc.graphics.MAssigner

Gets the atoms which are assigned by this object.

getAssociatedNonQueryFormat() - Method in class chemaxon.formats.MFileFormat

Gets the associated non-query format.

getAssociatedQueryFormat() - Method in class chemaxon.formats.MFileFormat

Gets the associated query format.

getAsString() - Method in class chemaxon.descriptors.DescriptorGenerator

Returns the generated descriptor in its native string representation.

getAsymmetricAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the number of asymmetric atoms.

getAsymmetricAtoms() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines the asymmetric atoms.

getAsymmetricEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the asymmetric Euclidean distance.

getAsymmetricEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Calculates the asymmetric Euclidean distance.

getAsymmetricEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP

Calculates the asymmetric Euclidean distance.

getAsymmetricEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

getAsymmetricFBPA(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the asymmetric FBPA convolution product based distance of the fingerprint from an other (given as parameter).

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

Gets the asymmetry factor used in the current parametrized asymmetric metrics.

getAtno() - Method in class chemaxon.struc.MolAtom

Gets the atomic number.

getAtom() - Method in class chemaxon.jep.context.AtomContext

Returns the input atom index.

getAtom() - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Gets the atom.

getAtom() - Method in class chemaxon.struc.graphics.MElectron

getAtom() - Method in class chemaxon.struc.graphics.MElectronContainer

All MElectron should belong to the same MolAtom, this returns the MolAtom reference of the first MElectron.

getAtom() - Method in class chemaxon.struc.sgroup.AttachmentPoint

Gets the atom on which the attachment point was placed.

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

Gets the nth atom.

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

Gets a node in the graph union.

getAtom(int) - Method in class chemaxon.struc.RxnMolecule

Gets a node.

getAtom(int) - Method in class chemaxon.struc.Sgroup

Gets an atom in the S-group.

getAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets the atom at the terminus of an arrow.

getAtom1() - Method in class chemaxon.struc.MolBond

Gets the first endpoint.

getAtom1(int) - Method in interface chemaxon.struc.Smolecule

Gets the index of the first atom of the specified bond.

getAtom1Index() - Method in class chemaxon.marvin.alignment.atrop.BondInfo

Atom index for first end atom.

getAtom2() - Method in class chemaxon.struc.MolBond

Gets the second endpoint.

getAtom2(int) - Method in interface chemaxon.struc.Smolecule

Gets the index of the second atom of the specified bond.

getAtom2Index() - Method in class chemaxon.marvin.alignment.atrop.BondInfo

Atom index for second end atom.

getAtomArray() - Method in class chemaxon.struc.graphics.MAtomSetPoint

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

Creates an array of atoms.

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

Gets the array of atoms in the S-group.

getAtomCount() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the number of atoms in the multiplet.

getAtomCount() - Method in class chemaxon.core.util.BondTable

Returns the number of atoms in the molecule this bond table represents.

getAtomCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

getAtomCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the number of atoms in the input molecule.

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

Gets the number of atoms.

getAtomCount() - Method in class chemaxon.struc.RgMolecule

Gets the number of nodes in the root structure.

getAtomCount() - Method in class chemaxon.struc.RxnMolecule

Returns the number of nodes in the graph union.

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

Gets the number of atoms in the S-group.

getAtomCount() - Method in interface chemaxon.struc.Smolecule

Gets the number of atoms.

getAtomCount() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the number of atoms in the found common substructure.

getAtomCount(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the number of atoms with given atomic number (including its isotopes).

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

Gets the number of atoms with the given atomic number.

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

Gets the number of atoms with the given atomic number in the root structure.

getAtomCount(int) - Method in class chemaxon.struc.RxnMolecule

Gets the number of atoms with the given atomic number in the unified molecule graph of the reaction.

getAtomCount(int, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the number of atoms with given atomic number in the molecule isotope with the specified mass number.

getAtomFont() - Method in class chemaxon.marvin.common.UserSettings

Gets the atom symbol font name.

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

Gets the atomic number of the given atom.

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

Gets the atomic number of the given atom.

getAtomicNumber(String) - Static method in class chemaxon.struc.MolAtom

Deprecated.

As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String).
The recommended method does not work for symbol not representing a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.

getAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem

Returns the atomic number of the element in the periodic system specified by its symbol or -1 if not found.

getAtomicRadius(int) - Static method in class chemaxon.struc.PeriodicSystem

Atomic radius of the element Angstroms.

getAtomicSurfaceAreaIncrement(int) - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the 3D surface area increments.

getAtomIndex() - Method in class chemaxon.calculations.nmr.Shift

Returns the atom index.

getAtomIndex() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

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

Returns the index of the ith atom of this multiplet.

getAtomIndex(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the atom index in the standardized molecule, or the atom index itself if the input molecule has not been standardized.

getAtomIndexes() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the atom indices of the NMR active nuclei.

getAtomIndexMap() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

getAtomIndexMapping() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns an immutable function of the current atom index mapping from the original molecule to standardized one.

getAtomIndices() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the indices of the atoms of this multiplet.

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

Returns an iterator over the atoms in this molecule in proper sequence.

getAtomIterator() - Method in class chemaxon.struc.RgMolecule

Returns an iterator over the atoms in this molecule in proper sequence.

getAtomIterator() - Method in class chemaxon.struc.RxnMolecule

Returns an iterator over the atoms in this molecule in proper sequence.

getAtomlogPHIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin

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

Increments of implicit H-s are not calculated. Returns the same value as logPPlugin.getAtomlogPIncrement(int)

getAtomlogPIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the logP increment for the specified atom.

getAtomMap() - Method in class chemaxon.calculations.nmr.Multiplet

getAtomMap() - Method in class chemaxon.struc.MolAtom

Gets the atom-atom mapping number.

getAtomMap(int) - Method in interface chemaxon.struc.Smolecule

Gets the atom-atom mapping number.

getAtomMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the atom mapping of the found common substructure.

getAtomMappingMethod() - Method in class chemaxon.marvin.common.UserSettings

Gets the atom mapping method.

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

Determines the atom numbering.

getAtomNumberingType() - Method in class chemaxon.marvin.common.UserSettings

Gets the atom numbering type.

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

Returns atom numbering type.

getAtomOf(MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct

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

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

Use MoleculeGraph.atoms() instead.

getAtomReverseMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the reverse atom mapping of the found common substructure.

getAtoms() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getAtoms() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getAtoms() - Method in class chemaxon.struc.graphics.MAtomSetPoint

Gets the atoms.

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

getAtoms(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets the atom or atoms at the terminus of an arrow.

getAtomSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane

Gets the color of an atom set.

getAtomSetColor(int) - Method in class chemaxon.struc.MDocument

Gets an atom set color.

getAtomSetColorMode(int) - Method in class chemaxon.struc.MDocument

Gets the atom set coloring mode.

getAtomSetColors() - Method in class chemaxon.descriptors.MolecularDescriptor

Determines the coloring of atoms.

getAtomSetColors() - Method in class chemaxon.descriptors.PFParameters

Gets the coloring of atoms as defined in the XML configuration file.

getAtomSetColors() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Determines the coloring of atoms.

getAtomSetFont(int) - Method in class chemaxon.struc.MDocument

Gets an atom set font.

getAtomSetIndexes(Molecule) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the individual atom color indexes.

getAtomSetIndexes(Molecule) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the individual atom colors by pharmcophore point type.

getAtomSetIndexes(Molecule, PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PFParameters

Gets the individual atom colors by pharmcophore point type.

getAtomSetNames() - Method in class chemaxon.descriptors.MolecularDescriptor

getAtomSetNames() - Method in class chemaxon.descriptors.PFParameters

Gets the name of atom sets (pharmacophore point type set), as defined in the configuration file/string.

getAtomSetNames() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

getAtomSetRGB(int) - Method in class chemaxon.struc.MDocument

Gets an atom set color.

getAtomSetSize() - Method in class chemaxon.struc.MDocument

Gets the size of the atom set.

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

Gets the atom size.

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

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

As of Marvin 5.2.2, replaced by MolPrinter.getAtomSize().

getAtomSize() - Method in class chemaxon.marvin.common.UserSettings

Gets the atom size in C-C bond length units.

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

Returns the atom size in units of regular bond length.

getAtomStereo(int) - Method in interface chemaxon.struc.Smolecule

Gets atom stereo properties as an integer.

getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.MolAtom

Gets the string representation of the atom symbol.

getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.sgroup.SgroupAtom

Gets the string representation of the atom symbol.

getAtomSymbolListAsString(MolAtom[]) - Static method in class chemaxon.struc.Sgroup

getAtomType(int) - Method in interface chemaxon.struc.Smolecule

Gets the type of an atom.

getAtropBonds() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

After the calculate method finished.

getAttach() - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.0 replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom).
If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.

getAttach(MolAtom) - Static method in class chemaxon.struc.Sgroup

Gets the attachment point information from the ExtraAtomProperties

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

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

As of Marvin 6.0, replaced by SuperatomSgroup.getBoundAttachAtoms().

getAttachCount(Integer) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets the attachment point count for the atom specified by the index

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

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

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

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

Gets the attached data.

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

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

Returns whether attached data (in data sgroups) should be used when comparing structures.

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

Returns the prefixes of the names of those data sgroups that will be used during structure comparison or null if all data sgroups should be checked.

getAttachFromExtraAtomProp() - Method in class chemaxon.struc.MolAtom

Gets the attachment information stored in the extra atom properties

getAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Gets the attachment point that's order is given as parameter

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

Gets the number of the attachment points.

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

Gets the orders with which attachment point exists

getAttachmentPointOrders(int) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Returns the attachment point orders of the atom specified by atomIndex.

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

Gets the attachment orders of the given attachment atom.

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

Gets the sorted copy of the attachment point list.

getAttachParentSgroup() - Method in class chemaxon.struc.MolAtom

Gets the smallest containing sgroup which can have the attachment point information of this atom.

getAttrFont(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument

Gets the font for the specified attribute object.

getAttribute(String) - Method in class chemaxon.struc.graphics.MAnalysisBox

getAttribute(String) - Method in class chemaxon.struc.graphics.MBracket

Gets the value of an attribute.

getAttribute(String) - Method in class chemaxon.struc.graphics.MEFlow

getAttribute(String) - Method in class chemaxon.struc.graphics.MElectron

getAttribute(String) - Method in class chemaxon.struc.graphics.MElectronContainer

getAttribute(String) - Method in class chemaxon.struc.graphics.MNameTextBox

Gets the value of an attribute.

getAttribute(String) - Method in class chemaxon.struc.graphics.MPolyline

Gets the value of an attribute.

getAttribute(String) - Method in class chemaxon.struc.graphics.MRectangle

Gets the value of an attribute.

getAttribute(String) - Method in class chemaxon.struc.graphics.MRoundedRectangle

Gets the value of an attribute.

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

Gets the value of an attribute.

getAttribute(String) - Method in class chemaxon.struc.MObject

Gets the value of an attribute.

getAttributes() - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets the attributes.

getAttributes(int, int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets attributes of the text of len length from start that are supposed to be set even if their values are "default".

getAutoScale() - Method in class chemaxon.marvin.beans.MSketchPane

Returns autoscale property.

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

Is tab scale automatically changed?

getAvailableCheckers() - Method in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Returns a list of checkers available

getAvailableCheckers() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory

This method returns all StructureChecker instances available by the current configuration

getAvailableFixers() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory

This method returns all StructureFixer instances available by the current configuration

getAvailableStandardizerActions() - Method in class chemaxon.standardizer.StandardizerActionFactory

Returns the list of standardizer actions that are available

getAvailableStyles() - Method in class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI

Gets the list of available DocumentStyle names

getAverageNonZeroRatio() - Method in class chemaxon.descriptors.MDGenerator

Gets the average percentage of cells that have non-zero value taken all descriptors generated since the initialization of the generator into account.

getAveragePolarizabilityComponent() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the average polarizability component (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).

getAWTFont() - Method in class chemaxon.struc.graphics.MFont

Gets an AWT font instance.

getBackground() - Method in class chemaxon.struc.MObject

Gets the background color of the object.

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

Returns the current background color.

getBalabanIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

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

Gets the ball radius in units of covalent radius.

getBallRadius() - Method in class chemaxon.marvin.common.UserSettings

Gets the ball radius for ball and stick mode.

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

Gets the ball radius for "ball and stick" mode.

getBaseElectronContainerIndex() - Method in class chemaxon.struc.graphics.MEFlow

getBaseElectronIndexInContainer() - Method in class chemaxon.struc.graphics.MEFlow

getBaseFont() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the base font.

getBaseFont() - Method in class chemaxon.struc.graphics.MTextBox

Gets the base font.

getBaseFontFamily() - Method in class chemaxon.struc.graphics.MTextBox

Gets the base font family.

getBaseFontStyle() - Method in class chemaxon.struc.graphics.MTextBox

Gets the base font style.

getBasicElectronCount() - Method in enum class chemaxon.struc.BondType

Returns the electron count given by an atom at the end of bond into the bond if it can be determined unambiguously, otherwise returns 0.

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

Gets the smallest best scale value in the molecule table.

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

Gets the best scale value for a molecule cell.

getBicycloStereo() - Method in class chemaxon.struc.MolAtom

Gets the previously stored bicyclo stereo information of this atom.

getBit(int) - Method in class chemaxon.descriptors.CustomDescriptor

getBitCount() - Method in class chemaxon.descriptors.CFParameters

Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.

getBitCount() - Method in class chemaxon.descriptors.RFParameters

Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.

getBitPosition() - Method in class chemaxon.descriptors.ECFPFeature

Gets the generated bit position for this ECFP feature.

getBitPosition(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup

Returns the corresponding bit position for the given integer identifier.

getBitPosition(MolAtom, int) - Method in class chemaxon.descriptors.ECFPFeatureLookup

Returns the corresponding bit position for the given atom neighborhood.

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

Gets the C-C bold bond width in pt units.

getBoldBondWidth() - Method in class chemaxon.marvin.common.UserSettings

Gets the bold bond width in pt.

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

Represented bond info.

getBond() - Method in class chemaxon.struc.sgroup.AttachmentPoint

Gets the bond that is binded to this attachment point (crossing bond).

getBond(int) - Method in class chemaxon.struc.MolAtom

Gets the i-th bond.

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

Gets the nth bond.

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

Gets an edge in the graph union.

getBond(int) - Method in class chemaxon.struc.RxnMolecule

Gets an edge.

getBond(int) - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator

Returns a bond of a specified index.

getBond(int) - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Returns a bond of a specified index.

getBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets the bond at the terminus of an arrow.

getBondArray() - Method in class chemaxon.struc.MolAtom

Gets the bonds connected to this atom.

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

Creates an array of bonds.

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

Gets all bonds connecting two atoms that are both in the Sgroup

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

Gets a bond triplet which stores the crossing bond and flip information.

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

Gets four bonds that store the crossing bond and flip information.

getBondCount() - Method in class chemaxon.descriptors.CFParameters

Gets the preset path length (number of adjacent bonds) parameter.

getBondCount() - Method in class chemaxon.descriptors.RFParameters

Gets the preset path length (number of adjacent bonds) parameter.

getBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the bond count.

getBondCount() - Method in class chemaxon.struc.MolAtom

Gets the number of bonds/ligands.

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

Gets the number of bonds.

getBondCount() - Method in class chemaxon.struc.RgMolecule

Gets the number of edges in the root structure.

getBondCount() - Method in class chemaxon.struc.RxnMolecule

Gets the number of edges in the graph union.

getBondCount() - Method in interface chemaxon.struc.Smolecule

Gets the number of bonds.

getBondCount() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the number of bonds in the found common substructure.

getBondFlags() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

getBondFlags(int) - Method in interface chemaxon.struc.Smolecule

Gets the bond descriptor flags.

getBondHashSpacing() - Method in class chemaxon.marvin.common.UserSettings

Gets the bond hash spacing.

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

Returns the bond hash spacing that is the distance hashes in a hashed bond.

getBondIndex() - Method in class chemaxon.marvin.alignment.atrop.BondInfo

Bond index.

getBondIndex(int, int) - Method in class chemaxon.core.util.BondTable

Returns the index of the bond connecting two atoms, or -1 if the two atoms are not connected.

getBondIndex(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the index of the bond connecting two atoms, -1 if the two atoms are not connected by bond.

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

Gets the index of the bond between the specified atoms.

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

Returns an iterator over the bonds in this molecule in proper sequence.

getBondIterator() - Method in class chemaxon.struc.RgMolecule

Returns an iterator over the bonds in this molecule in proper sequence.

getBondIterator() - Method in class chemaxon.struc.RxnMolecule

Returns an iterator over the bonds in this molecule in proper sequence.

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

Gets the C-C bond length in pt units.

getBondLength() - Method in class chemaxon.marvin.common.UserSettings

Gets the bond length in pt.

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

Returns the actual bond length in pt.

getBondMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the bond mapping of the found common substructure.

getBondReverseMapping() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the reverse bond mapping of the found common substructure.

getBonds() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getBonds() - Method in interface chemaxon.checkers.result.StructureCheckerResult

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

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

Returns the bonds attached to the given atom.

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

Returns the bonds attached to the given atom in this molecule graph.

getBondSetColor(int) - Method in class chemaxon.struc.MDocument

Gets a bond set color.

getBondSetColorMode(int) - Method in class chemaxon.struc.MDocument

Gets the bond set coloring mode.

getBondSetRGB(int) - Method in class chemaxon.struc.MDocument

Gets a bond set color.

getBondSetSize() - Method in class chemaxon.struc.MDocument

Gets the bond set size.

getBondSetThickness(int) - Method in class chemaxon.struc.MDocument

Gets a bond set thickness.

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

Gets the bond spacing.

getBondSpacing() - Method in class chemaxon.marvin.common.UserSettings

Gets the double bond spacing.

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

Returns the double bond spacing that is the distance of the two lines representing a double bond.

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

Gets the bond (edge) table.

getBondTable() - Method in class chemaxon.struc.RgMolecule

Gets the bond table of the root structre.

getBondTable() - Method in class chemaxon.struc.RxnMolecule

Gets the bond table for the graph union.

getBondTo(MolAtom) - Method in class chemaxon.struc.MolAtom

Finds the bond that connects this atom to another atom.

getBondType() - Method in class chemaxon.struc.MolBond

Gets the type of the bond.

getBondType(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines the type of a bond (aromatic bonds are automatically recognized)

getBondType(int) - Method in interface chemaxon.struc.Smolecule

Gets the type of a bond.

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

Gets the type of a bond between the two specified atoms.

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

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

as of Marvin 4.1, replaced by MarvinPane.getBondSpacing()

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

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

as of Marvin 4.1, replaced by MolPrinter.getBondSpacing()

getBoolean(String) - Static method in class chemaxon.sss.search.SearchOptions

Returns value as a boolean flag.

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

Gets the width of the border between cells.

getBottomMargin() - Method in class chemaxon.struc.PageSettings

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

Gets atoms with attachment point having crossing bond.

getBoundingRectangle(MoleculeGraph[]) - Method in class chemaxon.marvin.MolPrinter

Returns the bounding rectangle of the specified molecules using the current scale factor.

getBoundRectSize() - Method in class chemaxon.marvin.beans.MSketchPane

Gets the size of the bounding rectangle.

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

Gets the number of brackets in this S-group.

getBracketOrientation() - Method in class chemaxon.struc.graphics.MBracket

Gets the orientation of the bracket.

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

Gets all graphic brackets from this Sgroup

getBreakingChars() - Method in class chemaxon.struc.graphics.MNameTextBox

Gets the breaking characters after that the text in the text box can be broken if it doesn't fit into the text box.

getBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox

Gets the breaking characters after that the text in the text box can be broken if it doesn't fit into the text box.

getBrightestMolId() - Method in class chemaxon.descriptors.MDGenerator

Gets the id of that molecule which had the maximum number of non-zero cells among all descriptors generated since the initialization of the generator object.

getBrightness() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the brightness of the fingerprint.

getBrightness() - Method in class chemaxon.descriptors.ECFP

Gets the brightness of the fingerprint.

getBrightness() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the brightness of the fingerprint.

getBuildDate() - Static method in class com.chemaxon.version.VersionInfo

Returns the build date as string (in local time zone).

getBuildTime() - Static method in class com.chemaxon.version.VersionInfo

Returns the build time as string (in local time zone).

getBuildTimestamp() - Static method in class com.chemaxon.version.VersionInfo

Returns the build date and time.

getBuildTimestampStr() - Static method in class com.chemaxon.version.VersionInfo

Returns the build date and time as string in UTC time zone.

getBuildYear() - Static method in class com.chemaxon.version.VersionInfo

Returns the year of the build date as string.

getByIndex(int) - Static method in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

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

Gets the state of a checkbox in a GridBagView table.

getCacheCapacity() - Method in class chemaxon.marvin.view.MDocStorage

Gets the maximum number of cached documents.

getCachedDoc(int, String) - Method in class chemaxon.marvin.view.MDocStorage

Gets the specified document if it is present in the memory.

getCachedDocIndices() - Method in class chemaxon.marvin.view.MDocStorage

Gets the indices of cached records.

getCachedResults(Molecule, boolean) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns cached results, separated from the plugin object, so that no further enqueries needed to the plugin to get the result.

getCacheLock() - Method in class chemaxon.marvin.view.MDocStorage

Gets the synchronization lock for caching operations.

getCalcMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the molecule used in the calculation.

getCanvasComponent() - Method in class chemaxon.marvin.beans.MSketchPane

Determines canvas component of MarvinSketch.

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

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

as of Marvin 3.0, replaced by getVisibleCellComponent

getCapacity() - Method in class chemaxon.marvin.view.MDocStorage

Gets the total capacity.

getCarboaliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).

getCarboaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).

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

Returns the visibility style of the C labels on Carbon atoms.

getCarboRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the carbo ring count.

getCarboRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).

getCarboRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).

getCarboRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.

getCASNumber() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the CAS number via public web service.

getCategory(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCategories

Calculates the solubility category of molecule.

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

Gets the number of molecule cells in the table.

getCellEditorValue() - Method in class chemaxon.marvin.beans.MViewEditor

Returns the edited molecule that is a Molecule instance.

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

Gets the number of bits of an atomic cell in the descriptor.

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

Gets the geometrical center of a reaction component.

getCenterAtom() - Method in class chemaxon.descriptors.ECFPFeature

Gets the center atom of the represented substructure.

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

Gets the central atom of this sgroup.

getChainAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the chain atom count.

getChainBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the chain bond count.

getChangedAtomIndexes() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the indexes of the atoms changed during tautomerization.

getChangeList() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Gets the list of applied changes

getChangeMap() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

The map containing the applied changes for each applied actions

getChanges() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

getChanges() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Gets the list of changes applied on the molecule.

getChangeSupport() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Returns the changeSupport

getCharge() - Method in class chemaxon.struc.MolAtom

Gets the charge.

getCharge() - Method in class chemaxon.struc.sgroup.SgroupAtom

Returns the sum of the charges in the corresponding superatom s-group.

getCharge(int) - Method in interface chemaxon.struc.Smolecule

Gets the charge of an ion.

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

Gets the charge of the given atom.

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

Gets the charge of the given atom.

getChargeAngle() - Method in class chemaxon.struc.MolAtom

getChargeCategory() - Method in class chemaxon.marvin.calculations.logDPlugin

getChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.

getChargeDistribution() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the charge distribution array over pH values.

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

Gets the charge's font.

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

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

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

Returns the charge location attribute of the S-group.

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

Get the charge matching option value

getChargePlusMinusDistribution() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the plus and the minus parts of the charge distribution array over pH values.

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

getChartImage(int, int) - Method in class com.chemaxon.calculations.gui.MChart

getChecker(String, Map<String, String>) - Method in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

This method creates a requested (type represented in checkerId) StructureChecker instance with the give parameters

getCheckerConfigFileName() - Method in class chemaxon.marvin.common.UserSettings

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

Use UserSettings.getCheckerConfigURL() instead. Deprecated in 5.12.

getCheckerConfiguration() - Method in interface chemaxon.checkers.runner.CheckerRunner

Gets the list of available checkers

getCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings

Returns the URL of configuration for Checkers in marvin sketch.

getCheckerList() - Method in class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader

getCheckerList() - Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader

getCheckerList() - Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader

getCheckerMarks() - Method in class chemaxon.struc.MDocument

Returns the array of checker marks NOTE: checker marks will be reset on any molecule change

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

Get the sp-hybridization state option

getChemicalHashedFingerprint(int[], int) - Static method in class chemaxon.descriptors.ReactionFingerprint

Creates chemical hashed fingerpint from reaction fingerprint.

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

Gets the Chemical Terms filtering expression

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

Gets the configuration string for Chemical Terms filter.

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

FOR INTERNAL USE ONLY.

getChild() - Method in interface chemaxon.common.util.MProgressMonitor

Gets the child of this progress monitor.

getChildSgroup(int) - Method in class chemaxon.struc.Sgroup

Gets a child S-group.

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

Gets the number of child S-groups.

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

Gets the children of this S-group.

getChiralCenterCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of tetrahedral stereogenic centers.

getChiralCenters() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines the chiral center atoms.

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

Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

getChirality(int) - Method in interface chemaxon.struc.Smolecule

Gets the chirality of an atom.

getChiralityOfOriginalLigand() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

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

Gets chirality support level.

getChiralitySupport() - Method in class chemaxon.marvin.common.UserSettings

Gets the chirality support parameter.

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

Returns the current chirality display mode.

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

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

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

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

Returns the stereo center value.

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

getClassName() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

Returns the full class name of the service

getClassName() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Gets the name of the standardizer class

getClassName() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

Gets the name of the checker class

getClean2dOpts() - Method in class chemaxon.marvin.common.UserSettings

Gets the 2D cleaning options.

getClean3dOpts() - Method in class chemaxon.marvin.common.UserSettings

Gets the 3D cleaning options.

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

Gets the number of space dimensions for cleaning.

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

Gets the list of atoms changed during the standardization procedure, and needs to be cleaned

getClip(CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Gets the clipping rectangle.

getClonedValue(String) - Method in class chemaxon.jep.ConstantTable

Returns the value of a constant.

getClosestMElectronRef(DPoint3) - Method in class chemaxon.struc.graphics.MElectronContainer

getClosestMElectronRef(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

getCoarseReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

Returns the tanimoto distance of the reaction centers.

getCode() - Method in enum class chemaxon.standardizer.actions.AromatizeAction.Type

Gets the MoleculeGraph constant value of the aromatization

getCode() - Method in enum class com.chemaxon.search.AromatizationMethod

Gets the int code of the aromatization method.

getColor() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties

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

getColor() - Method in class chemaxon.struc.MObject

Gets the color of the object.

getColoredLargestConjugatedSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns a Molecule in which the atoms of largest conjugated system are colored.

getColoring() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the hit coloring options.

getColoringScheme() - Method in class chemaxon.marvin.alignment.ShapeData

getColors() - Method in class chemaxon.marvin.alignment.Pharmacophore3D

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

Gets the color scheme.

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

Returns the current color scheme.

getColumn(int) - Static method in class chemaxon.core.ChemConst

The column or group of an element in the periodic system.

getColumn(int) - Static method in class chemaxon.struc.MolAtom

The column or group of an element in the periodic system.

getColumnCount() - Method in class chemaxon.struc.PageSettings

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

Gets the default column width.

getColumnWidth(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Gets the default width of a specified column.

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

Gets a parameter string containing column widths.

getCommandKeyStroke(int) - Static method in class chemaxon.marvin.util.SwingUtil

Gets the command keystroke preferred on the current platform.

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

Gets the comment.

getComment() - Method in class chemaxon.struc.RgMolecule

Gets the comment of the root molecule.

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

Deprecated.

getCommonActions() - Method in class chemaxon.marvin.beans.MSketchPane

Deprecated.

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

Deprecated.

getCommonBitCount(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

getCommonBitCount(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

getCompatibleAttributes(MTextAttributes, MFont, MTextAttributes.MFontCreator, int) - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the compatible attributes.

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

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

This option is no longer supported. This method always returns true.

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

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

Complex number support will be removed without replacement.

getComponent() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Returns the parameter panel component.

getComponent() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Returns the parameter panel component.

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

Gets a reactant, product or agent.

getComponent(long) - Method in class chemaxon.struc.RxnMolecule

Gets a reactant, product or agent.

getComponent(Molecule, int) - Method in class chemaxon.checkers.AtomChecker

getComponent(Molecule, int) - Method in class chemaxon.checkers.BondChecker

getComponent(Molecule, int) - Method in class chemaxon.checkers.ComponentChecker

Gets the component from the molecule with index i.

getComponentCount(int) - Method in class chemaxon.struc.RxnMolecule

Gets the number of reactants, products or agents.

getComponentCount(Molecule) - Method in class chemaxon.checkers.AtomChecker

getComponentCount(Molecule) - Method in class chemaxon.checkers.BondChecker

getComponentCount(Molecule) - Method in class chemaxon.checkers.ComponentChecker

Gets the number of the components in the molecule

getComponentFlags(long) - Method in class chemaxon.struc.RxnMolecule

Gets the reaction component type flags from the ID.

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

Gets the reaction component ID of an atom.

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

Gets the reaction component ID of a bond.

getComponentID(Molecule) - Method in class chemaxon.struc.RxnMolecule

Gets the ID of a reaction component.

getComponentIds() - Method in class chemaxon.checkers.result.ReactionCheckerResult

Deprecated.

Returns the List of the ids of the components affected by the problem

getComponentIndex(long) - Method in class chemaxon.struc.RxnMolecule

Gets the reactant, product or agent index from the ID.

getComponents(Molecule) - Static method in class chemaxon.checkers.StructureCheckerUtility

A recursive algorithm collecting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.

getComponents(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction

A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.

getComponents(Molecule) - Method in class chemaxon.standardizer.actions.ExpandAction

getComponents(Molecule) - Method in class chemaxon.standardizer.actions.MapAction

getComponents(Molecule) - Method in class chemaxon.standardizer.actions.MapReactionAction

getComponents(Molecule) - Method in class chemaxon.standardizer.actions.NeutralizeAction

getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RearrangeReactionAction

Every action that needs to do something on a reaction as a whole needs this, otherwise reaction components will be processed one-by-one.

getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

getComponents(Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

getComponents(Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

getComponents(Molecule) - Method in class chemaxon.standardizer.advancedactions.TransformAction

getComponentType(long) - Method in class chemaxon.struc.RxnMolecule

Gets the reaction component type from the ID.

getComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

getConfig() - Method in class chemaxon.sss.screen.StrucFPConfig

Creates a configuration string according to the internal values.

getConfiguration() - Method in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

getConfiguration() - Method in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader

Gets the configuration defined by the pre-set configuration file.

getConfiguration() - Method in class chemaxon.standardizer.configuration.reader.StandardizerXMLReader

getConfiguration() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

getConfiguration() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Gets the configuration of the runner

getConfiguration() - Method in class chemaxon.standardizer.Standardizer

Gets the configuration of the standardizer.

getConformer(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns a conformer.

getConformerCount() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the number of different conformers.

getConformers() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns all conformers in a Molecule[] array.

getConformerWithConformerInfoProperty(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Deprecated.

Only intended for internal use.

getConfTryCountLimit() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties

getConnectedObject(int) - Method in class chemaxon.struc.MDocument

Gets an object from the document or from the chemical structure of the document.

getConnectedObjectCount() - Method in class chemaxon.struc.MDocument

Gets the number of objects in this document and in the chemical structure of this document.

getConnectionAtom() - Method in class chemaxon.struc.BicycloStereoDescriptor

Returns the ring atom connected to the ligand.

getConnectionAtomIndex() - Method in class chemaxon.struc.BicycloStereoDescriptor

Returns the ring atom index connected to the ligand.

getConnectionAtoms() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets the indexes of atoms connection to any atoms

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

Gets S-group connectivity.

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

getContainerOfMelectron(MElectron) - Static method in class chemaxon.struc.graphics.MElectronContainer

getContext() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the context of the data sgroup.

getContextFunctionNames() - Method in interface chemaxon.jep.ChemContext

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

This method is the legacy option for specifying the supported context functions. Use the ChemContext.ProvidesFunction annotation instead.

getContextFunctionNames() - Method in class chemaxon.jep.context.AtomContext

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

Use the ChemContext.ProvidesFunction annotation instead.

getContextFunctionNames() - Method in class chemaxon.jep.context.MolContext

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

Use the ChemContext.ProvidesFunction annotation instead.

getContextFunctionNames() - Method in class chemaxon.jep.context.ReactionContext

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

Use the ChemContext.ProvidesFunction annotation instead.

getContextId() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the id of the context of the data sgroup.

getCoordinateBondStyle() - Method in class chemaxon.marvin.common.UserSettings

Gets the "coordinative" bond line style when both atoms are single.

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

Gets the coordinate bond line style when both atoms are single.

getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.common.UserSettings

Gets the "coordinative" bond line style when one of the atoms is multicenter.

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

Gets the coordinate bond line style.

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

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

getCopyAsFormat() - Method in class chemaxon.marvin.common.UserSettings

Gets the selected format from the Copy As dialog.

getCorrectionLibraryIds() - Static method in class chemaxon.marvin.calculations.pKaPlugin

Returns the id's of available pKa correction libraries.

getCount() - Method in class com.chemaxon.calculations.gui.PluginFactory

Returns the number of plugin records.

getCouplingConstants() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns coupling constants.

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

Returns the coupling constants of the ith atom in this multiplet.

getCouplingConstants(int, NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.Multiplet

Returns the coupling constants of the ith atom in this multiplet.

getCouplingConstants(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns coupling constants in the given unit.

getCouplingNeeded() - Method in class chemaxon.calculations.nmr.Multiplet

Returns whether spin-spin couplings are taken into account.

getCovalentRadius(int) - Static method in class chemaxon.struc.PeriodicSystem

Covalent radius of the element in Angstroms.

getCovalentRadius(int, int) - Static method in class chemaxon.struc.PeriodicSystem

Covalent radius of the element in specific bond type in Angstroms.

getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.Sgroup

Gets the atoms that have crossing bonds.

getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Gets the atoms from the S-group that have crossing bonds.

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

Gets the Complete Set of Smallest Ring atom indexes array.

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

Get the cssr ring indexes in which the atom (specified with it's index) can be located.

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

Gets the connection table.

getCtab() - Method in class chemaxon.struc.RgMolecule

Gets the connection table of the root structure.

getCtab() - Method in class chemaxon.struc.RxnMolecule

Gets the connection table for the graph union.

getCTAtom1() - Method in class chemaxon.struc.MolBond

Gets the first atom for cis/trans stereo calculation.

getCTAtom4() - Method in class chemaxon.struc.MolBond

Gets the fourth atom for cis/trans stereo calculation.

getCurrent() - Method in interface chemaxon.checkers.runner.CheckerRunner

getCurrent() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

getCurrent() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Gets the current progress percent

getCurrentActionName() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

getCurrentActionName() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Gets which StandardizerAction instance run currently

getCurrentCheckerName() - Method in interface chemaxon.checkers.runner.CheckerRunner

getCurrentDefaultFontMetrics() - Method in class chemaxon.struc.graphics.MTextBox

Gets the current default FontMetrics.

getCurrentForeground() - Method in class chemaxon.struc.graphics.MTextBox

Gets the current color.

getCurrentFrameIndex() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets the current frame index.

getCurrentHeight() - Method in class chemaxon.struc.graphics.MTextBox

Gets the current height of the text.

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

getCurrentMolecule() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets the stored molecule graph.

getCurrentScriptCount(int) - Method in class chemaxon.struc.graphics.MTextBox

Gets the number of subscripts or superscripts on the last normal character.

getCurrentSubLevel() - Method in class chemaxon.struc.graphics.MTextBox

Gets the current subscript/superscript level.

getCurrentTarget() - Method in class chemaxon.marvin.swing.MAction

Is the current action coming from a pop-up menu item?

getCurrentTextAttributes(int) - Method in class chemaxon.struc.graphics.MTextBox

Gets the common attributes of the selected text or attributes for the next character to be typed.

getCurrentWidth() - Method in class chemaxon.struc.graphics.MTextBox

Gets the current width of the text.

getCursorColumn() - Method in class chemaxon.struc.graphics.MTextBox

Gets the cursor's column number.

getCursorPos() - Method in class chemaxon.struc.graphics.MTextBox

Gets the cursor position.

getCursorRow() - Method in class chemaxon.struc.graphics.MTextBox

Gets the cursor's row number.

getCustomFuzzyIncrements(int, int) - Method in class chemaxon.descriptors.PFParameters

Gets fuzzy increments for the fuzzy smoothing with a user-defined custom distribution (fuzzy smoothing vector).

getCustomMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns the factory that is used to create custom matcher (if specified).

getCustomName() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the customName

getCyclomaticNumber() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the smallest number of graph edges which must be removed such that no circuit remains.

getDarkestMolId() - Method in class chemaxon.descriptors.MDGenerator

Gets the id of that molecule which had the minimum number of non-zero cells among all descriptors generated since the initialization of the generator object.

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

Gets the byte array which is used for conversions between internal and external data formats.

getData() - Method in class chemaxon.sss.search.MarkushFeature

Deprecated.

Returns the feature data.

getData() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the data value to be set.

getData() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData

Gets the data field.

getDataCollectionConsent() - Method in class chemaxon.marvin.common.UserSettings

getDataCollectionServer() - Method in class chemaxon.marvin.common.UserSettings

getDataFromClipboard(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Returns the Molecule from the Transferable object.

getDataLine(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Gets a line of data.

getDataLineCount() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the number of data lines.

getDataToClipboard(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Returns the clipboard representation of the given Molecule.

getDaviesHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin

Returns the HLB value calculated by Davies method.

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

Gets the debugging level.

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

Gets the formatter object that is capable of formatting fractions with given precision.

getDecompositions() - Method in class chemaxon.sss.search.RgDecompResults

Returns the Decomposition objects corresponding to the targets.

getDefault() - Static method in enum class chemaxon.sss.search.options.TautomerEqualityMode

getDefault() - Static method in enum class chemaxon.sss.search.options.TautomerTransformationMode

getDefault() - Static method in class com.chemaxon.search.mcs.McsSearchOptions

Returns the default search options object.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.BCUT

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.CustomDescriptor

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ECFP

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ScalarDescriptor

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ShapeDescriptor

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.BCUTParameters

Gets the default XML configuration string.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.CDParameters

Gets the XML configuration string.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.CFParameters

Gets the default XML configuration string.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.ECFPParameters

Get the default XML configuration string.

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

Gets the default XML configuration string.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.PFParameters

Gets the default XML configuration string.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.RFParameters

Get the default XML configuration string.

getDefaultDocumentFrame() - Method in class chemaxon.descriptors.ShapeParameters

Get the default XML configuration string.

getDefaultFont() - Method in class chemaxon.struc.graphics.MTextDocument

Gets the default font.

getDefaultMetricIndex() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the index of the default metric.

getDefaultMetricIndex() - Method in class chemaxon.descriptors.ECFP

Gets the index of the default metric.

getDefaultMetricIndex() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the index of the default metric.

getDefaultMetricIndex() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the index of the default metric.

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

Gets the value of the given key in the default configuration or null if the key does not exist.

getDefaultSaveFormat() - Method in class chemaxon.marvin.common.UserSettings

Gets the default molecule format in the "Save As" dialog.

getDefaultScale() - Static method in class chemaxon.marvin.beans.MSketchPane

Returns the default scale factor which is equivalent to 100% magnification.

getDefaultSize() - Method in class chemaxon.marvin.view.swing.TableSupport

Gets the default size of an MViewPane containing the generated table.

getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.ECFPParameters

Gets the default configuration of the standardizer.

getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.MDParameters

Gets the default configuration of the standardizer.

getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.PFParameters

Gets the default configuration of the standardizer.

getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.ShapeParameters

Gets the default configuration of the standardizer.

getDefaultThreshold(int) - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets a metric dependent default threshold value.

getDefaultThreshold(int) - Method in class chemaxon.descriptors.ECFP

Gets a metric dependent default threshold value.

getDefaultThreshold(int) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets a metric dependent default threshold value.

getDefaultThreshold(int) - Method in class chemaxon.descriptors.ReactionFingerprint

Gets a metric dependent default threshold value.

getDefaultThreshold(int) - Method in class chemaxon.descriptors.ScalarDescriptor

Gets a metric dependent default threshold value.

getDefaultThreshold(int) - Method in class chemaxon.descriptors.ShapeDescriptor

Gets a metric dependent default threshold value.

getDefaultValue() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the default value of the multiplet function.

getDefaultValue() - Method in class chemaxon.calculations.nmr.NMRSpectrum

getDehydrogenizer() - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns a dehydrogenizer transformer.

getDensityCounts() - Method in class chemaxon.descriptors.MDGenerator

Gets the array of bit density.

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

Gets the R-group definition's index which depends on the referenced R-group definition.

getDescent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the descent of this portion.

getDescription() - Method in class chemaxon.checkers.AbstractStructureChecker

getDescription() - Method in class chemaxon.checkers.InvalidChecker

getDescription() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getDescription() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getDescription() - Method in interface chemaxon.checkers.StructureChecker

getDescription() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the description

getDescription() - Method in class chemaxon.fixers.AbstractStructureFixer

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

getDescription() - Method in interface chemaxon.fixers.StructureFixer

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

getDescription() - Method in class chemaxon.fixers.StructureFixerDescriptor

Returns the description

getDescription() - Method in class chemaxon.formats.MFileFormat

Gets the format description.

getDescription() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the description (tooltip) of service descriptor

getDescription() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the description.

getDescription() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the description of the action

getDescriptor() - Method in class chemaxon.checkers.AbstractStructureChecker

getDescriptor() - Method in class chemaxon.checkers.InvalidChecker

getDescriptor() - Method in interface chemaxon.checkers.StructureChecker

Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker

getDescriptor() - Method in class chemaxon.fixers.AbstractStructureFixer

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

getDescriptor() - Method in interface chemaxon.fixers.StructureFixer

Gets the descriptor object of the fixer.

getDescriptor() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor

Returns the ServiceDescriptor represented by editor state or null if the editor is in not valid state

getDescriptor() - Method in class chemaxon.standardizer.AbstractStandardizerAction

getDescriptor() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

getDescriptor() - Method in interface chemaxon.standardizer.StandardizerAction

Gets the descriptor of the standardizer action.

getDescriptorLongName(String) - Static method in class chemaxon.descriptors.DescriptorGenerator

Returns the long name for the given molecular descriptor type.

getDescriptorTypeName(String) - Static method in class chemaxon.descriptors.MDParameters

Takes the descriptor type name from the root element of the XML configuration.

getDescriptorTypes() - Static method in class chemaxon.descriptors.DescriptorGenerator

Returns the list of the built-in molecular descripor types.

getDescriptorURI() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor

Gets the URI of the JSON RPC descriptor file

getDescrType() - Method in class chemaxon.descriptors.CDParameters

Gets the type of the descriptor.

getDesiredLength() - Method in class chemaxon.struc.MolBond

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

since 5.11, replaced by MolBond.desiredLength(int, int, int, int).

getDesiredLength(boolean) - Method in class chemaxon.struc.MolBond

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

since 5.11, replaced by MolBond.desiredLength(int, int, int, int).

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

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

As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int) and MoleculeGraph.getDim().
Usage:

             MolBond.desiredLength(atno1, atno2, type, getDim());
             

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

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

As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int), MolBond.getType() and MoleculeGraph.getDim().
Usage:

             MolBond.desiredLength(atno1, atno2, b.getType, getDim());
             

getDf1() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

getDf2() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

getDialog(Component, ServiceDescriptor) - Method in interface chemaxon.marvin.services.ServiceDialogProvider

Returns dialog with argument editor and result view

getDiameter() - Method in class chemaxon.descriptors.ECFPFeature

Gets the diameter of the represented substructure.

getDiameter() - Method in class chemaxon.descriptors.ECFPParameters

Gets the preset diameter parameter.

getDihedral(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the dihedral of 4 atoms.

getDihedral(int, int, int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the dihedral of 4 atoms.

getDihedralScanResults() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Get results of executed dihedral scans.

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

Gets the dimension.

getDim(String) - Static method in class chemaxon.marvin.plugin.gui.ResultView

Returns the text width - height in a Dimension.

getDipole() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the length of the dipole moment vector.

getDipoleVector() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the dipole moment vector.

getDipoleX() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the x component of the dipole moment vector.

getDipoleY() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the y component of the dipole moment vector.

getDipoleZ() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the z component of the dipole moment vector.

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

Sets the working directory.

getDisabledGroupTypes() - Method in class chemaxon.marvin.beans.MSketchPane

getDisplay() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

getDisplay(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets a display object, loads it if needed.

getDisplayedChars() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the number of characters to be displayed(1...999 or 0 for all)

getDisplayedLines() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the number of lines to be displayed (0: show all)

getDisplayMolecule() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the molecule object to be used for GUI display.

getDisplayMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the molecule object to be used for GUI display.

getDisplayMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the molecule object to be used for GUI display.

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

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

since Marvin 6.4 only high quality exists

getDisplayVersion() - Static method in class com.chemaxon.version.VersionInfo

Returns the display version.

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

Gets display options.

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

Returns the actual display options.

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

Returns the actual extended display options.

getDissimilarity() - Method in class com.chemaxon.search.mcs.McsSearchResult

Returns a Tanimoto-like dissimilarity metric score of the input molecules based on the found maximum common substructure.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.BCUT

Calculates the dissimilarity ratio between two BCUT objects using the current default metric.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the dissimilarity between two chemical fingerprints using the default distance measure.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFP

Calculates the dissimilarity ratio between two ECFP objects using the current default metric.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.MolecularDescriptor

Calculates the dissimilarity ratio between two MolecularDescriptor objects using the default metric.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ReactionFingerprint

Calculates the dissimilarity between two reaction fingerprints using the default distance measure.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ScalarDescriptor

Calculates the dissimilarity between two scalar descriptor using the default metrics In the present implementation it is always the absolute difference between them.

getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.BCUT

Calculates the dissimilarity between two BCUT objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the dissimilarity between two chemical fingerprints using the specified distance metric.

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.CustomDescriptor

Calculates the dissimilarity between two descriptors using the specified parametrized dissimilarity metric.

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ECFP

Calculates the dissimilarity between two ECFP objects using the specified metric, apart from that it is the same as getDissimilarity(final MolecularDescriptor other).

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.MolecularDescriptor

Calculates the dissimilarity between two MolecularDescriptor objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the dissimilarity between two pharmacophore fingerprints using the specified parametrized distance metric.

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ReactionFingerprint

Calculates the dissimilarity between two reaction fingerprints using the specified distance metric.

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ScalarDescriptor

Calculates the dissimilarity between two scalar descriptor using the specified metric.

getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ShapeDescriptor

getDissimilarity(T) - Method in class chemaxon.descriptors.SimilarityCalculator

Gets the dissimilarity value according to previously defined metric and its parameters.

getDissimilarityMetricIndex(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the internal index of the given metric.

getDissimilarityMetrics() - Method in class chemaxon.descriptors.BCUT

Gets the dissimilarity metric names introduced for this class of MolecularDescriptor.

getDissimilarityMetrics() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the dissimilarity metric names

getDissimilarityMetrics() - Method in class chemaxon.descriptors.CustomDescriptor

Gets the dissimilarity metric names.

getDissimilarityMetrics() - Method in class chemaxon.descriptors.ECFP

Gets the dissimilarity metric names introduced for this class of MolecularDescriptor.

getDissimilarityMetrics() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the dissimilarity metric names in an array.

getDissimilarityMetrics() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the dissimilarity metric names.

getDissimilarityMetrics() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the dissimilarity metric names

getDissimilarityMetrics() - Method in class chemaxon.descriptors.ScalarDescriptor

Gets the dissimilarity metric names

getDissimilarityMetrics() - Method in class chemaxon.descriptors.ShapeDescriptor

getDissimilarityMetricsParamDefault() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the dissimilarity metric parameter names -> no parameters.

getDissimilarityMetricsParamHelp() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the dissimilarity metric parameter names -> no parameters.

getDissimilarityMetricsParamNames() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the dissimilarity metric parameter names -> no parameters.

getDissimilarityMetricsParamNum() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the dissimilarity metric parameter number -> no parameters.

getDissimilarityMetricsParamRanges() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the dissimilarity metric parameter ranges -> no parameters.

getDistance(int[]) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the distance of 2 atoms.

getDistance(int, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the distance of 2 atoms.

getDistanceCount(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Counts the given value in a row of the distance matrix.

getDistanceDegree(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.

getDoc(int, String) - Method in class chemaxon.marvin.view.MDocStorage

Gets the specified document.

getDoc(int, String, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage

Gets the specified document.

getDocLabel(int, MDocument) - Method in class chemaxon.marvin.io.MDocSource

Returns the display label for the given document and document index.

getDocLabel(int, MDocument) - Method in class chemaxon.marvin.view.MDocStorage

Returns the display label for the given document and document index.

getDocSource() - Method in class chemaxon.marvin.view.MDocStorage

Gets the document source.

getDocSourcePosition() - Method in class chemaxon.marvin.view.MDocStorage

Gets the current position in the input.

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

Gets the sparse dynamic document storage.

getDocStorage() - Method in class chemaxon.marvin.view.swing.TableSupport

Gets the sparse dynamic document storage.

getDocument() - Method in class chemaxon.marvin.beans.MSketchPane

Gets the document.

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

Gets the document object.

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

Gets the nth document.

getDocument(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns encapsulating document, creates it if needed.

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

Gets the parent document for a child molecule graph.

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

Gets the array of documents.

getDocumentStyleName() - Method in class chemaxon.marvin.common.UserSettings

getDomainMax() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the upper end of this multiplet.

getDomainMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the upper end of the spectrum.

getDomainMin() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the lower end of this multiplet.

getDomainMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the lower end of the spectrum.

getDominantTautomerDistribution(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the distribution of the dominant tautomer.

getDonorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the overall donor atom count (without multiplicity) in the molecule.

getDonorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin

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

Use HBDAPlugin.getDonorSiteCount() instead!

getDonorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin

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

Use HBDAPlugin.getDonorSiteCount(int) instead!

getDonorSiteCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the overall donor count (with multiplicity) in the molecule.

getDonorSiteCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the atomic donor count corresponding to the specified atom index.

getDotDisconnectedFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the dot-disconnected molecular formula of a multifragment molecule with its formal charge.

getDotDisconnectedFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the dot-disconnected molecular formula of a multifragment molecule.

getDotDisconnectedIsotopeFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.

getDotDisconnectedIsotopeFormalChargeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.

getDotDisconnectedIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the dot-disconnected isotope formula of a multifragment molecule.

getDotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the dot-disconnected isotope formula of a multifragment molecule.

getDoubleArray() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Gets the integer value.

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

Get the double bond stereo matching mode.

getDoublePrecision() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the precision.

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

Gets the wedge bond display convention.

getDownWedge() - Method in class chemaxon.marvin.common.UserSettings

Gets the wedge bond display convention.

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

Gets the down wedge orientation.

getDraggedObject() - Method in class chemaxon.struc.MDocument

Gets the dragged object

getDreidingEnergy() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the energy of the conformer.

getDx() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the x shift.

getDy() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the y shift.

getEccentricity(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.

getEditable() - Method in class chemaxon.marvin.beans.MViewEditor

Returns the mode that determines if the structure is editable.

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

Returns the mode that determines if the structure is editable.

getEditor() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor

Returns the editor component for the ServiceDescriptor

getEditor(Class<T>) - Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider

Returns a ServiceDescriptorEditor instance for specified ServiceDescriptor class

getEditorClassName() - Method in class chemaxon.checkers.AbstractStructureChecker

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

getEditorClassName() - Method in class chemaxon.checkers.InvalidChecker

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

getEditorClassName() - Method in interface chemaxon.checkers.StructureChecker

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

This method isn't needed anymore and will be removed in 6.0

getEditorClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the editorClassName

getEditorClassName() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Returns the editorClassName

getEditorClassName() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Gets the name of the editor of the standardizer class

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

Gets the name of the editor of the checker class

getEditorComponent() - Method in class chemaxon.marvin.beans.MViewEditor

Returns the editor component.

getEFlowsFromAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow

Returns all the EFlow from this atom.

getEFlowsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow

Returns all the EFlows that are started from this atom or pointing to this atom.

getEFlowsToAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow

Returns all the EFlows to this atom.

getEigenVector() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Deprecated.

Use HuckelAnalysisPlugin.getHMOEigenVector()

getElectronContainersOf(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct

getElectronCount() - Method in class chemaxon.struc.MDocument

Returns the number of electrons.

getElectronDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the electron density of an atom calculated with HMO, Double.NaN for no value.

getElectronProp() - Method in class chemaxon.struc.MolAtom

Returns the number of lone pairs on this atom.

getElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.

getElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Deprecated.

Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)

getElementCount() - Static method in class chemaxon.struc.PeriodicSystem

Number of elements in the periodic system

getEnableStandardization() - Method in class chemaxon.descriptors.RFParameters

Shows if standardization should be applied of not.

getEnantiomer(T) - Static method in class chemaxon.calculations.stereo.Stereochemistry

Get the enantiomer pair of the given molecule

getEncapsulatedReader() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the encapsulated record reader if it exists.

getEncapsulatedReader() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the encapsulated record reader if it exists.

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

Gets the cube that encloses the atoms of molecule graph.

getEncoding() - Method in class chemaxon.marvin.io.MolExportModule

Gets the output encoding.

getEncoding() - Method in class chemaxon.marvin.io.MRecord

Gets the encoding.

getEncoding() - Method in class chemaxon.marvin.io.PositionedInputStream

Gets the encoding.

getEncodingFromOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil

Gets the encoding that was explicitly given as an import option.

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

Gets the x shift at the end.

getEndLineCount() - Method in class chemaxon.marvin.io.MRecord

Gets the line number at the ending point.

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

Gets the position of the last character + 1.

getEndPosition() - Method in class chemaxon.marvin.io.MRecord

Gets the end position in the input file.

getEndPosition() - Method in class chemaxon.struc.MDocument

Gets the end position of this document in the input file.

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

Gets the end position of this molecule in the input file.

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

Observed rotational energy barrier.

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

Represented energy.

getEnergy() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the energy of the lowest energy conformer in kcal/mol.

getEnergy(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the energy of the i-th conformer in kcal/mol.

getEnhancedStereo() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup

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

Returns the enhanced stereo group (optional).

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

Returns the enhanced stereo flags of the molecule.

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

Gets the EnhancedStereoGroup to which the specified flag is mapped.

getEnumCodeNeeded() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Tests whether unique Markush enumeration code should be generated

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

Get the error for the best alignment

getError(int) - Method in class chemaxon.jep.ChemJEP

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

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

getErrorCode() - Method in class chemaxon.checkers.AbstractStructureChecker

getErrorCode() - Method in class chemaxon.checkers.ExternalStructureChecker

getErrorCode() - Method in class chemaxon.checkers.InvalidChecker

getErrorCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult

getErrorCode() - Method in interface chemaxon.checkers.result.ExternalStructureCheckerResult

This function returns a String which identifies the problems thus this must be unique for each class that implements this interface

getErrorCode() - Method in interface chemaxon.checkers.StructureChecker

Returns the String represented error code of the checker (this error code should be used for external implementation support instead of StructureChecker.getErrorType())

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

Returns a component with the appropriate error message.

getErrorCount() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

Return the error count.

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

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

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

getErrorDescription(int) - Method in class chemaxon.checkers.AbstractStructureChecker

Generate the error description depends on erroCount

getErrorDescription(StructureCheckerDescriptor, int) - Static method in class chemaxon.checkers.result.DefaultStructureCheckerResult

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

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

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

getErrorMessage() - Method in class chemaxon.checkers.InvalidChecker

Gets the error message of the checker instance

getErrorMessage() - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the calculation error information message if ChargePlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

getErrorMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the calculation error information message if HBDAPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the calculation error information message if HuckelAnalysisPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the calculation error information message if IonChargePlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the calculation error information message if IsoelectricPointPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

getErrorMessage() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the calculation error information message if logDPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the calculation error information message if logPPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Returns the calculation error information message or the empty string if there is no error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the calculation error information message or the empty string if there is no error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the calculation error information message if MSAPlugin.run() returned false (calculation error).

getErrorMessage() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the calculation error information message if OrbitalElectronegativityPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the calculation error information message if pKaPlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the calculation error information message if PolarizabilityPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the calculation error information message if RefractivityPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the calculation error information message or the empty string if there is no error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the calculation error information message or the empty string if there is no error.

getErrorMessage() - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the calculation error information message if TPSAPlugin.run() returned false (calculation error): hydrogen valence error.

getErrorMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).

getErrorMessage() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

Gets the error message of the standardizer instance

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

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

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

getErrorType() - Method in class chemaxon.checkers.AbstractStructureChecker

getErrorType() - Method in class chemaxon.checkers.InvalidChecker

getErrorType() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getErrorType() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getErrorType() - Method in interface chemaxon.checkers.StructureChecker

getErrorType() - Method in class chemaxon.checkers.SubstructureChecker

getErrorTypeDefaultFixerMap() - Method in class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader

getErrorTypeDefaultFixerMap() - Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader

getErrorTypeDefaultFixerMap() - Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader

getEstimatedStereoisomerCount() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

Gets the number of stereoisomers, if molecule does not contain pseudo stereocenters.
# of stereoisomer = 2 ^ stereocenter count

getEuclidean(BCUT) - Method in class chemaxon.descriptors.BCUT

Calculates the Euclidean distance.

getEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the Euclidean distance.

getEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Calculates the Euclidean distance.

getEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP

Calculates the Euclidean distance.

getEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the Euclidean distance.

getEuler() - Method in class chemaxon.struc.CTransform3D

Gets the Euler angles from the rotation transformation.

getExactMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.

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

Calculates the molecular weight of the molecule using the mass of the most frequent natural isotope of the atoms.

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

Get the identifiers of those special atoms that should match exactly during structure comparison.

getException() - Method in exception chemaxon.marvin.plugin.PluginException

Returns the wrapped exception.

getExcluded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Gets the excluded abbreviations

getExcluded() - Method in class chemaxon.checkers.AttachedDataChecker

Any attached data that matches this descriptor won't appear as the result of this checker.

getExcluded() - Method in class chemaxon.checkers.PseudoAtomChecker

getExcludeString() - Method in class chemaxon.standardizer.actions.AbstractSgroupAction

Gets the exclude string of action

getExcludeString() - Method in class chemaxon.standardizer.actions.ContractSgroupsAction

getExcludeString() - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction

getExcludeString() - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

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

Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.

getExplicitHcount() - Method in class chemaxon.struc.MolAtom

Gets number of hydrogen connections.

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

Gets the total number of explicit hydrogens attached to the molecule.

getExplicitHcount(int) - Method in interface chemaxon.struc.Smolecule

Gets the number of explicit hydrogen atom neighbors of the given atom.

getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

getExplicitLonePairCount() - Method in class chemaxon.struc.MDocument

Returns the number of Lone Pair electrons set by the user.

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

Deprecated.

For internal use only.

getExpression() - Method in class chemaxon.marvin.services.DynamicArgument

Returns the expression used for evaluations

getExtensionList() - Method in class chemaxon.formats.MFileFormat

Gets the extension list.

getExtensions() - Method in class chemaxon.formats.MFileFormat

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

getExternalCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings

Returns the URL of the configuration file containing the list of external Checkers in marvin sketch.

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

Gets the number of bonds of a specified atom where the neighbor atom doesn't belong to the S-group.

getExtraLabel() - Method in class chemaxon.struc.MolAtom

Gets the label string (also called atom value): "result" or "result1|result2".

getExtraLabelColor() - Method in class chemaxon.struc.MolAtom

Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

getExtraLabelColor(int) - Method in class chemaxon.struc.MolAtom

Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue).

getExtraLabelColor(long, int) - Static method in class chemaxon.struc.MolAtom

Gets extra label color from composed color value.

getExtraLabelSetColorMode(int) - Method in class chemaxon.struc.MDocument

Gets the coloring mode of extra label set sequences.

getExtraLabelSetFont(int) - Method in class chemaxon.struc.MDocument

getExtraLabelSetRGBs(int) - Method in class chemaxon.struc.MDocument

getExtraLabelSetSeq() - Method in class chemaxon.struc.MolAtom

getExtraLabelSetSize() - Method in class chemaxon.struc.MDocument

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

Gets E/Z stereo information for the given double bond.

getFamily() - Method in class chemaxon.struc.graphics.MFont

Gets the font family name.

getFeatureCount() - Method in class chemaxon.descriptors.ECFP

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

As of JChem 5.4.1, replaced by ECFP.getIdentiferCount().

getFeaturesFromBitPosition(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup

Returns the substructural features represented by the given bit position.

getFeaturesFromIdentifier(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup

Returns the substructural features represented by the given integer identifier.

getFieldAccessor() - Method in class chemaxon.marvin.view.MDocStorage

Gets the field accessor.

getFieldFont(String) - Method in class chemaxon.marvin.beans.MViewPane

Gets the font of a named field in a table.

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

Gets the field font size.

getFieldName() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the data field name.

getFields(int, Molecule, String[], MProp[]) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Extracts properties.

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

Are SDfile fields shown in table?

getFieldType() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the field type.

getFile() - Method in class chemaxon.formats.MolImporter

Gets the file object for the input.

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

Gets the current molecule file.

getFileExtensionLC(File) - Static method in class chemaxon.formats.MFileFormatUtil

Gets the file extension in lower case.

getFileExtensionLC(String) - Static method in class chemaxon.formats.MFileFormatUtil

Gets the file extension in lower case.

getFileName() - Method in class chemaxon.formats.MolImporter

Gets the name of the input file

getFilePointer() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Get the file pointer.

getFilePointer() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the current position in the input file.

getFilePointer() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the current position in the input file.

getFilePointer() - Method in class chemaxon.marvin.io.PositionedInputStream

Get the file pointer.

getFinalCause() - Method in exception chemaxon.formats.MolFormatException

Gets the final cause of the exception.

getFingerprint() - Method in class chemaxon.jep.context.MolContext

Returns the input molecule fingerprint.

getFingerprint(Molecule) - Method in interface chemaxon.jep.FingerprintGenerator

Returns the fingerprint of the structure.

getFingerprint(Object) - Method in class chemaxon.jep.context.MolContext

Returns the input molecule fingerprint if argument is the input molecule, null otherwise.

getFiveLongRings() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

This method returns the five long rings in the molecule represented by a List of List of MolAtom

getFixedLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint

Gets the fixed location in the polyline.

getFixer(String) - Method in class chemaxon.fixers.StructureFixerFactory

Deprecated.

This method returns a StructureFixer instance identified by fixerId parameters

getFixerClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the fixerClassName

getFixers() - Method in class chemaxon.fixers.StructureFixerFactory

Deprecated.

This method returns all StructureFixer instances available by the current configuration

getFixers(StructureCheckerResult) - Method in interface chemaxon.checkers.runner.CheckerRunner

Returns all the StructureFixer instances which associated with the StructureCheckerErrorType of the result

getFixers(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner

Deprecated.

getFixMode() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the fixMode

getFlags() - Method in class chemaxon.formats.MFileFormat

Gets the format descriptor flags.

getFlags() - Method in class chemaxon.marvin.io.MRecord

Gets the record descriptor flags.

getFlags() - Method in class chemaxon.struc.graphics.MPolyline

Gets the flags.

getFlags() - Method in class chemaxon.struc.MolAtom

Gets flags.

getFlags() - Method in class chemaxon.struc.MolBond

Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits), bond set (5 bits) and reacting center (7 bits) information.

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

Gets the dimension and chiral flags.

getFlags() - Method in class chemaxon.struc.RgMolecule

Gets the dimension and chiral flags.

getFlexibilityMode() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties

getFlexibleRingRotatableBondCount() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

getFlexibleRingSize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

getFloat(int) - Method in class chemaxon.descriptors.CustomDescriptor

getFocus() - Method in class chemaxon.struc.MDocument

Gets the focused object

getFogFactor() - Method in class chemaxon.marvin.common.UserSettings

Gets the fog factor.

getFont() - Method in class chemaxon.struc.prop.MFontProp

getFontFamily() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the font family name.

getFontMetrics(Graphics, MFont) - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets and updates the font metrics of a document section.

getFontScale() - Method in class chemaxon.struc.graphics.MTextBox

Gets the font scaling factor.

getFooterAsString() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the footer of the file as a string.

getFooterAsString() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the footer of the file as a string.

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

Gets the first parent.

getForeground() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the foreground color.

getFormalCharge() - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the formal charge of the molecule.

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

Gets the (total) formal charge of the molecule.

getFormalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the formal charge of a specified atom.

getFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular formula with formal charge.

getFormalChargeFormula(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates a fixed digit sortable molecular formula with formal charge.

getFormat() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder

Dipole export format.

getFormat() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Spectrum export format.

getFormat() - Method in class chemaxon.formats.MolExporter

Gets the output file format.

getFormat() - Method in class chemaxon.formats.MolImporter

Get the file format.

getFormat() - Method in class chemaxon.formats.MolInputStream

Get the molecule file format.

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

Gets the default molecule file format.

getFormat() - Method in class chemaxon.marvin.io.MolExportModule

Returns the output format.

getFormat() - Method in class chemaxon.marvin.io.MRecord

Gets the full format string of the record.

getFormat() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the file format.

getFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil

Gets the file format descriptor for the specified codename.

getFormatNamesWithExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil

getFormatter() - Method in class chemaxon.calculations.dipole.DipoleCalculator

getFormatter() - Method in class chemaxon.calculations.nmr.NMRCalculator

getFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.

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

Gets the molecular formula.

getFormula() - Method in class chemaxon.struc.RgMolecule

Gets the molecular formula in Hill order.

getFormula() - Method in class chemaxon.struc.RxnMolecule

Gets the molecular formula in Hill order.

getFormula(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates a fixed digit sortable molecular formula.

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

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

As of Marvin 5.6, replaced by MoleculeGraph.getFragCount(int) and MoleculeGraph.FRAG_KEEPING_MULTICENTERS.
Usage:

             mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
             

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

Returns the number of fragments for the given fragmentation type.

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

Gets an array containing the fragment id for each atom for the given fragmentation type.

getFragmentCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the number of fragments (disconnected parts) of the molecule.

getFragmentCount() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the number of fragments in the found common substructure.

getFreeAtomSetIndex() - Method in class chemaxon.struc.MDocument

Returns the first unused atomset index.

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

Gets the atoms with free attachment points.

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

Gets the number of free attachment points.

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

Gets the increasingly sorted orders of the free attachment points.

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

Gets the sorted free attachment orders of the given attachment atom.

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

Returns the number of the free attachment points for the given atom.

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

Returns the number of the free attachment points for the given atom.

getFreeBondSetIndex() - Method in class chemaxon.struc.MDocument

Returns the first unused bondset index.

getFreeElectronCount() - Method in class chemaxon.struc.graphics.MElectronContainer

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

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

As of Marvin 6.0, replaced by SuperatomSgroup.getFreeAttachAtoms().

getFrequency() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the freuency in MHz.

getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Gets the NMR frequency.

getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator

Returns NMR measurement frequency.

getFrequency() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the NMR measurement frequency in MHz unit.

getFrequencyCounts() - Method in class chemaxon.descriptors.MDGenerator

Gets the absolute frequence count array for all descriptors generated.

getFsp3() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons

getFsp3() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons

getFunction() - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

Returns the function itself or its clone.

getFunction(String) - Method in class chemaxon.jep.ChemJEP

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

The function table will become an internal API. No replacement.

getFunctionalGroupDisplayMolTable() - Method in class chemaxon.jep.Evaluator

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

Was only intended for internal use, will be removed.

getFunctionData() - Method in class chemaxon.jep.Evaluator

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

Was only intended for internal use, will be removed.

getFunctionData(boolean) - Method in class chemaxon.jep.Evaluator

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

Was only intended for internal use, will be removed.

getFunctionParameterData() - Method in class chemaxon.jep.Evaluator

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

Was only intended for internal use, will be removed.

getFunctionScale() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the scaling parameter for the function of this multiplet.

getFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum

getFusedAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.

getFusedAliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of fused aliphatic rings in the molecule (rings s).

getFusedAliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.

getFusedAliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).

getFusedAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.

getFusedAromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of fused aromatic rings in the molecule (rings s).

getFusedAromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.

getFusedAromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).

getFusedRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.

getFuzzyExponents() - Method in class chemaxon.descriptors.PFParameters

Gets the precalculated fuzzy exponent used in the Fuzzy Bipolar Autocorrelogram (FBPA) metric.

getFuzzyLowerBound() - Method in class chemaxon.descriptors.PFParameters

getFuzzySmoothingFactor() - Method in class chemaxon.descriptors.PFParameters

Gets the fuzzy smoothing factor used in the construction of fuzzy fingerprints.

getGaussianFuzzyIncrements() - Method in class chemaxon.descriptors.PFParameters

Gets fuzzy increments for the fuzzy smoothing with a normal distribution.

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

Gets the IUPAC name font size.

getGlobalChecker() - Static method in interface chemaxon.calculator.TaggedCalculator

Returns the global input checker that will be used by all calculators implementing this interface.

getGlobalGUIProperties() - Method in class chemaxon.marvin.view.MDocStorage

Gets the Global GUI properties.

getGlobalProperties() - Method in class chemaxon.formats.MolImporter

Gets the global properties in a container that was retrieved from the input stream, earlier.

getGlobalProperties() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the global properties.

getGrabbedLines() - Method in class chemaxon.marvin.io.PositionedInputStream

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

getGrabbedMoleculeString() - Method in class chemaxon.formats.MolImporter

Gets the last grabbed molecule string with LF style line endings by default.

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

Gets a molecule graph containing all the atoms and bonds.

getGraphUnion() - Method in class chemaxon.struc.RgMolecule

Gets a graph containing all the atoms and bonds.

getGraphUnion() - Method in class chemaxon.struc.RxnMolecule

Gets a graph containing all the atoms and bonds.

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

Gets a selection molecule containing all the atoms and bonds.

getGriffinHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin

Returns the HLB value calculated by Griffin method.

getGrinv() - Method in class chemaxon.struc.graphics.MNameTextBox

Gets an invariant the text box depends on.

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

Gets the graph invariants array.

getGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph

Gets the graph invariants (canonical labels).

getGrinv(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

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

As of Marvin 4.0, replaced by MoleculeGraph.getGrinv(int[], int).
Usage:

             getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
             

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

Gets the graph invariants (canonical labels).

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

Gets the graph invariant change count.

getGrinvCC() - Method in class chemaxon.struc.MProp

Gets the graph invariant change count at the moment of creation.

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

Gets graph invariant calculation options passed to the module.

getGroup() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets the definition of the group.

getGroup(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the menu group for a plugin.

getGroupCount() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Gets the count of the groups of the action

getGroupedDotDisconnectedFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the grouped dot-disconnected molecular formula of a multifragment molecule.

getGroupHit() - Method in class chemaxon.sss.search.Decomposition

Returns the group hit corresponding to the R-group decomposition.

getGroupHit() - Method in class chemaxon.sss.search.SearchHit

Returns the group hit view of the hit object.

getGroupIndices() - Method in class chemaxon.checkers.result.DataSgroupCheckerResult

getGroupList() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Gets the list of groups set for the action

getGroupMnemonic(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the group mnemonic for a plugin.

getGroups() - Method in class chemaxon.standardizer.actions.AliasToGroupAction

Gets the abbreviated groups of the action

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

Gets the group names associated to an action separated by , character

getGroupsOf(String, List<GroupDefinition>) - Static method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets the group from a list of group definitions, based on the abbreviation.

getGUIPropertyContainer() - Method in class chemaxon.struc.MDocument

getHalfWidth() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the half-width of the NMR lines.

getHalfWidth() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns NMR half-width.

getHararyIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.

getHashCode(Molecule) - Method in class chemaxon.sss.screen.HashCode

Gets hash code with default recursion level.

getHashCode(Molecule, int) - Method in class chemaxon.sss.screen.HashCode

Gets the hash code.

getHashCode(Molecule, int[]) - Method in class chemaxon.sss.screen.HashCode

Gets hash code with default recursion level.

getHashCode(Molecule, int[], int) - Method in class chemaxon.sss.screen.HashCode

Gets the hash code.

getHBond(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns a hydrogen bond.

getHBondCount() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the number of intramolecular hydrogen bonds.

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

Get the interpretation of H count in the query.

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

Gets the head crossing bonds.

getHeader() - Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit

Returns the table header.

getHeader() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Returns the table header.

getHeader() - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the table header.

getHeader() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the table header.

getHeader() - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the table header.

getHeaderAsString() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the header of the file as a string.

getHeaderAsString() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the header of the file as a string.

getHeaderNewLineCount() - Method in class chemaxon.marvin.io.MRecord

Gets the number of new lines in the molecule header part.

getHeight() - Method in class chemaxon.struc.PageSettings

getHelpText() - Method in class chemaxon.checkers.AbstractStructureChecker

getHelpText() - Method in class chemaxon.checkers.InvalidChecker

getHelpText() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getHelpText() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getHelpText() - Method in interface chemaxon.checkers.StructureChecker

Gets the help text of the checker

getHelpText() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the help text

getHelpText() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the help text of the action

getHeteroaliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).

getHeteroaliphaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).

getHeteroaliphaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).

getHeteroaliphaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).

getHeteroaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the heteroaromatic ring count.

getHeteroaromaticRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).

getHeteroaromaticRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).

getHeteroaromaticRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).

getHeteroRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the hetero ring count.

getHeteroRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

getHeteroRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

getHeteroRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getHidrophobicity() - Method in class chemaxon.marvin.calculations.logDPlugin

getHighBridgeAtomIndexes() - Method in class chemaxon.struc.BicycloStereoDescriptor

Return the atom indexes of the atoms of the bridge with the higher index.

getHighBridgeAtoms() - Method in class chemaxon.struc.BicycloStereoDescriptor

Return the atoms of the bridge with the higher index.

getHighestEigenvalue(int, int) - Method in class chemaxon.descriptors.BCUT

Gets the specified highest eigenvalue.

getHighestEigenvaluesCount(int) - Method in class chemaxon.descriptors.BCUTParameters

Gets the number of highest eigenvalues calculated.

getHistogramSimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor

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

use ShapeDescriptor.getShapeSimilarity(MolecularDescriptor) instead

getHitIndexType() - Method in class chemaxon.sss.search.MolSearchOptions

Returns the representation on which the hit indexes are given in case of Markush search.

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

Returns the hit ordering type.

getHitsAsMarkush() - Method in class chemaxon.sss.search.RgDecompResults

Returns a single RgMolecule that consists of the scaffold and all the possible ligands as rgroup-definitions.

getHitsAsRgDecomp() - Method in class chemaxon.sss.search.RgDecompResults

Returns All ligands of all targets.

getHitsAsTable() - Method in class chemaxon.sss.search.RgDecompResults

Returns the table elements in Molecule[][] format.

getHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin

Returns the HLB value.

getHMOChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.

getHMOEigenVector() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the eigenvector.

getHMOElectronDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the electron density of an atom calculated with HMO, Double.NaN for no value.

getHMOElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.

getHMOElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the electrophilic order of an atom, -1 for no value.

getHMOHuckelOrbitalCoefficients() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the huckel orbital coefficients.

getHMONucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.

getHMONucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the nucleophilic order of an atom, -1 for no value.

getHMORealEigenValue() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the real part of the eigenvalue.

getHMOTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the total pi energy of the input molecule.

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

Get target-side homology matching option.

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

Get query-side homology matching option, which homology atoms can match specific atoms.

getHorizontalAlignment() - Method in class chemaxon.struc.graphics.MTextBox

Gets the horizontal alignment.

getHPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the sum of the implicit H atom polarizability values around the given heavy atom.

getHResult(int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Returns the sum result of the H neighbours of the given atom.

getHuckelOrbitalCoefficients() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Deprecated.

Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()

getHybridizationState() - Method in class chemaxon.struc.MolAtom

Gets the hybridization state.

getHybridizationState(int) - Method in interface chemaxon.struc.Smolecule

Gets the hybridization state of an atom.

getHydrogen() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

getHydrogenizeOption() - Method in class chemaxon.formats.GeneralExportOptions

Gets the hydrogenization method.

getHyperWienerIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the hyper Wiener index of the molecule.

getIcon() - Method in class chemaxon.checkers.AbstractStructureChecker

getIcon() - Method in class chemaxon.checkers.InvalidChecker

getIcon() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getIcon() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getIcon() - Method in interface chemaxon.checkers.StructureChecker

Gets the Icon of the current checker

getIcon() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the Icon related to iconPath property

getIcon() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

getIcon() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the icon of service descriptor or null if no icon

getIcon() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor

getIcon() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Returns the Icon related to iconPath property

getIcon(int) - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo

Returns a MarvinSketch icon in 16x16 or 32x32 size.

getIcon(int) - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo

Returns a MarvinView icon in 16x16 or 32x32 size.

getIconPath() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the icon path

getIconPath() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the path of icon associated to the action

getId() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the id of the action

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

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

getId(String) - Static method in class chemaxon.marvin.services.json.JsonServiceDescriptor

Gets an ID for a method name, to make sure the client can identify the answer for the request.

getID() - Method in class chemaxon.standardizer.AbstractStandardizerAction

Gets the identifier string of the standardizer action.

getID() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

getID() - Method in interface chemaxon.standardizer.StandardizerAction

Gets the identifier of the standardizer task

getID() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Gets the id of the standardizer class

getID() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

Gets the id of the checker class

getIDBackgroundRGBA(int) - Method in class chemaxon.marvin.view.MDocStorage

Gets the background color's RGBA value in a record.

getIdentiferCount() - Method in class chemaxon.descriptors.ECFP

Gets the number of integer identifers generated for the fingerprint.

getIdentifier() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the checker identifier

getIdentifier() - Method in class chemaxon.descriptors.ECFPFeature

Gets the generated integer identifier for this ECFP feature.

getIdentifier() - Method in class chemaxon.fixers.StructureFixerDescriptor

Returns the fixer identifier

getIdentifier(MolAtom, int) - Method in class chemaxon.descriptors.ECFPFeatureLookup

Returns the corresponding integer identifier for the given atom neighborhood.

getIdentityTransformer() - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns an identity transformer.

getIDForegroundRGBA(int) - Method in class chemaxon.marvin.view.MDocStorage

Gets the foreground color's RGBA value in a record.

getIgnoreRotatableBonds() - Method in class chemaxon.descriptors.PFParameters

getImage(double) - Method in class chemaxon.marvin.beans.MSketchPane

Gets the canvas contents as an image using a scale factor.
Examples:
To get an image with a scale factor equivalent to 100% magnification: getImage(getDefaultScale());
To get an image with the actual scale factor: getImage(getScale());

getImage(Dimension) - Method in class chemaxon.marvin.beans.MSketchPane

Gets the canvas contents as an image scaled to fit in the specified rectangle.

getImageExportParameterStringForStyle(String) - Method in class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI

Creates a string used for Image Export, without format.

getImageImportServiceURL() - Method in class chemaxon.marvin.common.UserSettings

getImageMolecule() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the molecule to be used for legend image.

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

Query the display method of implicit hydrogens.

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

Returns the display method of implicit hydrogens.

getImplicitHcount() - Method in class chemaxon.struc.MolAtom

Gets the number of implicit hydrogens attached.

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

Gets the total number of implicit hydrogens attached to the molecule.

getImplicitHcount(int) - Method in interface chemaxon.struc.Smolecule

Gets the number of implicit Hydrogens of an atom.

getImplicitHCount(boolean) - Method in class chemaxon.struc.MolAtom

Gets the implicit Hydrogen count of the atom.

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

Gets the number of implicit hydrogens attached to the given atom.

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

Gets the number of implicit hydrogens attached to the given atom.

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

Get option for matching implicit and explicit hydrogens

getImplicitizableHList(Molecule, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Gets which atom is an implicitizable hydrogen.

getImplicitizeFlag() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult

Returns the flag which can used to identify which hydrogens should be implicitize.

getIncludedIds() - Method in class chemaxon.sss.search.RgDecompResults

Returns indexes of those targets that are matched by query.

getIndex() - Method in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

getIndex() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Returns the index of the actual action of the configuration

getIndexOfOriginalLigand() - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

getInnerPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle

getInputCount() - Method in class chemaxon.formats.MolConverter.Builder

Gets the number of input files/streams.

getInputCount() - Method in class chemaxon.formats.MolConverter.Options

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

getInputFormat() - Method in class chemaxon.marvin.io.MRecord

Gets the input format.

getInputFormat() - Method in class chemaxon.struc.MDocument

Gets the input file format.

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

Gets the input file format.

getInputMolDim() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the input molecule dimension.

getInputMolecule() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Returns the input molecule (the molecule before standardization).

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

Gets the input molecule.

getInputPriority() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Priority of the MTransferable object when importing from clipboard.

getInputStreamFromClipboard() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Gets an InputStream from the clipboard data if the format is supported by this MTransferable

getInstance() - Static method in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Returns the default factory instance.

getInstance() - Static method in class chemaxon.structurechecker.factory.CheckerFixerFactory

Creates a CheckerFixerFactory based on the CheckerFixerFactory.DEFAULT_CONFIGURATION_PATH and the user defined checkers/fixers located at the default user

getInstance(String, String) - Static method in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Returns the factory instance for specified paths.

getInt(int) - Method in class chemaxon.descriptors.CustomDescriptor

getIntArray() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Gets the integer value.

getIntegralValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the value of the NMR integral function at a given x point.

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

Returns the intensity of the ith line.

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

Gets the MolecularDescriptor specific metric index of the current parametrized metric.

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

Gets the required memory size to store the descriptor according to the specified parameters.

getInternalVersionId() - Static method in class com.chemaxon.version.VersionInfo

Returns the internal version identifier.

getIntesityPattern() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the intensity pattern of this multiplet.

getIntValue() - Method in enum class chemaxon.struc.AtomProperty.Radical

Gets the integer representation of the radical.

getIntValue() - Method in enum class chemaxon.struc.stereo.EZConfiguration

Gets the integer value of the stereo configuration.
As the configuration represents a CIS/TRANS stereo configuration as well therefore the corresponding constants are returned: 0 for EZConfiguration.NONE StereoConstants.TRANS for EZConfiguration.E StereoConstants.CIS for EZConfiguration.Z StereoConstants.CIS | StereoConstants.TRANS for EZConfiguration.E_OR_Z StereoConstants.TRANS | StereoConstants.CTUNSPEC for EZConfiguration.E_OR_UNSPEC StereoConstants.CIS | StereoConstants.CTUNSPEC for EZConfiguration.Z_OR_UNSPEC

getInverseName() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the inverse option name.

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

Gets the visibility of the specified atom sets.

getIonizerErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Returns the calculation error information message or the empty string if there is no error.

getIonizerErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the calculation error information message or the empty string if there is no error.

getIsotope(int, int) - Static method in class chemaxon.struc.PeriodicSystem

Retrieves an isotope of the element

getIsotopeComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the molecular composition (w/w%).

getIsotopeComposition(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the molecular composition (w/w%).

getIsotopeCount() - Static method in class chemaxon.struc.PeriodicSystem

Number of isotopes in the periodic system

getIsotopeCount(int) - Static method in class chemaxon.struc.PeriodicSystem

Number of isotopes of the element

getIsotopeDistribution() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the isotopic distributions for the molecule.

getIsotopeFormalChargeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular formula (isotopes are separated).

getIsotopeFormalChargeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular formula with formal charge (isotopes are separated).

getIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular formula (isotopes are separated).

getIsotopeFormula(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular formula (isotopes are separated).

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

Get option for matching isotopes

getIterator() - Method in class chemaxon.marvin.io.formats.MoleculeImporter

Returns an iterator that iterates through all molecules in the file/stream.

getItsArrow() - Method in class chemaxon.struc.RxnMolecule

Gets the reaction arrow of this reaction.

getJar() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Gets the jar containing the standardizer class

getJar() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

Gets the jar containing the checker class

getJavaVersionStr() - Static method in class com.chemaxon.version.VersionInfo

Returns the Java VM version information as string.

getJChemTableVersion() - Static method in class com.chemaxon.version.VersionInfo

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

No longer supported, use chemaxon.jchem.version.JChemVersionInfo instead.

getKeepCounts() - Method in class chemaxon.descriptors.ECFPParameters

Gets the counts (multiplicity) parameter.

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

Returns the plugin key.

getKey(int) - Method in class chemaxon.struc.MPropertyContainer

Gets a property key.

getKey(int) - Method in class chemaxon.struc.prop.MHashProp

Gets a key.

getKey(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the menu key for a plugin.

getKeys() - Method in class chemaxon.struc.MPropertyContainer

Returns the property keys.

getKeys(int, Molecule) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Gets the keys in a record.

getKnownExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil

Returns the file extension if it is a known extension.

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

Gets a label.

getL(int, int) - Method in class chemaxon.marvin.view.MDocStorage

Gets a text label in a record.

getLabel() - Method in class chemaxon.struc.NoStructure

The label for the noStructure.

getLabelCenter() - Method in class chemaxon.struc.sgroup.SgroupAtom

Gets the index of the character in the label the bonds should point to.

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

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

use isAtomSymbolsVisible() instead

getLabels(double[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Returns formatted array.

getLargestConjugatedSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the largest conjugated system in the molecule.

getLargestConjugatedSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the largest conjugated system size (number of pi electron pairs).

getLargestRing() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the atoms of the largest ring (number of atoms) in the molecule.

getLargestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the largest ring size.

getLargestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the size of largest ring containing the specified atom.

getLargestRingSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the atoms of the largest ring system (number of rings) in the molecule.

getLargestRingSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the size of the largest ring system (number of rings) in the molecule.

getLastEOL() - Method in class chemaxon.marvin.io.PositionedInputStream

getLastIndexOfAction(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets the last index of an action defined by the provided action string

getLastLicense() - Method in class chemaxon.marvin.common.UserSettings

For internal use only.

getLastProcessedLineNum() - Method in class chemaxon.formats.recognizer.Recognizer

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

as of Marvin 2014.07.21.0 not used

getLastSketchFrameSize() - Method in class chemaxon.marvin.common.UserSettings

getLastViewFrameSize() - Method in class chemaxon.marvin.common.UserSettings

getLeftBracket(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket

getLeftMargin() - Method in class chemaxon.struc.PageSettings

getLeftName() - Method in class chemaxon.struc.sgroup.SgroupAtom

Gets the string that will be shown at the left side of the molecule.

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

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

As of Marvin 6.0, replaced by SuperatomSgroup.getAllAttachAtoms().

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

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

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

Returns the number of cells forming the descriptor.

getLength() - Method in class chemaxon.struc.MolBond

Gets the actual length of the bond.

getLevel() - Method in interface chemaxon.common.util.MProgressMonitor

Gets the level of this progress monitor.

getLevelCount() - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Gets the number of levels.

getLibrarySizeString() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the display string representation of the Markush library size (number of all enumerated structures).

getLicenseEnvironment() - Method in class chemaxon.standardizer.Standardizer

Gets the license environment of the standardizer

getLigand(int) - Method in class chemaxon.struc.MolAtom

Gets the i-th ligand of this atom.

getLigand(AtomReference, int) - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence

Gets the n-th ligand of the given atom.

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

Gets the n-th ligand of the given atom.

getLigandAtno(AtomReference, int) - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence

Gets the atomic number of the n-th ligand of the given atom.

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

Gets the atomic number of the n-th ligand of the given atom.

getLigandBondType(AtomReference, int) - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence

Gets the type of the n-th ligand bond of the given atom.

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

Gets the type of the n-th ligand bond of the given atom.

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

Gets the number of ligands of the given atom.

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

Gets the number of ligands of the given atom.

getLigandIds() - Method in class chemaxon.sss.search.Decomposition

Returns the target ligand IDs.

getLigandIndex(MolAtom) - Method in class chemaxon.struc.MolAtom

Returns the index of the specified ligand in this atom.

getLigandOrder(MolAtom) - Method in class chemaxon.struc.MolAtom

Gets the order of a specified ligand.

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

Gets the ligand order visibility setting.

getLigands() - Method in class chemaxon.sss.search.Decomposition

Returns the R-ligand array.

getLigands() - Method in class chemaxon.struc.MolAtom

Returns the atoms connected to this atom by a bond.

getLigands() - Method in class chemaxon.struc.StereoActivePart

Get the ligands of the stereo active atom which take part in the stereo description.

getLigands(Integer) - Method in class chemaxon.struc.SelectionMolecule

getLigandsNumber() - Method in class chemaxon.sss.search.RgDecompResults

Returns the number of ligands in one target structure.

getLigandTableHeader(int, int) - Method in class chemaxon.sss.search.RGroupDecomposition

Returns ligand table header.

getLigandTableHeader(int, int, String) - Method in class chemaxon.sss.search.RGroupDecomposition

Returns ligand table header.

getLimitedStructureCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the number of structures to be generated.

getLine(int) - Method in class chemaxon.struc.graphics.MTextBox

Gets a line.

getLineColor() - Method in class chemaxon.struc.MObject

Gets the line color of the object.

getLineCount() - Method in class chemaxon.formats.MolImporter

Gets the current line number.

getLineCount() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Get the current line number.

getLineCount() - Method in class chemaxon.marvin.io.MolImportModule

Returns the line count in the molecule input stream.

getLineCount() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the current line number in the input file.

getLineCount() - Method in interface chemaxon.marvin.io.MRecordReader

Get the current line number.

getLineCount() - Method in class chemaxon.marvin.io.PositionedInputStream

Gets the current line number.

getLineCount() - Method in class chemaxon.struc.graphics.MTextBox

Gets the number of lines.

getLineMiddlePoint(DPoint3, DPoint3) - Static method in class chemaxon.struc.graphics.MPolyline

getLineNumber() - Method in class chemaxon.marvin.io.MRecordReader.Position

Gets the line number.

getLineNumberInFile() - Method in exception chemaxon.formats.MolFormatException

Gets the line number relative to the first line of the file.

getLineNumberInRecord() - Method in exception chemaxon.formats.MolFormatException

Gets the line number relative to the first line of the record.

getLineNumberMap() - Method in class chemaxon.marvin.io.MRecord

Gets the line number to original line number mapping.

getLineOnScreen(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Returns the i-th row of the data sgroup label, as displayed on the screen (with tag, query operator, units etc.)

getLinkNodeOuterAtom(int) - Method in class chemaxon.struc.MolAtom

Gets the index of one of the link node's outer neighbor atoms.

getList() - Method in class chemaxon.checkers.util.AtomLabels

Gets the list of atom labels

getList() - Method in class chemaxon.struc.MolAtom

Gets the atom list.

getList() - Method in class chemaxon.struc.prop.MListProp

Gets the array.

getListeners() - Method in class chemaxon.marvin.view.MDocStorage

getLoadSaveLocation() - Method in class chemaxon.marvin.common.UserSettings

Gets the load/save filechooser working directory selection method names, based on the preferences dialog.

getLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings

Gets the filechooser's default working directory, if it is set, and the filechooser working directory selection method is saveCustomLocation.

getLocalMaximumPlaces() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the local maximum places of the multiplet in ascending order.

getLocalMaximumPlaces() - Method in class chemaxon.calculations.nmr.NMRSpectrum

getLocalMenuName() - Method in class chemaxon.checkers.AbstractStructureChecker

getLocalMenuName() - Method in class chemaxon.checkers.InvalidChecker

getLocalMenuName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getLocalMenuName() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getLocalMenuName() - Method in interface chemaxon.checkers.StructureChecker

Gets the local menu name of the checker

getLocalMenuName() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the local menu name

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

Computes the local parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

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

Computes the local parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

getLocalParity(int) - Method in class chemaxon.struc.RxnMolecule

Computes the local parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

getLocation() - Method in class chemaxon.struc.MolAtom

Gets the coordinates.

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

Gets the origin of the molecule.

getLocation() - Method in class chemaxon.struc.MPoint

Gets the point's location.

getLocation() - Method in class chemaxon.struc.NoStructure

Returns the clone of the location of the NoStructure.

getLocation(CTransform3D) - Method in class chemaxon.struc.MPoint

Gets the point's location.

getLocation(DPoint3) - Method in class chemaxon.struc.MolAtom

Gets the coordinates.

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Gets the location.

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Gets the location.

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MElectron

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint

Gets the location.

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint.Sticky

Gets the location.

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky

Gets the location.

getLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint

Gets the point's location.

getLock() - Method in class chemaxon.struc.MolAtom

Get lock object for synchronization.

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

Gets the lock object for synchronization.

getlogD() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the logD value for the pH specified in logDPlugin.setpH(double).

getlogDpI() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the logD value at pI.

getlogDs() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the logD array.

getLogger() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder

Returns the dipole calculator logger.

getLogger() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Gets the calculator logger.

getLogger() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

Returns the current logger.

getLogicalValue(Object) - Static method in class chemaxon.jep.ChemJEP

Returns the logical correspondent of the specified result object: ChemJEP.TRUE, ChemJEP.FALSE or ChemJEP.UNDECIDED.

getLogPercentageLimit() - Method in class chemaxon.marvin.calculations.pKaPlugin

getlogPMicro() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the micro logP value.

getlogPNonionic() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the logP value for the non-ionic form.

getLogPTrainingIds() - Static method in class chemaxon.marvin.calculations.logDPlugin

Returns the id's of available logP trainings.

getlogPTrue() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the most typical logP among logD at pI, micro logP and nonionic logP.

getLonePairCount() - Method in class chemaxon.struc.MDocument

Returns the number of Lone Pair electrons.

getLonePairCount() - Method in class chemaxon.struc.MolAtom

Returns the automatically calculated lone pair count of this atom.

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

Deprecated.

use MolAtom.getLonePairCount() instead

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

Gets the number of lone pairs.

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

Tests whether lone pairs are visible.

getLowBridgeAtomIndexes() - Method in class chemaxon.struc.BicycloStereoDescriptor

Return the atom indexes of the atoms of the bridge with the lower index.

getLowBridgeAtoms() - Method in class chemaxon.struc.BicycloStereoDescriptor

Return the atoms of the bridge with the lower index.

getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.MolecularDescriptor

Calculates an estimate for the minimum value of the distance using the default distance metric.

getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the lower bound estimate of the dissimilarity from the given fingerprint.

getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.ReactionFingerprint

Calculates the lower bound estimate of the dissimilarity from the given fingerprint.

getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.ScalarDescriptor

Calculates the lower bound estimate of the dissimilarity from the given descriptor.

getLowestEigenvalue(int, int) - Method in class chemaxon.descriptors.BCUT

Gets the specified lowest eigenvalue.

getLowestEigenvaluesCount(int) - Method in class chemaxon.descriptors.BCUTParameters

Gets the number of lowest eigenvalues calculated.

getLowestEnergyConformer() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the calculated lowest energy conformer.

getLowestEnergyConformer() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the lowest energy conformer of the molecule.

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

Gets the nth molecule in memory.

getM(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Gets the nth molecule in a text format.

getMacroDistributions() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the macrospecies distribution arrays for all macro pKa values: the i-th row is the disrtibution vector of the i-th ionization state as function of the pH.

getMacroDistributions(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the i-th macrospecies distribution as function of the pH

getMacropKaValues(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Calculates the acidic pKa values in ascending order or the basic pKa values in descending order.

getMacropKaValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin

Calculates the least acidic pKa values in ascending order or the biggest basic pKa values in descending order.

getMacroSpeciesCharge(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the formal charges of a given macrospecies.

getMacroSpeciesCount() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the number of macrospecies count.

getMag() - Method in class chemaxon.marvin.beans.MSketchPane

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

As of Marvin 2.8.1, replaced by getScale()

getMainDoc(int) - Method in class chemaxon.marvin.view.MDocStorage

Gets the document at the specified position.

getMainDoc(int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage

Gets the document at the specified position.

getMainMolecule(int, Molecule) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Gets the main molecule object in a record.

getMainMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

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

Use CalculatorPlugin.createModifiedInputMolecule(Molecule) instead

getMainMoleculeGraph() - Method in class chemaxon.struc.MDocument

Gets the main molecule graph.

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

Tests whether the main molecule is a field.

getMajorMicrospecies() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the major microspecies at the pH set in MajorMicrospeciesPlugin.setpH(double).

getMap() - Method in class chemaxon.struc.prop.MHashProp

Gets the map.

getMap() - Method in interface com.chemaxon.search.transformation.util.IntMapper

getMap(MoleculeGraph) - Method in class chemaxon.struc.prop.MHCoords3DProp

Gets a map containing MolAtom objects as keys and DPoint3 arrays as values.

getMappingStyle() - Method in class chemaxon.standardizer.actions.MapAction

Returns the mapping style of the underlying mapper.

getMappingStyle() - Method in class chemaxon.standardizer.actions.MapReactionAction

Returns the mapping style of the underlying mapper.

getMappingStyle() - Method in class com.chemaxon.mapper.AutoMapper

Returns the mapping style of the mapper.

getMappingStyle() - Method in class com.chemaxon.mapper.AutoMapper.Options

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

Gets the documents margin size.

getMarginSize() - Method in class chemaxon.marvin.common.UserSettings

Gets the documents margin size.

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

Gets the Markush aromatic search behavior.

getMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Calculates the molecular weight of the molecule.

getMass() - Method in class chemaxon.struc.MolAtom

Gets the atomic weight.

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

Calculates the molecular weight of the molecule.

getMass() - Method in class chemaxon.struc.RgMolecule

Calculates the molecular weight of the molecule.

getMass() - Method in class chemaxon.struc.RxnMolecule

Calculates the molecular weight of the molecule.

getMass(int) - Static method in class chemaxon.struc.PeriodicSystem

Atomic weight of the element based on the natural abundance of its isotopes

getMass(int, int) - Static method in class chemaxon.struc.PeriodicSystem

Atomic weight of an isotope

getMassno() - Method in class chemaxon.struc.MolAtom

Gets the mass number.

getMassno(int) - Method in interface chemaxon.struc.Smolecule

Gets the mass number of an atom.

getMassPrecision(int) - Static method in class chemaxon.struc.PeriodicSystem

The precision of an elemental mass is the number of measured digits after the decimal separator.

getMassPrecision(int, int) - Static method in class chemaxon.struc.PeriodicSystem

The precision of an isotopic mass is the number of measured digits after the decimal separator.

getMatchCount() - Method in class chemaxon.sss.search.Search

The number of times the query molecule appears in the target molecule.

getMatchedQueryAtoms() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the indices of the query atoms that are part of the found common substructure.

getMatchedQueryBonds() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the indices of the query bonds that are part of the found common substructure.

getMatchedTargetAtoms() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the indices of the target atoms that are part of the found common substructure.

getMatchedTargetBonds() - Method in class com.chemaxon.search.mcs.McsSearchResult

Gets the indices of the target bonds that are part of the found common substructure.

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

Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.

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

Get maximum value of columns in the table.

getMaxConsideredRingSize() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns the maximum size of rings considered during search for the specified ring handling mode.

getMaxDimCached() - Method in class chemaxon.marvin.view.MDocStorage

Gets the maximum molecule dimension.

getMaxDist() - Method in class chemaxon.descriptors.PFParameters

Gets the miximum distance of pharmacophore points that is considered.

getMaxDist() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

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

Observed largest energy.

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

getMaximalProjectionArea() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the maximal projection area in Angstrom^2.

getMaximalProjectionRadius() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the radius of the circle surrounding the maximal projection in Angstrom.

getMaximum() - Method in interface chemaxon.common.util.MProgressMonitor

Gets the maximum value.

getMaximumBitRatio() - Method in class chemaxon.descriptors.MDGenerator

Gets the maximum percentage of non-zero cells in descriptors generated.

getMaxRepetitions() - Method in class chemaxon.struc.MolAtom

Gets the maximum number of repetitions for a link atom.

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

Returns the maximal attachment point order of R-group attachment point atoms in this molecule graph.

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

Get maximum value of rows in the table

getMaxs() - Method in class chemaxon.marvin.alignment.ShapeData

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

Get the maximum number of molecules displayed in the table.

getMaxThreadCount() - Method in class com.chemaxon.mapper.AutoMapper.Options

getMaxZ() - Method in class chemaxon.marvin.calculations.GeometryPlugin

getMChemicalStruct() - Method in class chemaxon.struc.MDocument

getMcsSimilarityLimit() - Method in class chemaxon.marvin.alignment.MMPAlignmentProperties

getMDocumentStream() - Method in class chemaxon.formats.MolImporter

Creates an MDocument Stream with the iterator of the importer.

getMDocumentStream() - Method in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Creates a stream of MDocuments from the imported molecuels.

getMDocumentStream() - Method in class chemaxon.marvin.io.MDocSource

getMeaningfulFrequencies() - Static method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the array of meaningful NMR measurement frequencies in MHz.

getMeasure() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

Gets the measure of the action

getMediumReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

Returns the tanimoto distance of the reaction centers and their neighbouring atoms and bonds.

getMElectron() - Method in class chemaxon.struc.graphics.MEFlow

getMElectronContainer() - Method in class chemaxon.struc.graphics.MEFlow

getMElectronContainerIndexInAtom(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct

getMElectronContainerOf(MElectron) - Method in class chemaxon.struc.graphics.MChemicalStruct

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

getMElectronRef() - Method in class chemaxon.struc.graphics.MEFlow

getMenu(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the menu string for a plugin.

getMergedst() - Method in class chemaxon.marvin.beans.MSketchPane

Gets the merge distance.

getMessage() - Method in interface chemaxon.calculator.CalculatorError

Returns the message that describes this error.

getMessage() - Method in exception chemaxon.sss.search.SearchException

Returns the detailed message string of this exception, plus all the causes concatenated.

getMessage() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport

Returns an error message.

getMetalAtoms() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

This method returns the metallocene relevant metal atoms represented by a List of MolAtom.

getMethod() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

Gets the method of the action

getMethod() - Method in class chemaxon.standardizer.actions.TautomerizeAction

getMethodName() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the method name to call

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

Gets the index of the given parametrized metric.

getMetricIndex(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the index of the given parameterized metric.

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

Gets the user defined symbolic name of the current parametrized metric.

getMetricName() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the name of the current parameterized metric.

getMetricName(int) - Method in class chemaxon.descriptors.MDParameters

Gets the user defined symbolic name of the specified parametrized metric.

getMetricName(int) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the name of a metric specified parameterized metric by its index.

getMicrospecies(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the microspecies molecule.

getMicrospeciesCount() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the number of microspecies

getMidPointLocation(int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Gets the middle point of the arc.

getMIMEType() - Method in class chemaxon.formats.MFileFormat

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

as of Marvin 2014.07.21.0 not used

getMinDist() - Method in class chemaxon.descriptors.PFParameters

Gets the minimum distance of pharmacophore points that is considered.

getMinDist() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

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

Observed lowest energy.

getMinFragmentSize() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns the minimum required size of the fragments of the common substructures.

getMinimalProjectionArea() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the minimal projection area in Angstrom^2.

getMinimalProjectionRadius() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the radius of the circle surrounding the minimal projection in Angstrom.

getMinimumBitRatio() - Method in class chemaxon.descriptors.MDGenerator

Gets the minimum percentage of non-zero cells in descriptors generated.

getMinimumHeight() - Method in class chemaxon.struc.graphics.MTextBox

Gets the minimum height of the text.

getMinRepetitions() - Method in class chemaxon.struc.MolAtom

Gets the minimum number of repetitions for a link node.

getMins() - Method in class chemaxon.marvin.alignment.ShapeData

getMinZ() - Method in class chemaxon.marvin.calculations.GeometryPlugin

getMirroredArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline

Mirror transformation for arrow heads.

getMMFF94Energy() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the MMFF94 energy of the structure (default: kcal/mol).

getMnemonic() - Method in class chemaxon.marvin.swing.MAction

Gets the mnemonic.

getMnemonic(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the menu mnemonic for a plugin.

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

Gets the list of modified atoms during the standardization procedure

getMol() - Method in class chemaxon.marvin.beans.MSketchPane

Returns the clone of the current molecule being on the canvas.

getMol(String) - Method in class chemaxon.marvin.beans.MSketchPane

Gets the molecule in a text format.

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

Gets the molecule background color.

getMolBytes() - Method in class chemaxon.marvin.io.MRecord

Gets the molecule bytes, with preprended header and appended footer if appropriate.

getMolCenter(int, String) - Method in class chemaxon.marvin.view.MDocStorage

Gets a molecule center.

getMolCrd() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

getMolecule() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the input molecule of the dipole moment computation.

getMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the molecule under examination.

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

Retrieves the input molecule

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

Retrieves the input molecule

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

Retrieves the input molecule

getMolecule() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getMolecule() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getMolecule() - Method in class chemaxon.checkers.runner.SketchCheckerRunner

Deprecated.

getMolecule() - Method in class chemaxon.jep.context.MolContext

Returns the input molecule.

getMolecule() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Returns the target molecule

getMolecule() - Method in class chemaxon.struc.graphics.MAnalysisBox

getMolecule() - Method in class chemaxon.struc.prop.MMoleculeProp

Gets the molecule.

getMolecule() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult

Returns the input molecule.

getMolecule(int) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Gets the molecule at the provided index

getMolecule(int) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Gets the molecule at the provided index

getMolecule(int) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Gets the molecule at the provided index

getMolecule(int) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets the specified frame.

getMolecule1Aligned() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult

getMolecule2Aligned() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult

getMoleculeCount() - Method in class chemaxon.descriptors.MDGenerator

Gets the number of molecules processed (that is, the number of descriptors generated) since the initialization of the object.

getMoleculeCount() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets the number of frames.

getMoleculeGraph() - Method in class chemaxon.struc.graphics.MChemicalStruct

Gets the stored molecule graph.

getMoleculeIterator() - Method in class chemaxon.marvin.io.MDocSource

Gets a molecule iterator for this document source.

getMoleculeIterator(MolImporter) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory

Gets a molecule iterator from the importer.

getMoleculeIterators(MolImporter[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory

Gets molecule iterators from the importers in an array.

getMoleculeMovie() - Method in class chemaxon.struc.MDocument

Gets the molecule movie.

getMoleculeName() - Method in class chemaxon.marvin.io.MRecord

Returns the name of the molecule in the record.

getMoleculeOrig() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

Gets back a clone of the unmodified input structure.

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

getMolecules() - Method in class chemaxon.sss.screen.StrucFPConfig

Gets the Molecule objects for the keys

getMolecules() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets all molecules.

getMoleculeString() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the last molecule as a string.

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

After the alignment result molecule can be obtained.

getMolfileExtensions() - Static method in class chemaxon.formats.MFileFormatUtil

Gets the array of known molecule file extensions.

getMolfileFormats() - Static method in class chemaxon.formats.MFileFormatUtil

Gets the array of known molecule file formats.

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

Gets the molfile version.

getMolID() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

getMolImportModule() - Method in class chemaxon.formats.MolImporter

getMolImportModule() - Method in class chemaxon.marvin.io.MRecordImporter

getMolIndex() - Method in exception chemaxon.marvin.io.MolExportException

Returns the molecule index.

getMolInputStream() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the molecule input stream.

getMolInputStream() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the molecule input stream.

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

Gets the molecule name font size.

getMolObject(int) - Method in class chemaxon.struc.graphics.MEFlow

Gets the electron source or sink.

getMolPainter(int, String) - Method in class chemaxon.marvin.view.MDocStorage

Gets a molecule painter.

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

Returns the underlying panel.

getMolPanel() - Method in class chemaxon.marvin.beans.MSketchPane

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

getMolPolarizability() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the molecular polarizability value.

getMolStream() - Method in class chemaxon.formats.MolImporter

Creates a Molecule Stream with the iterator of the importer.

getMolStream() - Method in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Creates a Molecule Stream from the imported molecules.

getMolStream() - Method in class chemaxon.marvin.io.MDocSource

getMolString() - Method in class chemaxon.marvin.io.MRecord

Gets the molecule string, with preprended header and appended footer if appropriate.

getMolStrings() - Method in class chemaxon.sss.screen.StrucFPConfig

Gets the original strings for the keys

getMoreErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the more error message

getMostFrequentNaturalIsotope(int) - Static method in class chemaxon.struc.PeriodicSystem

Returns the mass number of the most frequent natural isotope of the element

getMostLikelyMolFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil

Gets the most likey molecule file format from the file name extension.

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

Gets the simplified molecule object even if there is a parent document with other objects.

getMostSimplifiedMolecule() - Method in class chemaxon.struc.RgMolecule

Gets the simplified molecule object even if there is a parent document with other objects.

getMProp() - Method in class chemaxon.struc.MDocument

Gets the document as a property.

getMrvWithSettings() - Method in class chemaxon.marvin.beans.MSketchPane

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

use MSketchPane.getMol(String) instead

getMsAcceptorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the average acceptor counts over the microspecies distribution for different pH-s.

getMsCount() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the number of microspecies and/or distributions.

getMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the microspecies distribution array.

getMsDistributions() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the microspecies distribution arrays for all microspecies: the i-th element is the disrtibution array of the i-th microspecies.

getMsDonorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the average donor counts over the microspecies distribution for different pH-s.

getMSketchPane() - Method in class chemaxon.marvin.beans.MSketch

getMSLogic() - Method in class chemaxon.struc.RxnMolecule

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

Multi-step reactions not supported. Method performs no operations.

getMsMolecule(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the microspecies molecule.

getMultiplets() - Method in class chemaxon.calculations.nmr.NMRSpectrum

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

Returns the multiplicities of the ith atom of the multiplet.

getMultiplier() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets the multiplier.

getMViewPane() - Method in class chemaxon.marvin.beans.MView

getMViewParam() - Method in class chemaxon.marvin.beans.MViewParams

Generates the parameter string that can be set to MViewPane.

getName() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the name of the NMR spectrum.

getName() - Method in class chemaxon.calculations.pka.PKaTrainingResult

getName() - Method in class chemaxon.checkers.AbstractStructureChecker

getName() - Method in class chemaxon.checkers.InvalidChecker

getName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getName() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getName() - Method in interface chemaxon.checkers.StructureChecker

Gets the name of the checker

getName() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the checker name

getName() - Method in class chemaxon.descriptors.BCUT

Gets the name of the BCUT descriptor object.

getName() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the name of the ChemicalFingerprint object.

getName() - Method in class chemaxon.descriptors.CustomDescriptor

Gets the name of the CustomDescriptor object.

getName() - Method in class chemaxon.descriptors.ECFP

Gets the name of the ECFP fingerprint object.

getName() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the name of the descriptor.

getName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the name of the PharmacophoreFingerprint object.

getName() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the nice name of the ReactionFingerprint descriptor object.

getName() - Method in class chemaxon.descriptors.ScalarDescriptor

Gets the name of the ScalarDescriptor object.

getName() - Method in class chemaxon.descriptors.scalars.HAcc

Gets the name of the HAcc descriptor object.

getName() - Method in class chemaxon.descriptors.scalars.HDon

Gets the name of the HDon descriptor object.

getName() - Method in class chemaxon.descriptors.scalars.Heavy

Gets the name of the HeavyAtomCount descriptor object.

getName() - Method in class chemaxon.descriptors.scalars.LogD

Gets the name of the LogD descriptor object.

getName() - Method in class chemaxon.descriptors.scalars.LogP

Gets the name of the LogP descriptor object.

getName() - Method in class chemaxon.descriptors.scalars.Mass

Gets the name of the Mass descriptor object.

getName() - Method in class chemaxon.descriptors.scalars.TPSA

Gets the name of the TPSA descriptor object.

getName() - Method in class chemaxon.descriptors.ShapeDescriptor

Gets the name of the ShapeDescriptor fingerprint object.

getName() - Method in class chemaxon.fixers.AbstractStructureFixer

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

getName() - Method in interface chemaxon.fixers.StructureFixer

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

getName() - Method in class chemaxon.fixers.StructureFixerDescriptor

Returns the fixer name

getName() - Method in class chemaxon.formats.MFileFormat

Gets the codename of the format.

getName() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Gets the name of the represented MTransferable.

getName() - Method in class chemaxon.marvin.services.ServiceArgument

Returns the name of the argument

getName() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the name of the service

getName() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the option name.

getName() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the name of the action

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

Gets the molecule name/title that was set by Molecule.setName(String).

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

Gets the molecule title/name.

getName() - Method in class chemaxon.struc.RgMolecule

Gets the name of the root molecule.

getName() - Method in interface chemaxon.struc.Smolecule

Gets the molecule title/name.

getName() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData

Gets the name.

getName(int) - Static method in class chemaxon.struc.PeriodicSystem

Name of the element

getNameIOServiceURL() - Method in class chemaxon.marvin.common.UserSettings

getNameList() - Method in class chemaxon.formats.MFileFormat

Gets all the codenames of the format.

getNames() - Method in class chemaxon.formats.MFileFormat

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

Use MFileFormat.getNameList() instead.

getNameSpace() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Returns the namespace

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

Gets the mouse drag action.

getNDists() - Method in class chemaxon.descriptors.PFParameters

Gets the number of histograms bars, that is that number of distance values disguished.

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

Gets the index of a neighbor of an atom.

getNeighborCount(int) - Method in interface chemaxon.struc.Smolecule

Gets the number of neighbors of an atom.

getNetIntensity() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the net intensity of this multiplet which corresponds to the number of atoms in the multiplet.

getNewOldIndexMap() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

getNewToOld() - Method in class chemaxon.standardizer.Standardizer

Returns the new -> old atom index mapping.

getNewToOld() - Method in interface com.chemaxon.search.transformation.AtomIndexMapper

Returns a mapper from new to old atom indexes.

getNewToOldMap() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Returns the new -> old atom index mapping.

getNext() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer

Returns the next input molecule.

getNextAromatizedStructure() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the next enumerated structure.

getNextStructure() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the next enumerated structure, or null if no more structures.

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

getNodeCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

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

getNoErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the no error message of the concerning checker

getNominalMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.

getNonQueryImplicitHcount() - Method in class chemaxon.struc.MolAtom

Gets the number of implicit hydrogens attached.

getNotAbsoluteRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets the not absolute (contains non-"and" enhanced) (R) or (S) chiral centers

getNotAbsoluteRSChiralCenters(List<MolAtom>) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets the not absolute (contains non-"and" enhanced) (R) or (S) chiral centers

getNotSpec() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties

getNucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.

getNucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Deprecated.

Use HuckelAnalysisPlugin.getHMONucleophilicOrder(int)

getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Gets the nucleus type.

getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator

Returns the NMR active nucleus.

getNucleusString() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the nucleus type string.

getNucleusType() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the type of the nucleus under examination.

getNumber() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo

Number of type.

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

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

This feature will be removed without replacement.

getNumberFormat() - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

getNumberOfFeatures() - Method in class chemaxon.descriptors.PFParameters

The number of pharmacophore features (aka types, properties) used in the fingerprints.

getNumberOfFeatures() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

getNumberOfIntegersNeeded() - Method in class chemaxon.sss.screen.StrucFPConfig

Indicates the number of 32 bit units needed to store the fingerprint.

getNumberOfKeys() - Method in class chemaxon.sss.screen.StrucFPConfig

Indicates the number of structural keys.

getNumberOfLines() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the number of NMR lines in this multiplet.

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

Gets the total number of parametrized metrics available in the present configuration.

getNumberOfMetrics() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the number of parameterized metrics available for the particular descriptor.

getNumberOfMetrics() - Method in class chemaxon.descriptors.SDParameters

Gets the total number of parametrized metrics available in the present configuration.

getNumberOfNMRActiveNuclei() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns number of the NMR active nuclei.

getNumberOfParameters() - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

Returns the number of required parameters, or -1 if any number of parameters is allowed.

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

Gets the number of weights the current parametrized metric takes.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.BCUTParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.CDParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.CFParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.ECFPParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.MDParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.PFParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(int) - Method in class chemaxon.descriptors.RFParameters

Gets the number of weight factors used by the specified metric.

getNumberOfWeights(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the number of weight factors used by the specified metric.

getNumElectrons() - Method in class chemaxon.struc.graphics.MEFlow

Gets the number of electrons the arrow represents.

getObject(int) - Method in class chemaxon.struc.MDocument

Gets an object from the document.

getObject(String) - Method in class chemaxon.struc.MPropertyContainer

Gets a property object.

getObjectAtPointer() - Method in class chemaxon.marvin.beans.MSketchPane

Get the object at the mouse pointer.

getObjectContainingSelection() - Method in class chemaxon.struc.MDocument

Gets the object that contains the selection.

getObjectCount() - Method in class chemaxon.struc.MDocument

Gets the number of objects in this document.

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

getObjectCount() - Method in class chemaxon.struc.RgMolecule

getObjectCount() - Method in class chemaxon.struc.RxnMolecule

getObjectsMiddle(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup

Calculates the middle point of the coordinates of objects this sgroup is associated to.

getOccurredException() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Gets the exception occurred during standardization process

getOffset() - Method in class chemaxon.marvin.view.MDocStorage

Gets the offset in the document source.

getOldNewIndexMap() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

getOldToNew() - Method in class chemaxon.standardizer.Standardizer

Returns the old -> new atom index mapping.

getOldToNew() - Method in interface com.chemaxon.search.transformation.AtomIndexMapper

Returns a mapper from old to new atom indexes.

getOldToNewMap() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Returns the old -> new atom index mapping.

getOneErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the one error message

getOppositeConfiguration(EZConfiguration) - Static method in enum class chemaxon.struc.stereo.EZConfiguration

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

getOption(String) - Method in class chemaxon.sss.search.SearchOptions

Returns option value in string format.

getOptionDescriptors(String) - Method in class chemaxon.marvin.io.MolExportModule

Gets an array of option descriptors for the specified format.

getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Gets the option descriptors.

getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.marvin.io.MolExportModule

Gets an array of option descriptors.

getOptionDescriptors(ResourceBundle, String, String, List<OptionDescriptor>) - Static method in class chemaxon.marvin.io.MolExportModule

Gets an array of option descriptors.

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

Returns the name of all available options which can be used to set/get option values with SearchOptions.setOption(String, String) and SearchOptions.getOption(String) methods.

getOptions() - Method in class chemaxon.formats.MolImporter

Gets the import options.

getOptions() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the import options.

getOptions() - Method in class chemaxon.marvin.io.MolExportModule

Returns the output options.

getOptions() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the options for the import module.

getOptions() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the import options.

getOptionSign() - Method in class chemaxon.marvin.io.MolExportModule

Gets the sign of the options.

getOptionsPane() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

getOptionsPane(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the options pane for a plugin, loads it if needed.

getOptionsToDeselect() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the options that must be deselected if this option is selected.

getOptionsToDisable() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the options that must be switched off if this option is selected.

getOptionsToEnable() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the options that must be switched off if this option is selected.

getOptionString() - Method in enum class chemaxon.sss.search.options.HaltOnErrorOption

getOptionString() - Method in enum class chemaxon.sss.search.options.HomologyTranslationOption

getOptionString() - Method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

getOptionString() - Method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption

getOptionString() - Method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

getOptionString() - Method in enum class chemaxon.sss.search.options.TautomerEqualityMode

getOrCreateUUID() - Method in class chemaxon.marvin.common.UserSettings

getOrder() - Method in class chemaxon.struc.graphics.MAssigner

Gets the order of an assigner.

getOrder() - Method in class chemaxon.struc.sgroup.AttachmentPoint

Gets the order of the attachment point.

getOrientation() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties

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

getOriginal() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets the original molecule of the group.

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

Gets the original molecule of the standardization process.

getOriginal() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Gets the original molecule

getOriginalMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

getOrigQueryAtom(int) - Method in class chemaxon.sss.search.MolComparator

Converts search internal atom index (in the query) to the original atom index in the query molecule.

getOrigQueryAtom1(int) - Method in class chemaxon.sss.search.MolComparator

Returns the index of the first atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).

getOrigQueryAtom2(int) - Method in class chemaxon.sss.search.MolComparator

Returns the index of the second atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).

getOrigQueryBond(int) - Method in class chemaxon.sss.search.MolComparator

Returns bond index in the query molecule for the given query bond (search internal bond index in the query).

getOrigQueryNeighbour(int) - Method in class chemaxon.sss.search.MolComparator

For a search internal atom index (in the query), returns a neighbour atom index (original atom index in the query molecule).

getOrigTargetAtom(int) - Method in class chemaxon.sss.search.MolComparator

Converts search internal atom index (in the target) to the original atom index in the target molecule.

getOrigTargetAtom1(int) - Method in class chemaxon.sss.search.MolComparator

Returns the index of the first atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).

getOrigTargetAtom2(int) - Method in class chemaxon.sss.search.MolComparator

Returns the index of the second atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).

getOrigTargetBond(int) - Method in class chemaxon.sss.search.MolComparator

Returns bond index in the target molecule for the given target bond (search internal bond index in the target).

getOrigTargetNeighbour(int) - Method in class chemaxon.sss.search.MolComparator

For a search internal atom index (in the target), returns a neighbour atom index (original atom index in the target molecule).

getOsVersionStr() - Static method in class com.chemaxon.version.VersionInfo

Returns the OS version information as string.

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

Gets the other end of the bond.

getOtherCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Gets the other bond if a bond is a crossing bond in a ladder-type polimer bracket.

getOtherEnd() - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Gets the atom at the other end point.

getOwnerCount() - Method in class chemaxon.marvin.common.UserSettings

Gets the current number of owners.

getP0() - Method in class chemaxon.struc.graphics.MTextBoxTransformation

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

Gets the specified PageFormat

getPageSettings() - Method in class chemaxon.struc.MDocument

Gets the page settings of multipage molecular document.

getParameter(String) - Method in class chemaxon.marvin.beans.MarvinPane

Gets a parameter.

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

Returns the parameter panel.

getParameterPanel() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

getParameterPanel(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets the parameter panel for a plugin, loads it if needed.

getParameters() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the parameters associated with the object.

getParameters() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

Gets the parameter map of the action

getParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Returns the parameters set by the user.

getParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Returns the plugin parameters.

getParameters(Properties) - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Returns the plugin parameters.

getParametersClassName() - Method in class chemaxon.descriptors.BCUT

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.CustomDescriptor

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.ECFP

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the name of the parameters class corresponding to the descriptor (prefixed with the package name as getClass().getName() would return).

getParametersClassName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.ScalarDescriptor

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.scalars.HAcc

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.scalars.HDon

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.scalars.LogD

Gets the name of the parameters class corresponding to the descriptor.

getParametersClassName() - Method in class chemaxon.descriptors.ShapeDescriptor

Gets the name of the parameters class corresponding to the descriptor.

getParametersOf(PKaTrainingResult.PKaType) - Method in class chemaxon.calculations.pka.PKaTrainingResult

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

Gets the parameter string.

getParent() - Method in class chemaxon.struc.MolAtom

Return the molecule graph that contains this atom.

getParent() - Method in class chemaxon.struc.MolBond

Gets the parent graph.

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

Gets the parent graph that contains this substructure.

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

Gets the document or the document of the parent graph.

getParentLine() - Method in class chemaxon.struc.graphics.MMidPoint

Gets the parent line.

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

Gets the parent molecule.

getParentRect() - Method in class chemaxon.struc.graphics.MRectanglePoint

Gets the parent rectangle.

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

Gets the parent S-group.

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

Deprecated.

as of Marvin 6.2, intended for internal use, similar functionality can be reached by SuperatomSgroup.getSgroupGraph()

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

Computes the parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

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

Computes the parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

getParity(int) - Method in class chemaxon.struc.RxnMolecule

Computes the parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

getParity(int) - Method in interface chemaxon.struc.Smolecule

Gets the parity of an atom.

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

Gets parity type.

getPath() - Method in class chemaxon.formats.MolInputStream

Gets the path or URL of the file.

getPeakDomainMax() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the array of peak upper ends.

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

Returns the upper end of the ith peak.

getPeakDomainMin() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the array of peak lower ends.

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

Returns the lower end of the ith peak.

getPeptideDisplayType() - Method in class chemaxon.marvin.common.UserSettings

Gets the current peptide display type

getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Returns the pH where the major microspecies should be taken.

getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the pH where the major microspecies should be taken.

getpH() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the pH where the major microspecies should be taken.

getPharmacophore() - Method in class chemaxon.marvin.alignment.Pharmacophore3D

getpHs() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the pH array.

getpHs() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the pH array.

getpHs() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the pH array.

getpHs() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the pH array.

getpI() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the isoelectric point.

getPiCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the pi charge of a specified atom.

getPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane

Gets the current molecule piece in the specified format.

getPiOEN(int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the pi orbital electronegativity of a specified atom.

getpKa(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the most significant pKa value for the given atom index.

getpKa(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Deprecated.

Use pKaPlugin.getpKaValues(int, int)

getpKaConc(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the so called concentration ionization constant.

getpKaMixed(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the so called mixed ionization constant

getpKaOfpI() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the pKa values of the calculated isoelectric point.

getpKaPrefixType() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the pKa prefix type.

getpKaType(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the pKa type: pKaPlugin.ACIDIC, pKaPlugin.BASIC or 0 if there is no pKa value for the given atom.

getpKaValues(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the pKa values for the given atom index and pKa type.

getPlaceholderText() - Method in class chemaxon.marvin.services.DynamicArgument

Returns the value placeholder text.

getPlacementOrigin(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup

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

getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument

Gets the document as plain text.

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

Gets the selected text as a plain text string.

getPlattIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.

getPlugin() - Method in class chemaxon.marvin.plugin.CalculatorPluginService

Returns the calculator plugin object.

getPlugin() - Method in exception chemaxon.marvin.plugin.concurrent.PluginExecutionException

Returns the plugin object.

getPlugin() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

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

getPlugin() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

getPlugin(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets a plugin, loads it if needed.

getPluginIDs() - Method in class chemaxon.jep.Evaluator

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

Was only intended for internal use, will be removed.

getPluginIndex(String) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets a plugin index from record key.

getPluginParameters() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the plugin parameter table (this should be set in the plugin).

getPluginResource(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the plugin JAR as resource URL, given the JAR file path relatively to the "plugins" directory.

getPMap(Molecule, PSymbols) - Method in class chemaxon.descriptors.PFGenerator

Gets pharmacophore map of the input molecule.

getPMAPTagName() - Method in class chemaxon.descriptors.PFGenerator

Gets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.

getPoint(int) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Gets the point.

getPoint(int) - Method in class chemaxon.struc.graphics.MChemicalStruct

Gets a point of the object.

getPoint(int) - Method in class chemaxon.struc.graphics.MEFlow

Gets a point of the line.

getPoint(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Gets the point.

getPoint(int) - Method in class chemaxon.struc.graphics.MElectron

getPoint(int) - Method in class chemaxon.struc.graphics.MElectronContainer

getPoint(int) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets a point of the object.

getPoint(int) - Method in class chemaxon.struc.graphics.MPolyline

Gets the clone of a point of the line.

getPoint(int) - Method in class chemaxon.struc.MObject

Gets a point of the object.

getPoint(int) - Method in class chemaxon.struc.MPoint

Gets the point.

getPointCount() - Method in class chemaxon.struc.graphics.MChemicalStruct

Gets the number of points (atoms).

getPointCount() - Method in class chemaxon.struc.graphics.MElectronContainer

getPointCount() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Gets the number of points (atoms).

getPointCount() - Method in class chemaxon.struc.graphics.MPolyline

Gets the number of points.

getPointCount() - Method in class chemaxon.struc.MObject

Gets the number of points.

getPointCount() - Method in class chemaxon.struc.MPoint

Gets the number of points.

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MElectron

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Gets a reference to a point or midpoint in the polyline.

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Gets an internal selectable point of the rectangle.

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle

Gets an internal selectable point of the rectangle.

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.MObject

Gets a reference to a point of the object.

getPointRef(int, CTransform3D) - Method in class chemaxon.struc.MPoint

Gets a point of the line.

getPointRefCount() - Method in class chemaxon.struc.graphics.MEFlow

Gets the number of point references.

getPointRefCount() - Method in class chemaxon.struc.graphics.MElectronContainer

getPointRefCount() - Method in class chemaxon.struc.graphics.MPolyline

Gets the number of point references.

getPointRefCount() - Method in class chemaxon.struc.graphics.MReactionSign

getPointRefCount() - Method in class chemaxon.struc.graphics.MRectangle

Gets the number of internal selectable point references.

getPointRefCount() - Method in class chemaxon.struc.graphics.MRoundedRectangle

Gets the number of internal selectable point references.

getPointRefCount() - Method in class chemaxon.struc.MObject

Gets the number of point references.

getPointRefCount() - Method in class chemaxon.struc.MPoint

Gets the number of point references.

getPoints() - Method in class chemaxon.struc.graphics.MPolyline

Gets the points.

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

Gets an array containing the atom coordinates.

getPoints(int) - Method in class chemaxon.struc.prop.MHCoords3DProp

Gets the Hydrogen locations for an atom.

getPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the atom polarizability value.

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

Are popup menus enabled?

getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets a portion of the document.

getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets a portion of the text relative to this portion.

getPortName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Returns the port name

getPos() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the data display DASP position (0...9).

getPosition() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the current position.

getPosition() - Method in exception chemaxon.marvin.io.MRecordParseException

Gets the position of the error.

getPosition() - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets the position in the document.

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

Returns the position of the ith NMR line.

getPositionInPolyline() - Method in class chemaxon.struc.graphics.MMidPoint

Gets the position in the polyline.

getPositionInRect() - Method in class chemaxon.struc.graphics.MRectanglePoint

Gets the position in the rectangle.

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

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

As of Marvin 6.0, replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom) and MolAtom.getAttachParentSgroup().
Usage:

 SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup());
 List&ltInteger&gt orders = group.getAttachmentPointOrders(molAtom);
             

getPossibleRotatableBondCount() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Rotatable bond count before the atrop isomer calculation.

getPreBreakingChars() - Method in class chemaxon.struc.graphics.MNameTextBox

Gets the breaking characters before that the text in the text box can be broken if it doesn't fit into the text box.

getPreBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox

Gets the breaking characters before that the text in the text box can be broken if it doesn't fit into the text box.

getPreferredIUPACName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the preferred IUPAC name.

getPreferredLabelDir(CTransform3D, int) - Method in class chemaxon.struc.MolAtom

Gets the preferred direction for an additional label.

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

Gets the preferred size of the component.

getPreferredView() - Method in class chemaxon.marvin.io.MolImportModule

Specifies which view style is preferred (for instance in MarvinView) for this format.

getPreferredWidth() - Method in class chemaxon.struc.graphics.MNameTextBox

Gets the preferred width of the text-box.

getPrefix() - Method in exception chemaxon.naming.NameFormatException

The part of the input name that was recognized, or null.

getPreviousNormalTextSectionIndex() - Method in class chemaxon.struc.graphics.MTextBox

Gets the index of the last `normal' text section before the current subscript/superscript section.

getPrimaryIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Gets the primary indexes.

getPrimaryMolecule() - Method in class chemaxon.struc.MDocument

Gets the primary molecule object.

getPrimaryMolecules() - Method in class chemaxon.struc.MDocument

Gets an array containing the primary molecule objects.

getPrincipalPolarizabilityComponents() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the principal components a(xx), a(yy), a(zz) of polarizability tensor (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).

getPriority() - Method in class chemaxon.fixers.StructureFixerDescriptor

Returns the fixer priority.

getPriority() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Gets the priority of the MTransferable object by exporting to clipboard.

getPriority(String) - Method in class chemaxon.formats.MFileFormat

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

as of Marvin 2014.07.21.0 use MFileFormat.getSubFormatPriority(String) instead

getProduct() - Method in exception chemaxon.license.LicenseException

getProduct(int) - Method in class chemaxon.struc.RxnMolecule

Gets a product.

getProductCount() - Method in class chemaxon.struc.RxnMolecule

Gets the number of products.

getProductName() - Method in class chemaxon.calculations.dipole.DipoleCalculator

getProductName() - Method in class chemaxon.calculations.nmr.NMRCalculator

getProductName() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

getProductName() - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

getProductName() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.ResonancePlugin

getProductName() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the product identifier of the plugin as given by LicenseGlobals.

getProductName() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

getProductName() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProductName() - Method in class chemaxon.marvin.calculations.TPSAPlugin

getProductName() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the product identifier of the plugin as given by LicenseManager.

getProducts() - Method in class chemaxon.struc.RxnMolecule

Gets all products in an array.

getProductTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

Returns the tanimoto distance of the product sides.

getProgessLength() - Method in interface chemaxon.checkers.runner.CheckerRunner

getProgessLength() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

getProgessLength() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Gets the length of the standardization process

getProgress() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Estimates the progress.

getProgressBar() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

getProgressMonitor(Component) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates a progress observer object to be used in CalculatorPlugin.setProgressMonitor(chemaxon.common.util.MProgressMonitor).

getPropArraySize() - Method in class chemaxon.struc.MDocument.Prop

Gets the array size.

getPropArraySize() - Method in class chemaxon.struc.MProp

Gets the array size.

getPropArraySize() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Gets the array size.

getPropArraySize() - Method in class chemaxon.struc.prop.MHashProp

Gets the array size.

getPropArraySize() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Gets the array size.

getPropArraySize() - Method in class chemaxon.struc.prop.MListProp

Gets the array size.

getProperties() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult

Returns the flag which can used to identify which properties should be fixed.

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

Returns the value for the given key.

getProperty(String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns a descriptor property

getProperty(String) - Method in class chemaxon.struc.MolAtom

Returns the property value to which the specified property key is mapped at this atom, or null if this atom has no mapping for this property key.

getProperty(String) - Method in class chemaxon.struc.MolBond

Returns the property value to which the specified property key is mapped at this bond, or null if this bond has no mapping for this property key.

getProperty(String) - Method in class chemaxon.struc.Molecule

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

As of Marvin 5.7, this method is deprecated. Replaced by MPropHandler.getPropertyString(MoleculeGraph, String).
Usage:

String property = MPropHandler.getPropertyString(mol, key);

getPropertyChangeSupport() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the property change support for this object

getPropertyChangeSupport() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor

Returns the PropertyChangeSupport associated with this editor

getPropertyContainer() - Method in class chemaxon.marvin.io.MRecord

Gets the properties.

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

Gets the total number of RDfile/SDfile properties.

getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo

Returns the property descriptor array.

getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo

Returns the property descriptor array.

getPropertyDescriptors(Class<?>, Vector<PropertyDescriptor>) - Method in class chemaxon.marvin.beans.MarvinPaneBeanInfo

Puts the descriptors of the common Marvin bean properties into the specified Vector.

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

Gets an RDfile/SDfile property key.

getPropertyKeys() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the array of property keys

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

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

As of Marvin 4.1, replaced by properties().getKeys() and properties().getKeyEnumeration().
One-to-one replacement is method getKeyEnumeration() but method getKeys() is simpler to use.

getPropertyMap() - Method in class chemaxon.marvin.common.UserSettings

Shortcut to getPropertyMap(UserSettings.PROPERTY_TYPE_ALL)

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

Returns a map of properties from the given type.

getPropertyObject(MoleculeGraph, String) - Static method in class chemaxon.marvin.io.MPropHandler

Returns the property object associated with the given key in the given molecule.

getPropertyObject(String) - Method in class chemaxon.struc.Molecule

Gets an RDfile/SDfile property object.

getPropertyString(MoleculeGraph, String) - Static method in class chemaxon.marvin.io.MPropHandler

Converts the property object associated with the given key in the given molecule to string.

getPropertyText(Molecule) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Returns molecule properties is text form.

getPropList() - Method in class chemaxon.struc.MPropertyContainer

Gets the list of basic properties.

getPropType() - Method in class chemaxon.struc.MDocument.Prop

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.MProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MBooleanProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MDoubleProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MFontProp

getPropType() - Method in class chemaxon.struc.prop.MHashProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MHCoords3DProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MIntegerProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MListProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MMoleculeProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MObjectProp

Gets the type name of the property.

getPropType() - Method in class chemaxon.struc.prop.MStringProp

Gets the type name of the property.

getPropValue() - Method in class chemaxon.struc.MDocument.Prop

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.MProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MBooleanProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MDoubleProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MFontProp

getPropValue() - Method in class chemaxon.struc.prop.MHashProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MHCoords3DProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MIntegerProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MListProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MMoleculeProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MObjectProp

Gets the property value as an object.

getPropValue() - Method in class chemaxon.struc.prop.MStringProp

Gets the property value as an object.

getPropXSDType() - Method in class chemaxon.struc.MDocument.Prop

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.MProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MBooleanProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MCollectionProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MFontProp

getPropXSDType() - Method in class chemaxon.struc.prop.MHCoords3DProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MMoleculeProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MObjectProp

Gets the XSD type name of the property.

getPropXSDType() - Method in class chemaxon.struc.prop.MStringProp

Gets the XSD type name of the property.

getPSymbols() - Method in class chemaxon.descriptors.PFParameters

Gets the pharmacophore type symbols used in the current configuration.

getQProp(String) - Method in class chemaxon.struc.MolAtom

Gets a query property.

getQPropAsInt(String) - Method in class chemaxon.struc.MolAtom

Gets a query property as an integer.

getQPropMinMax(String) - Method in class chemaxon.struc.MolAtom

Gets the minimum and maximum possible values of a query property.

getQPropNames() - Method in class chemaxon.struc.MolAtom

Gets the names of query properties with non-null values.

getQPropNameSet() - Method in class chemaxon.struc.MolAtom

Gets the names of query properties with non-null values, or null if no query properties are set.

getQuery() - Method in class chemaxon.sss.formula.FormulaSearch

Gets the chemical formula query string used for searching

getQuery() - Method in class chemaxon.sss.search.Decomposition

Returns the R-grouped query used in the R-group decomposition.

getQuery() - Method in class chemaxon.sss.search.MarkushGenerator

Returns the query.

getQuery() - Method in class chemaxon.sss.search.MolSearch

getQuery() - Method in class chemaxon.sss.search.RGroupDecomposition

Retrieves the original query structure.

getQuery() - Method in class chemaxon.sss.search.Search

Retrieves the query structure.

getQuery() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Gets the query structure.

getQueryAromaticity() - Method in class chemaxon.struc.MolAtom

Gets the aromatic/aliphatic query property.

getQueryAsString(Molecule) - Static method in class chemaxon.sss.search.Search

For internal purposes only.

getQueryAtom() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Gets the atom to be searched for by the action (the query atom)

getQueryCode() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the program code of the query option.

getQueryLabel() - Method in class chemaxon.struc.MolAtom

Gets the string representation of the query atom

getQueryMode() - Method in class chemaxon.formats.MolImporter

Gets query mode.

getQueryMode() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the query mode.

getQueryMoleculeErrorMessage(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

getQueryOp() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the data query operator.

getQuerystr() - Method in class chemaxon.struc.MolAtom

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

As of release 5.7, replaced by MolAtom.getQueryString()

getQuerystr() - Method in class chemaxon.struc.MolBond

Gets the query properties.

getQuerystr() - Method in class chemaxon.struc.QueryBond

Gets the query properties.

getQueryString() - Method in class chemaxon.struc.MolAtom

Returns s the query string assigned to this atom.

getQueryToPrint() - Method in class chemaxon.sss.search.Search

For internal purposes only.

getRadical() - Method in class chemaxon.struc.MolAtom

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

as of Marvin 6.2. use MolAtom.getRadicalValue() instead

getRadical(int) - Method in interface chemaxon.struc.Smolecule

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

Use Smolecule.getRadicalValue(int) instead.

getRadicalCount() - Method in class chemaxon.struc.MDocument

Returns the number of Radical electrons.

getRadicalCount() - Method in class chemaxon.struc.MolAtom

Gets the number of free electrons.

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

Gets the number of free electrons of the given atom.

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

Gets the number of free electrons of the given atom.

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

Get option for radical matching behavior.

getRadicalValue() - Method in class chemaxon.struc.MolAtom

Gets the AtomProperty.Radical enum value that represents the radical of the atom.

getRadicalValue(int) - Method in interface chemaxon.struc.Smolecule

Gets the radical value of an atom.

getRadius() - Method in class chemaxon.struc.graphics.MElectron

getRadius() - Method in class chemaxon.struc.graphics.MElectronContainer

Returns the radius of MElectrons.

getRandicIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.

getRandomSeed() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Gets the random seed value.

getRangeMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Maximal y value of the NMR spectrum function.

getRangeMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Minimal y value of the NMR spectrum function.

getRawValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the value of the unscaled NMR spectrum function at a given x point.

getReactant(int) - Method in class chemaxon.struc.RxnMolecule

Gets a reactant.

getReactantCount() - Method in class chemaxon.struc.RxnMolecule

Gets the number of reactants.

getReactants() - Method in class chemaxon.struc.RxnMolecule

Gets all reactants in an array.

getReactantTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

Returns the tanimoto distance of the reactant sides.

getReaction() - Method in class chemaxon.jep.context.ReactionContext

Returns the reaction.

getReaction(MoleculeGraph) - Static method in class chemaxon.struc.RxnMolecule

Returns the reaction represented by the given molecule if exists, otherwise null.

getReactionArrow() - Method in class chemaxon.struc.RxnMolecule

Gets a two-element array containing the endpoints of the reaction arrow.

getReactionArrow(boolean) - Method in class chemaxon.struc.RxnMolecule

Gets the reaction arrow of this reaction with the possibility to generate an arrow if the arrow is not yet set.

getReactionArrowList() - Method in class chemaxon.struc.RxnMolecule

Gets the list of the reaction arrows of this reaction.

getReactionArrowType() - Method in class chemaxon.struc.RxnMolecule

Gets the reaction arrow type.

getReactionArrowTypeName() - Method in class chemaxon.struc.RxnMolecule

Gets the reaction arrow type name.

getReactionSmarts() - Method in class chemaxon.checkers.result.SubstructureCheckerResult

Returns the reactionSmarts

getReactionSmarts() - Method in class chemaxon.checkers.SubstructureChecker

Returns the reactionSmarts

getReactionStereo() - Method in class chemaxon.struc.MolAtom

Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.

getReactionSupport() - Method in class chemaxon.marvin.beans.MSketchPane

Is reaction drawing supported?

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

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

since Marvin 5.1 when this and the MarvinPane.getSaveGlobalGUIProperties() function have been merged.

getRealBondCount() - Method in class chemaxon.struc.MolAtom

Gets the number of bonds connected to "real" atoms.

getRealEigenValue() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Deprecated.

Use HuckelAnalysisPlugin.getHMORealEigenValue()

getRealRotatableBondCount() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Rotatable bond count (atrop bonds excluded)

getRecognizedFormat() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Gets the recognized file format.

getRecognizedFormat() - Method in interface chemaxon.marvin.io.MRecordReader

Gets the recognized file format.

getRecognizer(int, int) - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Gets an element of the recognizer list at the specified level.

getRecordCount() - Method in class chemaxon.formats.MolImporter

Gets the current record number.

getRecordCount() - Method in class chemaxon.marvin.io.ArrayMDocSource

Gets the current record number.

getRecordCount() - Method in class chemaxon.marvin.io.MDocSource

Gets the current record number.

getRecordCount() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Gets the current record number.

getRecordCountMax() - Method in class chemaxon.formats.MolImporter

Gets the total number of records read.

getRecordCountMax() - Method in class chemaxon.marvin.io.ArrayMDocSource

Gets the total number of records.

getRecordCountMax() - Method in class chemaxon.marvin.io.MDocSource

Gets the total number of records.

getRecordCountMax() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Gets the total number of records.

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

Gets the highlight color of a record.

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

Gets the foreground color of a record.

getRecordIndex() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException

Gets the requested, unavailable record index.

getRecordIndexMax() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException

Gets the maximum available record index.

getRecordIndexMin() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException

Gets the minimum available record index.

getRecordNumber() - Method in class chemaxon.marvin.io.MRecordReader.Position

Gets the record number.

getRecordReader() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the record reader.

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

before getRotatedMolecule the AlignRigidEasy.align() method must be called

getReferenceMolecule() - Method in interface chemaxon.marvin.alignment.MCSAlignment

Reference molecule.

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

getReflogDs() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the reference logD array.

getRefpHs() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the reference pH array.

getRefractivity() - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the refractivity value.

getRefractivityHIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the refractivity increment on the H atoms attached to a given atom.

getRefractivityIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the refractivity increment for a given atom.

getRegNo() - Method in class chemaxon.struc.prop.MMoleculeStringProp

getRelativeNegativity() - Method in class chemaxon.struc.MolAtom

Check negativity compared to the neighbors.

getRemark() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.

getRemark() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns a warning message in case of arithmetical overflow (the number of enumerated structures exceeds Long.MAX_VALUE), null otherwise.

getRemark() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns a warning message if there are no resonants, null otherwise.

getRemark() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns a warning message if there are no tautomers, null otherwise.

getRemark() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.

getRemark() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the calculation remark.

getRemark() - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the calculation remark.

getRemark() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the calculation remark.

getRemark() - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the calculation remark.

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

Returns the calculation remark.

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

Gets the list of atoms removed during the standardization procedure

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

Gets the rendering style.

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

Returns the rendering style of atoms and bonds.

getRepeatingUnitAtom(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets a paradigmatic repeating unit atom.

getRepeatingUnitAtomCount() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets the number of atoms in the pararadigmatic repeating unit.

getRepeatingUnitAtoms() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets the repeating unit atoms.

getReplaceAtom() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Gets the atom to replaced with by the action

getRepresentation() - Method in class chemaxon.checkers.util.DataExclusionList

getRepresentationClass() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Gets the name of the representation class of the MTransferable.

getRequestMethod() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor

Gets the HTTP method of the request.

getRequiredHlbValue() - Method in interface chemaxon.marvin.calculations.HlbPlugin

Returns the Required HLB value calculated by chemaxon method.

getResidueAtomId() - Method in class chemaxon.struc.MolAtom

Gets the residue atom identifier.

getResidueSeq() - Method in class chemaxon.struc.MolAtom

Gets the residue sequence number.

getResidueType() - Method in class chemaxon.struc.MolAtom

Gets the residue type.

getResolution() - Method in class chemaxon.descriptors.PFParameters

Gets the resolution of histograms.

getResolution() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

getResourceBundle(String) - Static method in class chemaxon.marvin.beans.MarvinPane

Utility method to get a resource bundle.

getResult() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

getResult() - Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit

Returns the cached results.

getResult() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Returns the calculation result after the plugin has been CalculatorPlugin.run().

getResult() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit

Returns the plugin object itself.

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

Gets the result molecule of the standardization process

getResult(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the result item for the specified type and index.

getResult(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the result string for the given molecule.

getResult(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the result string for the given molecule.

getResult(Molecule) - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the result string for the given molecule.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the result item for the specified type and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the result item for the specified type and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the result item for the specified type and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the result item for the specified type and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the microsepcies if pH is different from Double.NaN, otherwise returns the input molecule itself.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the result item for the specified type and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the result item for the specified type and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

getResult(Object, int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the result item for the specified key and index.

getResult(Object, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the result item for the specified type and index.

getResult(Object, String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call ElementalAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call ElementalAnalyserPlugin.getResult(Object, int) with a 0 index.

getResult(Object, String) - Method in class chemaxon.marvin.calculations.GeometryPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call GeometryPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call GeometryPlugin.getResult(Object, int) with a 0 index.

getResult(Object, String) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call IsoelectricPointPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call IsoelectricPointPlugin.getResult(Object, int) with a 0 index.

getResult(Object, String) - Method in class chemaxon.marvin.calculations.logDPlugin

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

getResult(Object, String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call MarkushEnumerationPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call MarkushEnumerationPlugin.getResult(Object, int) with a 0 index.

getResult(Object, String) - Method in class chemaxon.marvin.calculations.pKaPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call pKaPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call pKaPlugin.getResult(Object, int) with a 0 index.

getResult(Object, String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call TopologyAnalyserPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call TopologyAnalyserPlugin.getResult(Object, int) with a 0 index.

getResult(Object, String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call CalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call CalculatorPlugin.getResult(Object, int) with a 0 index.

getResult(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

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

Some implementations of this method modify the state of the plugin, which is a very confusing behavior, so the method is now deprecated and should no longer be used. If you used this method with an index argument, parse the index instead, and call CalculatorPlugin.getResult(Object, int). Otherwise, call the appropriate setter method of the plugin to configure it with the argument, and call CalculatorPlugin.getResult(Object, int) with a 0 index.

getResultantImplicitHCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the implicit H charge around a central atom

getResultAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue): RED for acidic pKa, BLUE for basic pKa.

getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result in String format for the first result type.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the specified result molecule in SMILES format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Get a calculation result (returned by StructuralFrameworksPlugin.getResultMolecule() after a StructuralFrameworksPlugin.run() call in the given format StructuralFrameworksPlugin.setFormat(String)

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result in String format.

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

Returns the result component for display.

getResultCount() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

getResultCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the number of result items for the first result type.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the number of result items for the given result type.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the number of result items for the given result type.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the number of result items: 1.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the number of result items for the given result type.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the number of result items for the given result key.

getResultDomain() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.

getResultDomain() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the domain for the first result type.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the calculation domain CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the calculation domain CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULE in case of increments .

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the calculation domain.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the calculation domain CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.

getResultList() - Method in interface chemaxon.checkers.runner.CheckerRunner

getResultMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the plugin calculation error message, error or warning.

getResultMessage() - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the plugin calculation error message, error or warning.

getResultMessage() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the plugin calculation error message, error or warning.

getResultMessage() - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the plugin calculation error message, error or warning.

getResultMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

getResultMolecule() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

The result molecule will be 3D and aromatized version of the input molecules.

getResultMolecule() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

getResultMolecule() - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

getResultMolecule() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the major microspecies for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Get result structure

getResultMolecule() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the result molecule for display.

getResultMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the result molecule for display.

getResultMolecule(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the decorated result molecule for the given target molecule.

getResultMolecule(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the decorated result molecule for the given target molecule.

getResultMolecule(Molecule) - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the decorated result molecule for the given target molecule.

getResultMolecules() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.

getResultMolecules() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.

getResultMolecules() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the result molecule array for display.

getResultMolecules(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the result molecules for the given molecule.

getResultMolecules(Molecule) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the result molecules for the given target molecule.

getResultMolecules(Molecule) - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the result molecules for the given target molecule.

getResults(Object) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns result items for the given result type.

getResultsAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

getResultsAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result with possible subresults.

getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the specified result in GUI-specific String format: A for acceptor, D for donor.

getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the specified results in String format.

getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the specified result with possible subresults (both pKa values instead of the most significant pKa) in String format.

getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the specified result with possible subresults.

getResultSource() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the result as a document source object.

getResultSource() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the result as a document source object.

getResultSource() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the result as a document source object.

getResultSource() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the result as a document source object.

getResultSource() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the result as a document source object.

getResultSource() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the result as a document source object.

getResultSource() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the result as a document source object.

getResultTypeList() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the result types (possible types: "sigma", "pi", "total").

getResultTypes() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the string IDs of the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the result types (possible type: "charge").

getResultTypes() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the result types (possible types: "majority-ms").

getResultTypes() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the result types (possible types: "sigma", "pi").

getResultTypes() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the result types (possible types: pKa, acidic, basic, msdistr).

getResultTypes() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns the result types (possible types: sigma, pi, total).

getResultTypes() - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

getResultTypes() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the result types.

getResultTypes() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the result types.

getReturnTypes() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Returns the array of return types

getRgroup() - Method in class chemaxon.struc.MolAtom

Gets the R-group ID.

getRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MolAtom

Gets the attachment point order of an R-group attachment point.

getRgroupBridgeCount() - Method in class chemaxon.struc.RgMolecule

Returns the number of R-group bridges defined in this structure.

getRgroupBridgeIds() - Method in class chemaxon.struc.RgMolecule

Returns the list of R-group bridge IDs defined in this structure.

getRgroupBridgeMember(RgroupBridgeId, int) - Method in class chemaxon.struc.RgMolecule

Returns a definition member of the given R-group bridge.

getRgroupBridgeMemberCount(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule

Returns the number of definition members of the given R-group bridge.

getRgroupCount() - Method in class chemaxon.struc.RgMolecule

Gets the number of R-groups.

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

getRGroupedQuery() - Method in class chemaxon.sss.search.RGroupDecomposition

Returns the R-grouped query.

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

Gets the ID of an R-group.

getRgroupId(int) - Method in interface chemaxon.struc.Smolecule

Gets the R-group identifier of an atom.

getRgroupId(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule

getRgroupId1() - Method in class chemaxon.struc.RgroupBridgeId

Returns the ID of the first bridged R-group.

getRgroupId2() - Method in class chemaxon.struc.RgroupBridgeId

Returns the ID of the second bridged R-group.

getRgroupIds() - Method in class chemaxon.checkers.result.RgroupCheckerResult

Returns the list of affected R-group IDs.

getRgroupIndex(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule

Returns the index of the ordinary R-group that actually represents the given R-group bridge.

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

Gets an R-group member.

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

Gets the number of R-group members.

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

Gets an R-group member.

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

Gets the unique identifier of the R-group member that contains the specified atom.

getRightBracket(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket

getRightMargin() - Method in class chemaxon.struc.PageSettings

getRightName() - Method in class chemaxon.struc.sgroup.SgroupAtom

Set the string that will be shown at the right side of the molecule.

getRingAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the ring atom count.

getRingBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the ring bond count.

getRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the ring count.

getRingCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getRingCountOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.

getRingCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

Use TopologyAnalyserPlugin.getRingCount(int)

getRingHandlingMode() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns the ring handling mode.

getRings() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the rings in the molecule.

getRings(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies rings in the molecule having a given size.

getRingSystemCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the number of ring systems.

getRingSystemCount(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the number of ring systems having a given size (number of rings) in the molecule.

getRingSystemCountOfSize(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

Use TopologyAnalyserPlugin.getRingSystemCount(int)

getRingSystems() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the ring systems in the molecule.

getRingSystems(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

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

getRLigandCount() - Method in class chemaxon.sss.search.RGroupDecomposition

Returns the number of R-atoms in the R-grouped query (see RGroupDecomposition.getRGroupedQuery()).

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

Returns true if undefined R-atoms with the same R-group ID should match the same structure.

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

Gets R-logic flags.

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

Gets R-logic occurrence range.

getRLogicVisible() - Method in class chemaxon.marvin.common.UserSettings

Tells whether the R-logic is visible if exists

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

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

getRmsd() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult

getRoot() - Method in class chemaxon.struc.RgMolecule

Gets the root structure.

getRootG() - Method in class chemaxon.struc.RgMolecule

Gets the root structure.

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

Gets root s-groups (groups that are not embedded into another s-group).

getRotatableBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the rotatable bond count.

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

before getRotatedCoordinates the AlignRigidEasy.align() method must be called

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

before getRotatedMolecule the AlignRigidEasy.align() method must be called

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

Gets the rotation part of the transformation matrix.

getRotBondCount() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

getRow(int) - Static method in class chemaxon.struc.MolAtom

The row or or period of an element in the periodic system.

getRow(int) - Static method in class chemaxon.struc.PeriodicSystem

The row or or period of an element in the periodic system.

getRowCount() - Method in class chemaxon.struc.PageSettings

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

Gets the row height.

getrsChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets the (r) and (s) stereo centers of the molecule

getRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets the (R) and (S) chiral centers of the molecule

getSaltCount() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Gets the count of the salts of the action

getSaltID(int) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Gets the salt ID at the provided index

getSaltList() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Gets the custom salt list of the action

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

Checks whether we have to read GUI properties from a .MRV file

getSaveGUIPropertiesInMRV() - Method in class chemaxon.marvin.common.UserSettings

getSaveLoadZoomFactorToMRV() - Method in class chemaxon.marvin.common.UserSettings

Tells if marvin save the zoom factor to mrv or not.

getScaffold() - Method in class chemaxon.sss.search.Decomposition

Returns the scaffold in target.

getScaffold() - Method in class chemaxon.sss.search.RgDecompResults

Returns scaffold of the query (r-groups are added automatically if needed).

getScale() - Method in class chemaxon.marvin.beans.MSketchPane

Returns the scale factor of the current magnification.

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

Returns the scale factor in units of regular bond length.

getScale() - Method in class chemaxon.struc.CTransform3D

Gets the scale factor.

getScale() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the relative size of the font compared to the base font.

getScale() - Method in class chemaxon.struc.graphics.MTextBoxTransformation

getScaledAWTFont(Float) - Method in class chemaxon.struc.graphics.MFont

Gets an AWT font instance after scaling.

getScaledTanimoto(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Gets the Tanimoto dissimilarity coefficient.

getScaledTanimoto(PharmacophoreFingerprint, PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the scaled Tanimoto metric (adapted to hystograms).

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

Gets the scale factor used in the current parametrized scalable metrics.

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

Gets the scaling hypothesis used in scaled metrics.

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

Returns parts of the parameter values in string.

getScriptCount(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets the number of subscripts or superscripts on the last normal character.

getSearchMode() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Gets the current search mode.

getSearchOptions() - Method in class chemaxon.sss.search.MarkushGenerator

Returns the search options.

getSearchOptions() - Method in class chemaxon.sss.search.Search

Returns the SearchOptions object associated with this Search object.

getSearchOptions() - Method in class chemaxon.standardizer.advancedactions.TransformAction

Gets the search options of the action

getSearchOptions() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Returns the search options used by this instance.

getSearchType() - Method in class chemaxon.sss.formula.FormulaSearch

Gets the formula search type.

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

Returns the currently set global search operation mode.

getSearchType(String) - Static method in class chemaxon.sss.search.SearchOptions

Decodes the string representation of the search type and returns the predefined constant value defined in SearchConstants.

getSecondaryIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Gets the secondary indexes.

getSection(int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets a section of the document.

getSectionCount() - Method in class chemaxon.struc.graphics.MTextDocument

Gets the number of sections in the document.

getSectionIndexOfCharAt(int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets the section index of a character.

getSectionShiftY(int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets the y shift of a section.

getSelectedAtoms(int, String) - Method in class chemaxon.marvin.view.MDocStorage

Gets the selected atom indices.

getSelectedDocument() - Method in class chemaxon.struc.graphics.MTextBox

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

Gets the number of selected fields.

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

Get selected fields array which are selected in Table Options dialog box

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

Get type array of selected field types.

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

Gets the index of the molecule that is selected by the user.

getSelectedPage() - Method in class chemaxon.struc.PageSettings

getSelectedString() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selected substring.

getSelection() - Method in class chemaxon.marvin.beans.MSketchPane

Gets a clone of the selection.

getSelection() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport

Returns the selection of atoms.

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

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

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

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

Gets a selection which contains index of center atom and indexes of ligands.

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

getSelectionEndColumn() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selection's end column number.

getSelectionEndPos() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selection's end position.

getSelectionEndRow() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selection's end row number.

getSelectionStartColumn() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selection's start column number.

getSelectionStartPos() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selection's start position.

getSelectionStartRow() - Method in class chemaxon.struc.graphics.MTextBox

Gets the selection's start row number.

getSeparator(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Gets if a separator is required after the plugin menuitem in the Tools menu.

getSeries(ChartSample) - Method in class com.chemaxon.calculations.gui.MChart

getServiceHandler() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the default service handler instance for this descriptor.

getServicesConfigurationPath() - Method in class chemaxon.jep.Evaluator

Returns the custom services configuration path.

getServicesConfigURL() - Method in class chemaxon.marvin.common.UserSettings

Returns the URL of configuration for Services in marvin sketch

getSet() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the set of attributes used.

getSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane

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

as of Marvin 3.3, replaced by getAtomSetColor

getSetSeq() - Method in class chemaxon.struc.MolAtom

Gets the atom set sequence number.

getSetSeq() - Method in class chemaxon.struc.MolBond

Gets the bond set.

getSeverity() - Method in class chemaxon.checkers.StructureCheckerDescriptor

Returns the severity

getSgroup() - Method in class chemaxon.struc.sgroup.SgroupAtom

Gets the S-group corresponding to this superatom.

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

Gets an S-group.

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

Gets the array of S-groups.

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

Gets the number of S-groups.

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

Gets a COPY of the molecule graph.

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

Gets the molecule graph as a selection.

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

Returns an iterator over the s-groups in this molecule in proper sequence.

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

Gets the S-group's ligands if the structure represents an S-group.

getSgroups() - Method in class chemaxon.checkers.result.SgroupCheckerResult

Returns a List which contains the affected groups of the problem

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

Gets the S-group type.

getSgroupType(String) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Gets the S-group type.

getShapes(CTransform3D) - Method in class chemaxon.struc.graphics.MBracket

getShapeScore() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult

getShapeSimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor

getShapeTanimoto() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult

getShapeTanimoto() - Method in class chemaxon.marvin.alignment.PairwiseAlignment

getShapeTanimoto() - Method in interface chemaxon.marvin.alignment.PairwiseComparison

getShapeTanimoto() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

getShift() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the chemical shift.

getShift() - Method in class chemaxon.calculations.nmr.Shift

Returns the chemical shift.

getShiftError() - Method in class chemaxon.calculations.nmr.Multiplet

Returns the estimated error of the chemical shift.

getShiftError() - Method in class chemaxon.calculations.nmr.Shift

Returns the error (confidence interval radius) of the shift.

getShiftErrorClassification() - Method in class chemaxon.calculations.nmr.Multiplet

Returns error classification of the chemical shift.

getShiftErrorClassification() - Method in class chemaxon.calculations.nmr.Shift

Returns the error classification of the stored chemical shift.

getShifts() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns chemical shifts.

getShortestPath(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the shortest topological path (number of bonds) between two atoms.

getShortName() - Method in class chemaxon.descriptors.BCUT

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.ChemicalFingerprint

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.CustomDescriptor

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.ECFP

Gets the short name of the fingerprint.

getShortName() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.ReactionFingerprint

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.ScalarDescriptor

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.HAcc

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.HDon

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.Heavy

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.LogD

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.LogP

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.Mass

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.scalars.TPSA

Gets the short name of the descriptor.

getShortName() - Method in class chemaxon.descriptors.ShapeDescriptor

Gets the short name of the fingerprint.

getShortName() - Method in enum class chemaxon.struc.SgroupType

getShowLogPercentage() - Method in class chemaxon.marvin.calculations.pKaPlugin

getSigmaCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the sigma charge of a specified atom.

getSigmaOEN(int) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns the sigma orbital electronegativity of a specified atom.

getSimilarity() - Method in class com.chemaxon.search.mcs.McsSearchResult

Returns a Tanimoto-like similarity score of the input molecules based on the found maximum common substructure.

getSimilarity(T) - Method in class chemaxon.descriptors.SimilarityCalculator

Gets the similarity value according to previously defined metric and its parameters.

getSimpleName() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor

getSimpleName() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor

getSimpleName() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

getSimpleName() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the simple name of the service type

getSimpleName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

getSimpleName() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor

getSimpleParamString() - Method in enum class chemaxon.descriptors.MetricsType

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

Gets the simplified molecule object.

getSimpView() - Method in class chemaxon.marvin.beans.MSketchPane

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

as of Marvin 3.5, replaced by MSketchPane.isBondDraggedAlong()

getSingleHit() - Method in class chemaxon.sss.search.SearchHit

Returns the single hit view of the hit object.

getSingleMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the microspecies distribution at the specified pH value set in pKaPlugin.setpH(double).

getSink() - Method in class chemaxon.struc.graphics.MEFlow

Gets the destination of the electron-flow arrow (MolAtom, MolBond, or MolAtom[2] for incipient bond).

getSinkAtom() - Method in class chemaxon.struc.graphics.MEFlow

Gets the atom at the sink of this arrow.

getSinkAtoms() - Method in class chemaxon.struc.graphics.MEFlow

Gets the atom or atoms at the arrow sink.

getSinkBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets the bond at the sink of this arrow.

getSize() - Method in class chemaxon.marvin.view.MDocStorage

Gets the total number of entries.

getSize() - Method in interface com.chemaxon.search.transformation.util.IntMapper

Returns the number of elements that can be mapped by IntMapper.map(int).

getSizeDouble() - Method in class chemaxon.struc.graphics.MFont

Gets the font size.

getSketchAnyBond() - Method in class chemaxon.marvin.common.UserSettings

Gets the default any bond drawing style in the sketcher.

getSketchArrowHeadLength() - Method in class chemaxon.marvin.common.UserSettings

Gets the current arrow head length.

getSketchArrowHeadWidth() - Method in class chemaxon.marvin.common.UserSettings

Gets the current arrow head width.

getSketchArrowTailLength() - Method in class chemaxon.marvin.common.UserSettings

Gets the current arrow tail length.

getSketchArrowTailWidth() - Method in class chemaxon.marvin.common.UserSettings

Gets the current arrow tail width.

getSketchCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings

Gets the default carbon displaying style in the sketcher.

getSketchColorScheme() - Method in class chemaxon.marvin.common.UserSettings

Gets the sketcher's default color scheme.

getSketchImplicitH() - Method in class chemaxon.marvin.common.UserSettings

Gets the display method of implicit hydrogens for the sketcher.

getSketchLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings

Gets the default ligand order displaying style in the sketcher.

getSketchLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings

Based on the preferences this funtion returns the proper working directory for the MarvinSketch application's load filechooser.

getSketchMode() - Method in class chemaxon.marvin.beans.MSketchPane

Gets the sketching mode.

getSketchMolbg2d() - Method in class chemaxon.marvin.common.UserSettings

Gets the sketcher's default 2D molecule background color.

getSketchMolbg3d() - Method in class chemaxon.marvin.common.UserSettings

Gets the sketcher's default 3D molecule background color.

getSketchRecentFileList() - Method in class chemaxon.marvin.common.UserSettings

Gets the recent files' list at marvinsketch, the last item is the most recent.

getSketchRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings

Gets the recent file list requested size, based on a preferences setting

getSketchRendering2d() - Method in class chemaxon.marvin.common.UserSettings

Gets the rendering style for the 2D sketcher.

getSketchRendering3d() - Method in class chemaxon.marvin.common.UserSettings

Gets the rendering style for the 3D sketcher.

getSketchSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings

Not implemented yet don't use it.

getSkip(int) - Method in class chemaxon.struc.graphics.MPolyline

Gets the distance of the (visible) head or tail from the corresponding line end point.

getSkippedIds() - Method in class chemaxon.sss.search.RgDecompResults

Returns indexes of those targets that are not matched by query.

getSkippedTargetIndexes() - Method in class chemaxon.sss.search.MarkushGenerator

Returns the target array indexes of targets that have been skipped in the last RgMolecule generation in MarkushGenerator.generate().

getSmallestRing() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the smallest ring (number of stoms) in the molecule.

getSmallestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the smallest ring size.

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

Get the smallest ring size in which the atom (specified with it's index) can be located.

getSmallestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the size of smallest ring containing the specified atom.

getSmallestRingSystem() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Identifies the smallest ring system (number of rings) in the molecule.

getSmallestRingSystemSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns the size of the smallest ring system (number of rings) in the molecule.

getSmartsMode() - Method in class chemaxon.sss.screen.StrucFPConfig

Indicates if molecule strings should be interpreted as SMARTS.

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

Gets the SMILES font size.

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

Retrieves the input molecule

getSolubility() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult

Returns the solubility value.

getSolubility(SolubilityUnit) - Method in interface com.chemaxon.calculations.solubility.SolubilityResult

Returns the solubility value.

getSolubilityCategory() - Method in interface com.chemaxon.calculations.solubility.SolubilityResult

Returns the solubility category.

getSolubilityCategory(SolubilityCategories) - Method in interface com.chemaxon.calculations.solubility.SolubilityResult

Returns the solubility category.

getSolventCount() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Gets the count of the solvents of the action

getSolventID(int) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Gets the solvent ID at the provided index

getSolventList() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Gets the custom solvent list of the action

getSortedMicrospecies(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the microspecies molecule, sorted by descreasing distribution at the given pH.

getSortedMsDistribution(int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the microspecies distribution, sorted by descreasing distribution at the given pH.

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

Gets the sorted S-groups in parent-child order.

getSortedValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin

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

Use pKaPlugin.getMacropKaValues(int, double[], int[]) instead

getSource() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

getSource() - Method in interface chemaxon.checkers.result.StructureCheckerResult

getSource() - Method in class chemaxon.struc.graphics.MEFlow

Gets the origin of the electron-flow arrow (MolAtom or MolBond).

getSourceAtom() - Method in class chemaxon.struc.graphics.MEFlow

Gets the atom at the source of this arrow.

getSourceAtoms() - Method in class chemaxon.struc.graphics.MEFlow

Gets the atom or atoms at the arrow source.

getSourceBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets the bond at the source of this arrow.

getSpecResult(Molecule, String) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

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

This method depends on the now deprecated CalculatorPlugin.getResult(Object, String) method, so this is deprecated as well and will be removed.

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

Gets the type of the set of smallest rings to use

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

Gets the Smallest Set of Smallest Ring atom indexes array.

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

Gets the Smallest Set of Smallest Ring bond indexes array.

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

Gets the Smallest Set of Smallest Ring edges as an array of BitSets, one BitSet for each ring.

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

Get SSSR bond index bitset.

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

Deprecated.

as of 15.09.2014, use MoleculeGraph.getSSSRBondSet() instead

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

Get the sssr ring indexes in which the atom (specified with it's index) can be located.

getStandardError(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin

getStandardized() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Gets the standardized molecule

getStandardizerAction(String, Map<String, String>) - Method in class chemaxon.standardizer.StandardizerActionFactory

This method creates a requested (type represented in actionId) StandardizerAction instance with the give parameters

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

Get the index number of the molecule that is the first to be displayed.

getStartLineCount() - Method in class chemaxon.marvin.io.MRecord

Gets the line number at the starting point.

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

Gets the position of the first character.

getStartPosition() - Method in class chemaxon.marvin.io.MRecord

Gets the start position in the input file.

getStartPosition() - Method in class chemaxon.struc.MDocument

Gets the starting position of this document in the input file.

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

Gets the starting position of this molecule in the input file.

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

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

Represented scan steps.

getSteps() - Method in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy

getStereo(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates absolute stereo configuration of the given atom.

getStereo(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates absolute stereo configuration of the given double bond.

getStereo1(MolAtom) - Method in class chemaxon.struc.MolBond

Gets wedge bond type relative to the specified chiral atom.

getStereo2(int, int, int, int) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.

getStereo2(MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.

getStereo2(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans (Z/E) stereo information for the given bond.

getStereo2(MolBond, MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.

getStereo2(MolBond, MolAtom, int, int, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.

getStereo2(MolBond, MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.

getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.

getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.RgMolecule

getStereoActiveAtom() - Method in class chemaxon.struc.StereoActivePart

Get the active atom index.

getStereoActiveParts() - Method in interface chemaxon.struc.CIPStereoDescriptorIface

getStereoActiveRef() - Method in class chemaxon.struc.StereoActivePart

getStereoCare() - Method in class chemaxon.struc.MolAtom

Reports double bond stereo care information on the connected bonds.

getStereoCenter() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport

Returns an optional of stereo centers.

getStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup

getStereoDoubleBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the number of stereo double bonds.

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

Returns the current ratio of the font size of the stereo label compared to the normal atom label size.

getStereoGroupNumber() - Method in class chemaxon.struc.MolAtom

Gets the stereochemical group number for AND and OR groups of the enhanced stereo representation.

getStereoGroupType() - Method in class chemaxon.struc.MolAtom

Gets the stereochemical group type for the enhanced stereo representation.

getStereoisomer(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns a stereoisomer.

getStereoisomerCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the number of different stereoisomers.

getStereoisomerCount() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

Returns the number of stereoisomers.

getStereoisomers() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns the stereoisomers in a Molecule[] array.

getStereoisomers() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

Returns the list of generated stereoisomers.

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

Get the stereo model option.

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

Get the stereo search type option.

getStereoValue() - Method in class chemaxon.struc.BicycloStereoDescriptor

Return the bicyclo stereo value.

getStereoValue() - Method in interface chemaxon.struc.CIPStereoDescriptorIface

getStericEffectIndex(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.

getStericHindrance(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Calculates hindrance of an atom from covalent radii values and distances.

getStickdst() - Method in class chemaxon.marvin.beans.MSketchPane

Gets the sticking distance.

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

Gets the stick thickness.

getStickThickness() - Method in class chemaxon.marvin.common.UserSettings

Gets the stick diameter for ball and stick mode.

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

Gets the 3D stick's diameter.

getStoichiometry() - Method in class chemaxon.standardizer.actions.ExpandAction

Gets the stoichiometry value of the action

getStoredParameters(Properties) - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Returns the stored parameters.

getStoredParameters(Properties) - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Returns the stored parameters.

getStrategy() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Returns the strategy to use.

getStrictMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum

getStrictReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms and bonds, and the neighbours' neighbouring atoms and bonds.

getString() - Method in class chemaxon.marvin.io.MRecord

Gets the record text as string.

getString() - Method in class chemaxon.struc.graphics.MFont

Gets the string representation.

getString() - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets the text string.

getString(String) - Method in class chemaxon.struc.MPropertyContainer

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

As of Marvin 5.7, replaced by MPropHandler.convertToString(MPropertyContainer, String)

getStructurallogPIncrement() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the structural logP increment.

getStructure() - Method in class chemaxon.standardizer.advancedactions.TransformAction

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

getStructure(int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns a structure.

getStructure(int) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns a resonant structure.

getStructure(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns a tautomer.

getStructureCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the number of all enumerated structures, -1 in case of arithmetical overflow (if the number would exceed Long.MAX_VALUE).

getStructureCount() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns the number of different structures.

getStructureCount() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns the number of different resonant structures.

getStructureCount() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the number of different tautomers.

getStructureID() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the structure ID used in Markush code (enumeration ID) generation.

getStructures() - Method in class chemaxon.checkers.result.SubstructureCheckerResult

Returns the structures

getStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the enumerated structures.

getStructures() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns all structures.

getStructures() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns resonant structures in Molecule[] array.

getStructures() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

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

since Marvin 5.9 replaced by TautomerizationPlugin.getStructure(int)

getStyle() - Method in class chemaxon.struc.graphics.MFont

Gets the font style.

getSubDocument(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

getSubFormatPriority(String) - Static method in class chemaxon.formats.MFileFormat

Gets the priority of the specified subformat name.

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

Gets the number of all "submolecules".

getSubGraphCount() - Method in class chemaxon.struc.RgMolecule

Gets the number of all "submolecules".

getSubGraphCount() - Method in class chemaxon.struc.RxnMolecule

Gets the number of all "submolecules".

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

Gets all "submolecules".

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

Gets all "submolecules".

getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RgMolecule

Gets all "submolecules".

getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RxnMolecule

Gets all "submolecules".

getSubLevel() - Method in class chemaxon.struc.graphics.MTextAttributes

Gets the subscript/superscript level.

getSubscript() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the subscript for non-superatom S-groups.

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

Gets the subscript for non-superatom S-groups.

getSubscript() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets the subscript.

getSubstructure() - Method in class chemaxon.descriptors.ECFPFeature

Gets the corresponding substructure as a Molecule object.

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

Gets polymer S-group subtype.

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

Gets the superatom.

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

Gets the superscript for non-superatom S-groups.

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

Gets the superscript for Sru S-groups.

getSupportedDescriptors() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider

Returns a set of supported ServiceDescriptor classes.

getSurfaceArea() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns the surface area, calculation type is previously set in MSAPlugin.setSurfaceAreaType(int).

getSurfaceArea() - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns the surface area.

getSymbol() - Method in class chemaxon.struc.MolAtom

Gets the element symbol.

getSymbol() - Method in class chemaxon.struc.sgroup.SgroupAtom

Gets the abbreviated group symbol.

getSymbol(int) - Method in class chemaxon.descriptors.PFParameters

Gets the symbol associated with the specified Pharmacophore.

getSymbol(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

getSymbol(int) - Static method in class chemaxon.struc.PeriodicSystem

Symbol of the element

getSymbolIndex(String) - Method in class chemaxon.descriptors.PFParameters

Gets the index associated with the specified Pharmacophore symbol.

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

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

Use ChemJEP.constantTable() instead.

getSymbolTable() - Method in class chemaxon.jep.Evaluator

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

Use Evaluator.constantTable() instead.

getSymmetricFBPA(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the symmetric FBPA convolution product based distasnce of the fingerprint from an other (given as parameter).

getSzegedIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Szeged index of the molecule.

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

Gets a text field value in a GridBagView table.

getT(int, int) - Method in class chemaxon.marvin.view.MDocStorage

Gets a text field in a record.

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor

Sets up the editor component.

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer

The implementation of this method sets up the rendering component to display the passed-in molecule, and then returns the component.

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer

The implementation of this method sets up the rendering component to display the passed-in molecule, and then returns the component.

getTableOptions() - Method in class chemaxon.marvin.view.swing.TableSupport

Gets the table options component.

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

Gets an object that helps to build and use a viewer table.

getTableText(String, String[], double[][]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Returns table in string form.

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

Gets the magnification in the molecule cells.

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

Gets the magnification for a molecule cell.

getTag() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the tag character for footnote display (or space if blank).

getTags() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the tags associated to the action

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

Gets the tail crossing bonds.

getTanimoto(byte[], byte[]) - Static method in class chemaxon.sss.screen.Similarity

Calculates the Tanimoto coefficient of the two bit strings.

getTanimoto(byte[], byte[], int) - Static method in class chemaxon.sss.screen.Similarity

Calculates the Tanimoto coefficient of the two bit strings.

getTanimoto(int[], int[], int) - Static method in class chemaxon.sss.screen.Similarity

Calculates the Tanimoto coefficient of the two bit strings.

getTanimoto(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the Tanimoto metric.

getTanimoto(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Gets the Tanimoto dissimilarity coefficient.

getTanimoto(ECFP) - Method in class chemaxon.descriptors.ECFP

Calculates the Tanimoto distance.

getTanimoto(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the Tanimoto metric (adapted to hystograms)

getTarget() - Method in class chemaxon.sss.formula.FormulaSearch

Gets the chemical formula of the target used to search in

getTarget() - Method in class chemaxon.sss.search.Decomposition

Returns the target.

getTarget() - Method in class chemaxon.sss.search.MolSearch

getTarget() - Method in class chemaxon.sss.search.Search

Retrieves the target molecule.

getTarget() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Gets the target structure.

getTargetAsString(Molecule) - Static method in class chemaxon.sss.search.Search

For internal purposes only.

getTargetGroups() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Gets the target action groups of the standardizer

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

Returns the target homology matching mode.

getTargets() - Method in class chemaxon.sss.search.MarkushGenerator

Returns the targets.

getTargetToPrint() - Method in class chemaxon.sss.search.Search

For internal purposes only.

getTautomerEqualityMode() - Method in class chemaxon.sss.search.MolSearchOptions

Internal use only.

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

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

Indicates if tautomers of the query should be enumerated for search.

getTautomerTransformationMode() - Method in enum class chemaxon.sss.search.options.TautomerEqualityMode

getTCenter() - Method in class chemaxon.struc.graphics.MRectangle

Gets the transformed point.

getTemplates() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

Gets the template molecules of the clean action

getTemporaryObject(String) - Method in class chemaxon.struc.MolAtom

Gets a temporary object.

getTerminalBondDeletionStyle() - Method in class chemaxon.marvin.common.UserSettings

Gets the terminal bon deletion style.

getTerms() - Method in class chemaxon.struc.graphics.MAnalysisBox

getTermsFromString(String) - Static method in class chemaxon.struc.graphics.MAnalysisBox

getText() - Method in class chemaxon.struc.graphics.MTextBox

Gets the text stored.

getTextAttributesAtCursor() - Method in class chemaxon.struc.graphics.MTextBox

Gets the common attributes of the text on the cursor.

getTextDocument() - Method in class chemaxon.struc.graphics.MTextBox

Gets the text document.

getThickness() - Method in class chemaxon.struc.graphics.MPolyline

Gets the line thickness.

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

Gets the threshold value being set for the current parametrized version.

getThreshold() - Method in class chemaxon.descriptors.MolecularDescriptor

Gets threshold value of the current parameterized metric.

getThreshold(int) - Method in class chemaxon.descriptors.MDParameters

Gets a metric dependent threshold value.

getThreshold(int) - Method in class chemaxon.descriptors.MolecularDescriptor

Gets a metric dependent default threshold value.

getThrowable() - Method in interface chemaxon.util.iterator.MoleculeIterator

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

Not used. MoleculeIterator.next() throws NoSuchElementException in case of error.

getThrowable() - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns the throwable object.

getThrowable() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns the throwable object.

getThrowable() - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns the throwable object.

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

getTimeLimit() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Gets the maximum allowed MCS search time in milliseconds.

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

The search on a single target timeouts reaching this amount of time.

getTitle() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns the frame title.

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

Returns the frame title.

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

Gets the index of the top left cell.

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

getTopMargin() - Method in class chemaxon.struc.PageSettings

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

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

This method returns an internal representation which will be hidden in the future. No replacement.

getTopologyConstraint() - Method in class com.chemaxon.search.mcs.buildup.BuildupMcs

Gets the the maximum difference in topology the mapped part of the molecules can have.

getTOption() - Method in class chemaxon.struc.graphics.MRectangle

Gets the transformation options.

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

Gets the total (formal) charge of the molecule.

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

Calculates the sum of the charge values on the atoms in this S-group.

getTotalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns the total charge of a specified atom.

getTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Deprecated.

Use HuckelAnalysisPlugin.getHMOTotalPiEnergy()

getTPSA() - Method in class chemaxon.marvin.calculations.TPSAPlugin

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

as of Marvin 4.1, replaced by TPSAPlugin.getSurfaceArea()

getTraditionalName() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns the traditional IUPAC name.

getTrainingIds() - Static method in class chemaxon.marvin.calculations.logPPlugin

Returns the id's of available logP trainings.

getTransferData(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Returns the result of the transfer operation.

getTransferDataFlavors() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Returns the DataFlavors supported by the actual implementation.

getTransform() - Method in class chemaxon.standardizer.advancedactions.TransformAction

Gets the transformation molecule of the action

getTransformedGraphics() - Method in class chemaxon.struc.graphics.MTextBoxTransformation

getTversky(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the Tversky !!DISSIMILARITY!! index: (1-(commonly used tversky))

getTversky(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the Tversky !!DISSIMILARITY!! index

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

Gets Tversky alpha value for the given parametrized metric.

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

Gets Tversky beta value for the given parametrized metric.

getType() - Method in class chemaxon.checkers.AromaticityErrorChecker

Returns the type of the aromatization

getType() - Method in class chemaxon.descriptors.SDParameters

getType() - Method in class chemaxon.marvin.services.ServiceArgument

Returns the argument type

getType() - Method in class chemaxon.marvin.util.OptionDescriptor

Gets the option type.

getType() - Method in class chemaxon.sss.search.MarkushFeature

Deprecated.

Returns the feature type.

getType() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

Gets the type of absolute stereo action

getType() - Method in class chemaxon.standardizer.actions.AromatizeAction

Gets the type of aromatization

getType() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the type of the action as string.

getType() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

Gets the type of action

getType() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Gets the type value of the action

getType() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

Gets the type of action

getType() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

Gets the type of action

getType() - Method in class chemaxon.standardizer.advancedactions.TransformAction

Gets the type of transformation

getType() - Method in interface chemaxon.struc.CIPStereoDescriptorIface

getType() - Method in class chemaxon.struc.graphics.MBracket

Gets the bracket type.

getType() - Method in class chemaxon.struc.graphics.MRArrow

Returns the type of this arrow.

getType() - Method in class chemaxon.struc.MolBond

Gets the bond type.

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

Gets S-group type.

getType() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo

Gets the type of enhanced stereo flag.

getType(int) - Method in class chemaxon.descriptors.BCUTParameters

Gets the type of the BCUT descriptor.

getType(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Checks whether the atoms in the selection are all in reactants, products or agents.

getType(String) - Static method in enum class chemaxon.sss.search.options.TautomerEqualityMode

getType(String) - Static method in enum class chemaxon.struc.SgroupType

Returns an SgroupType for the given short name.

getTypeCount() - Method in class chemaxon.descriptors.BCUTParameters

Gets the count of descriptor types.

getTypes() - Method in class chemaxon.checkers.AtomTypeChecker

Returns the checked atom types

getTypeString(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

getTypeString(Object) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Returns a string representation of the given type.

getTypeString(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns a string representation of the given type.

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

Returns undefined R atom matching behavior mode.

getUndefinedrsChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets the undefined (r) and (s) stereo centers of the molecule

getUndefinedRSChiralCenters(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets the undefined (R) and (S) chiral centers of the molecule

getUndo() - Method in class chemaxon.marvin.beans.MSketchPane

Gets the maximum undo depth.

getUnguessableFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil

Gets the file format from the file name extension for formats that are not guessable from the file content.

getUnit() - Method in class chemaxon.calculations.dipole.DipoleResult

Returns the dipole moment unit.

getUnit() - Method in class chemaxon.calculations.nmr.Multiplet

Return the unit.

getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Gets the NMR unit.

getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator

Returns NMR spectrum unit.

getUnit() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the unit type.

getUnits() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the unit of this data field.

getUpperLeftPoint() - Method in class chemaxon.struc.PageSettings

getUpperLimit() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

getUpperLimit() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory

getUpperLimit() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory

The upper limit of category.

getURL() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns the service URL

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

Returns the user defined comparators.

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

Gets the user settings object.

getUserTypes() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the user defined result types.

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

Getter for vague bond level.

getValence() - Method in class chemaxon.struc.MolAtom

Gets the valence.

getValence(int) - Method in interface chemaxon.struc.Smolecule

Gets the valence.

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

Returns the options for valence checking.

getValenceCheckOptions() - Method in class chemaxon.struc.RgMolecule

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

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

As of Marvin 6.0, replaced by MoleculeGraph.getValenceCheckOptions() and MoleculeGraph.isValenceCheckEnabled().
Usage:

 // Same as getValenceCheckState() == ValenceCheckState.OFF:
 isValenceCheckEnabled() == true;
 // Same as getValenceCheckState() == ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED:
 getValenceCheckOptions.isLocalAromatic() == true;
 // Same as getValenceCheckState() == ValenceCheckState.FULL:
 getValenceCheckOptions.isLocalAromatic() == false;
             

getValenceProp() - Method in class chemaxon.struc.MolAtom

Gets the valence property.

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

Gets the valence property of the given atom.

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

Gets the valence property of the given atom.

getValencePropMinMax() - Method in class chemaxon.struc.MolAtom

Gets the minimum and maximum possible values of the valence property.

getValidSinkAtomPairsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom) .

getValidSinkAtomPairsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond) .

getValidSinkAtomsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom) .

getValidSinkAtomsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond) .

getValidSinkBondsForMolecule(Molecule, MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom) .

getValidSinkBondsForMolecule(Molecule, MolBond) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond) .

getValidSourceAtomPairsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtomPairs(Molecule) .

getValidSourceAtomsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtoms(Molecule) .

getValidSourceBondsForMolecule(Molecule) - Static method in class chemaxon.struc.graphics.MEFlow

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

As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceBonds(Molecule) .

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

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

Use ChemJEP.evaluate_double(ChemContext) instead.

getValue() - Method in class chemaxon.marvin.services.ServiceArgument

Returns the argument value

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

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

As of Marvin 14.9.15, replaced by AtropStereoCenter.getCIPValue().

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

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

As of Marvin 14.9.15, replaced by AxialStereoCenter.getCIPValue().

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

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

As of Marvin 14.9.15, replaced by CisTransStereoCenter.getCIPValue().

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

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

As of Marvin 14.9.15, replaced by StereoCenter.getCIPValue().

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

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

As of Marvin 14.9.15, replaced by TetrahedralStereoCenter.getCIPValue().

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

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

Use ChemJEP.evaluate(ChemContext) instead.

getValueAt(double) - Method in class chemaxon.calculations.nmr.Multiplet

Returns the value of the multiplet function at a given point.

getValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns the value of the NMR spectrum function at a given x point.

getVanDerWaalsRadius(int) - Static method in class chemaxon.struc.PeriodicSystem

Van der Waals radius of the element in Angstroms.

getVariable(String) - Method in interface chemaxon.jep.ChemContext

Returns the value of a variable.

getVDWSA() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns van der Waals surface area.

getVersion() - Static method in class com.chemaxon.version.VersionInfo

Returns the product version.

getVerticalAlignment() - Method in class chemaxon.struc.graphics.MTextBox

Gets the vertical alignment.

getViewAnyBond() - Method in class chemaxon.marvin.common.UserSettings

Gets the default any bond drawing style in the viewer.

getViewCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings

Gets the default carbon displaying style in the viewer.

getViewColorScheme() - Method in class chemaxon.marvin.common.UserSettings

Gets the viewer's default color scheme.

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

Gets the view handler type.

getViewImplicitH() - Method in class chemaxon.marvin.common.UserSettings

Gets the display method of implicit hydrogens for the viewer.

getViewLayout() - Method in class chemaxon.marvin.common.UserSettings

Gets the table layout of the Viewer.

getViewLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings

Gets the default ligand order displaying style in the viewer.

getViewLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings

Based on the preferences this funtion returns the proper working directory for the MarvinView application's load filechooser.

getViewMolbg2d() - Method in class chemaxon.marvin.common.UserSettings

Gets the viewer's default molecule background color for 2D.

getViewMolbg3d() - Method in class chemaxon.marvin.common.UserSettings

Gets the viewer's default molecule background color for 3D.

getViewNavmode2d() - Method in class chemaxon.marvin.common.UserSettings

Gets the navigation mode for the 2D viewer.

getViewNavmode3d() - Method in class chemaxon.marvin.common.UserSettings

Gets the navigation mode for the 3D viewer.

getViewRecentFileList() - Method in class chemaxon.marvin.common.UserSettings

Gets the recent files' list in MarvinView, the last item is the most recent.

getViewRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings

Gets the recent file list requested size, based on a preferences setting

getViewRendering2d() - Method in class chemaxon.marvin.common.UserSettings

Gets the rendering style for the 2D viewer.

getViewRendering3d() - Method in class chemaxon.marvin.common.UserSettings

Gets the rendering style for the 3D viewer.

getViewSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings

Not implemented yet, don't use it.

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

Gets the i-th button in the visible area of the viewer.

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

Gets the i-th checkbox in the visible area of the viewer.

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

Gets the canvas of the specified cell in a GridBag layout based table.

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

Gets the number of the visible cells in a GridBag layout based table.

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

Determines the visible cell index of a cell

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

Returns the coordinates of the given atom (contained in the molecule).

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

Returns the coordinates of the given atom (contained in the molecule).

getVisiblePointRef(int, CTransform3D) - Method in class chemaxon.struc.graphics.MBracket

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

getVisiblePointRefCount() - Method in class chemaxon.struc.graphics.MBracket

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

getVisualizable() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

For internal use only.

getVolume() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

getVolume() - Method in class chemaxon.marvin.calculations.GeometryPlugin

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

Calculates the volume score between the current orientation and conformation of the two molecules.

getVolumeTanimoto() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

getWarningMessage() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

Returns the calculation warning information message.

getWarningMessage() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns a warning message if there are no conformers, null otherwise.

getWarningMessage() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns a warning message if lowest energy conformer calculation was unsuccessful or aborted by user, null otherwise.

getWarningMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns the calculation warning information message if no H-bond donor/acceptor atoms found, returns the empty string otherwise.

getWarningMessage() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns the calculation warning information message.

getWarningMessage() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the calculation warning information message if no isoelectric point exists, returns the empty string otherwise.

getWarningMessage() - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the calculation warning message.

getWarningMessage() - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the calculation warning message.

getWarningMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the calculation warning information message.

getWarningMessage() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns a warning message if there are no stereoisomers, null otherwise.

getWarningMessage() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

getWarningMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the calculation warning information message.

getWebServiceName() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Returns the service name

getWeightedAsymmetricEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the weighted asymmetric Euclidean distance.

getWeightedAsymmetricEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Calculates the weighted asymmetric Euclidean distance.

getWeightedAsymmetricEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP

Calculates the weighted asymmetric Euclidean distance.

getWeightedAsymmetricEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the weighted asymmetric Euclidean distance.

getWeightedEuclidean(BCUT) - Method in class chemaxon.descriptors.BCUT

Calculates the weighted Euclidean distance.

getWeightedEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Calculates the weighted Euclidean distance.

getWeightedEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor

Calculates the weighted Euclidean distance.

getWeightedEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP

Calculates the weighted Euclidean distance.

getWeightedEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the weighted Euclidean distance.

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

Gets all weights for the given parametrized metric.

getWeights() - Method in class chemaxon.struc.graphics.MAtomSetPoint

Gets the atom weights used in average location calculation.

getWidth() - Method in class chemaxon.struc.PageSettings

getWienerIndex() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.

getWienerPolarity() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.

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

Gets the magnification in the zoom windows.

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

Gets the line thickness for wireframe mode.

getWireThickness() - Method in class chemaxon.marvin.common.UserSettings

Gets the bond thickness in wireframe mode.

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

Gets the line thickness for wireframe mode.

getWord(ByteBuffer, int) - Method in class chemaxon.marvin.io.PositionedInputStream

getWrapperException(Exception) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Returns a wrapper exception to be returned.

getWrapperException(Exception) - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit

Returns a wrapper exception to be returned.

getWrongLengthBonds() - Method in class chemaxon.checkers.result.BondLengthCheckerResult

Returns the internal representation of the bond length checker result, which contains all information required to fix bond length errors.

getWsdlURI() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Returns the WSDL URI

getX() - Method in class chemaxon.struc.MolAtom

Gets the X coordinate.

getX() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the X coordinate.

getXMLTokens() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Gets the XML tokens of the action

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

Gets the expanded/contracted state.

getY() - Method in class chemaxon.struc.MolAtom

Gets the Y coordinate.

getY() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets the Y coordinate.

getZ() - Method in class chemaxon.struc.MolAtom

Gets the Z coordinate.

gFuzzyIncrements - Variable in class chemaxon.descriptors.PFParameters

Fuzzy smoothing values for gaussian smoothing.

GLOBAL - Static variable in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

An options object with ValenceCheckOptions.isLocalAromatic() returning false and ValenceCheckOptions.isTraditionalNitrogensAllowed() returning true.

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

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

Identifier of parameter: "grinv".

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

Identifier of parameter: "grinvVisible".

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

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

Identifier of parameter: sketchGridVisible property.

GRINV_DONT_STORE - Static variable in class chemaxon.struc.MoleculeGraph

Graph invariant option to instruct that the graph invariant should not be stored in MoleculeGraph.

GRINV_NOHYDROGEN - Static variable in class chemaxon.struc.MoleculeGraph

Graph invariant option for ignoring explicit hydrogens.

GRINV_OLDSTEREO - Static variable in class chemaxon.struc.MoleculeGraph

Graph invariant option for calculating graph invariants using the old stereo method.

GRINV_STEREO - Static variable in class chemaxon.struc.MoleculeGraph

Graph invariant option for calculating graph invariants using stereo information.

GRINV_USEMAPS - Static variable in class chemaxon.struc.MoleculeGraph

Graph invariant option for calculating graph invariants considering atom maps also.

GRINV_VALUE_OPTIONS - Static variable in class chemaxon.struc.MoleculeGraph

Unified mask of graph invariant options affecting grinv value.

grinvCC - Variable in class chemaxon.struc.MoleculeGraph

Graph invariant change count.

GROUP_END_TOKEN - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

End of group list token of the action string

GROUP_LIST_KEY - Static variable in class chemaxon.standardizer.advancedactions.CreateGroupAction

Property key for group list modification

GROUP_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Group entry separator token of the action string

GROUP_START_TOKEN - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Start of group list token of the action string

GroupDefinition - Class in chemaxon.standardizer.advancedactions

Pattern of a group.

GroupDefinition() - Constructor for class chemaxon.standardizer.advancedactions.GroupDefinition

Creates an empty group pattern.

GroupDefinition(String, Molecule) - Constructor for class chemaxon.standardizer.advancedactions.GroupDefinition

Creates a new group pattern.

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

Result type with the string id "groupeddotdisconnectedformula".

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

guessFormat(String) - Method in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated.

guessFormat(String) - Method in class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated.

guessFormat(String) - Method in class chemaxon.formats.recognizer.Recognizer

Tries to guess the format of the given line.

guessFormat(String) - Method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated.

MODIFIING THIS METHOD REQUIRES TO UPDATE THE SMILESRecognizer.tryToRecognize(String, int) METHOD AS WELL!!

guessPeptideFormat(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer

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

GZIP - Static variable in class chemaxon.formats.MFileFormat

GZIP compressed file.

H

H - Static variable in class chemaxon.core.ChemConst

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

H_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator

Name of the 1H chemical shift atom property.

H1 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus

1H NMR

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

Number of heavy atoms.

HAcc - Class in chemaxon.descriptors.scalars

Implements hydrogen bond acceptor atom count as a scalar descriptor.

HAcc() - Constructor for class chemaxon.descriptors.scalars.HAcc

Creates a new, empty HAcc descriptor.

HAcc(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.HAcc

Copy constructor.

HAcc(HBParameters) - Constructor for class chemaxon.descriptors.scalars.HAcc

Creates a new instance according to the parameters given.

HAcc(String) - Constructor for class chemaxon.descriptors.scalars.HAcc

Creates a new instance according to the parameters given.

HALOAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

HALT - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy

Halts standardization process in case of standardization error

HaltOnErrorOption - Enum Class in chemaxon.sss.search.options

Option type describing the error handling behaviour.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ChargePlugin

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

This plugin handles multifrag molecules.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if the plugin handles multifragment molecules, false otherwise.

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

Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.

hasAlternativeName() - Method in class chemaxon.struc.sgroup.SgroupAtom

Checks whether there is an alternative name at all.

hasAromaticBond() - Method in class chemaxon.struc.MolAtom

Tests whether the atom has aromatic bonds.

hasAtom() - Method in class chemaxon.struc.graphics.MElectron

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

Is the specified atom an element of this group?

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

Is the specified atom an element of this group?

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

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

Tests whether the molecule graph has atom sets.

hasAtomSet() - Method in class chemaxon.struc.RgMolecule

Tests whether the molecule graph has atom sets.

hasAtomSet() - Method in class chemaxon.struc.RxnMolecule

Tests whether the molecule graph has atom sets.

HasAttachedDataFilter - Class in com.chemaxon.calculations.stereoanal.filters

Filter stereo centers which contains attached data.

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

hasBackground() - Method in class chemaxon.struc.graphics.MBracket

A bracket has no background.

hasBackground() - Method in class chemaxon.struc.graphics.MPolyline

A polyline has a background only if it is closed.

hasBackground() - Method in class chemaxon.struc.graphics.MTextBox

A text box has a background always.

hasBackground() - Method in class chemaxon.struc.MObject

Can the object have a background?

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

Tests whether the molecule graph has atom sets.

hasBondSet() - Method in class chemaxon.struc.RgMolecule

Tests whether the molecule graph has atom sets.

hasBondSet() - Method in class chemaxon.struc.RxnMolecule

Tests whether the molecule graph has atom sets.

hasBrackets() - Method in class chemaxon.struc.sgroup.DataSgroup

Brackets are painted if mouse runs over sgroup atoms.

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

Checks if brackets should be painted or not.

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

Does a bracket belong to this sgroup?

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

Checks if brackets should be painted or not.

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

Used in initializing searches.

hasCharge() - Method in class chemaxon.struc.MolAtom

hasColor() - Method in class chemaxon.struc.graphics.MPolyline

A polyline does not have a non-line, non-background color.

hasColor() - Method in class chemaxon.struc.graphics.MTextBox

A text box has a text color.

hasColor() - Method in class chemaxon.struc.MObject

Can the object have a color (non-line and non-background)?

hasContainerFreeMElectron() - Method in class chemaxon.struc.graphics.MElectronContainer

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

Tests if the molecule has contracted S-groups or not.

hasDistanceRanges() - Method in class chemaxon.marvin.alignment.ShapeData

hasElectronContainer(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct

hasElectrons() - Method in class chemaxon.struc.MDocument

Returns whether MDocument contains any electrons.

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

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

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

hasExplicitLonePairs() - Method in class chemaxon.struc.MDocument

Returns true if the MDocument has any electrons drawn by the user.

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

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

use MDocument.hasExplicitLonePairs() instead

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

hasFace() - Method in class chemaxon.struc.graphics.MPolyline

Is it 2 dimensional?

hasFace() - Method in class chemaxon.struc.graphics.MTextBox

Is it 2 dimensional?

hashCode() - Method in class chemaxon.calculations.pka.PKaTrainingResult

hashCode() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

hashCode() - Method in class chemaxon.checkers.AbstractStructureChecker

hashCode() - Method in class chemaxon.checkers.AromaticityErrorChecker

hashCode() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

hashCode() - Method in class chemaxon.checkers.AttachedDataChecker

hashCode() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

hashCode() - Method in class chemaxon.checkers.result.AromaticityCheckerResult

hashCode() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult

hashCode() - Method in class chemaxon.checkers.result.BondAngleCheckerResult

hashCode() - Method in class chemaxon.checkers.result.BondLengthCheckerResult

hashCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult

hashCode() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

hashCode() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult

hashCode() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

hashCode() - Method in class chemaxon.checkers.result.ReactionCheckerResult

Deprecated.

hashCode() - Method in class chemaxon.checkers.result.RgroupCheckerResult

hashCode() - Method in class chemaxon.checkers.result.SgroupCheckerResult

hashCode() - Method in class chemaxon.checkers.result.SubstructureCheckerResult

hashCode() - Method in class chemaxon.checkers.StructureCheckerDescriptor

hashCode() - Method in class chemaxon.checkers.util.AtomLabels

hashCode() - Method in class chemaxon.checkers.util.DataExclusionList

hashCode() - Method in class chemaxon.checkers.ValencePropertyChecker

hashCode() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

hashCode() - Method in class chemaxon.fixers.StructureFixerDescriptor

hashCode() - Method in class chemaxon.marvin.io.Encoding

hashCode() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

hashCode() - Method in class chemaxon.sss.search.Decomposition

hashCode() - Method in class chemaxon.sss.search.MarkushFeature

Deprecated.

hashCode() - Method in class chemaxon.sss.search.SearchHit

hashCode() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

hashCode() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

hashCode() - Method in class chemaxon.struc.AtropStereoDescriptor

hashCode() - Method in class chemaxon.struc.AxialStereoDescriptor

hashCode() - Method in class chemaxon.struc.CisTransStereoDescriptor

hashCode() - Method in class chemaxon.struc.CTransform3D

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

hashCode() - Method in class chemaxon.struc.graphics.MAtomSetPoint

hashCode() - Method in class chemaxon.struc.graphics.MEFlowBasePoint

hashCode() - Method in class chemaxon.struc.graphics.MElectron

hashCode() - Method in class chemaxon.struc.graphics.MElectronContainer

hashCode() - Method in class chemaxon.struc.graphics.MFont

hashCode() - Method in class chemaxon.struc.graphics.MMidPoint

hashCode() - Method in class chemaxon.struc.graphics.MRectanglePoint

hashCode() - Method in class chemaxon.struc.graphics.MTextAttributes

hashCode() - Method in class chemaxon.struc.MPoint

hashCode() - Method in class chemaxon.struc.prop.MBooleanProp

hashCode() - Method in class chemaxon.struc.prop.MCollectionProp

hashCode() - Method in class chemaxon.struc.prop.MDoubleArrayProp

hashCode() - Method in class chemaxon.struc.prop.MDoubleProp

hashCode() - Method in class chemaxon.struc.prop.MFontProp

hashCode() - Method in class chemaxon.struc.prop.MHashProp

hashCode() - Method in class chemaxon.struc.prop.MHCoords3DProp

hashCode() - Method in class chemaxon.struc.prop.MIntegerArrayProp

hashCode() - Method in class chemaxon.struc.prop.MIntegerProp

hashCode() - Method in class chemaxon.struc.prop.MListProp

hashCode() - Method in class chemaxon.struc.prop.MMoleculeProp

hashCode() - Method in class chemaxon.struc.prop.MMoleculeStringProp

hashCode() - Method in class chemaxon.struc.prop.MObjectProp

hashCode() - Method in class chemaxon.struc.prop.MStringProp

hashCode() - Method in class chemaxon.struc.RgroupBridgeId

hashCode() - Method in class chemaxon.struc.StereoActivePart

hashCode() - Method in class chemaxon.struc.TetrahedralStereoDescriptor

HashCode - Class in chemaxon.sss.screen

Hash code generator for molecules.

HashCode() - Constructor for class chemaxon.sss.screen.HashCode

Creates a new instance of HashCode

HASHED - Static variable in class chemaxon.struc.MolBond

"Hashed" attribute of the bond.

hasId(String) - Method in class chemaxon.struc.Molecule

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

Tests whether the molecule has implicit hydrogen atoms.

hasLineColor() - Method in class chemaxon.struc.graphics.MPolyline

A polyline have a line color always.

hasLineColor() - Method in class chemaxon.struc.MObject

Can the object have a line color?

hasMoreStructures() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns true if there are more structures.

hasNext() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer

Returns true if there are more molecules, false if end has been reached.

hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator

Decides whether the iteration has more element.

hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator

Decides whether the iteration has more element.

hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Decides whether the iteration has more element.

hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator

Decides whether the iteration has more element.

hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator

Decides whether the iteration has more element.

hasNext() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator

Decides whether the iteration has more element.

hasNext() - Method in interface chemaxon.util.iterator.MoleculeIterator

Tests whether the iteration has more elements.

hasNextResult() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Returns whether there are more results available.

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

Decides whether the central atom of the sgroup has a non-coordinate bond.

hasOrder(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

hasOutline() - Method in class chemaxon.struc.graphics.MPolyline

Does it have an outline?

hasParameters(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Returns true if plugin has parameter panel, false otherwise.

hasQProps() - Method in class chemaxon.struc.MolAtom

Does it have query properties?

hasQueryBonds() - Method in class chemaxon.struc.MolAtom

Tests whether the atom has query bonds ("ANY" bonds).

hasRadicals() - Method in class chemaxon.struc.MDocument

Returns true if the MDocument has any Radical Electrons.

hasResults() - Method in class chemaxon.sss.search.RgDecompResults

hasRgroupContainedBy(Set<?>) - Method in class chemaxon.struc.RgMolecule

Tests whether the molecule has an R-group that is a subset of the specified set of atoms.

hasRichText() - Method in class chemaxon.struc.graphics.MTextBox

Tests whether the document is rich text.

hasSameCharge(int) - Method in class chemaxon.struc.MolAtom

hasSelection() - Method in class chemaxon.struc.graphics.MChemicalStruct

Checks the existence of the selection.

hasSelection() - Method in class chemaxon.struc.graphics.MMoleculeMovie

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

hasSelection() - Method in class chemaxon.struc.graphics.MTextBox

Checks the existence of the selection.

hasSelection(MoleculeGraph) - Static method in class chemaxon.struc.graphics.MChemicalStruct

Checks the existence of the selection.

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

Tests whether the property list contains the molecule.

hasSMARTSProps() - Method in class chemaxon.struc.MolAtom

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

As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)

hasSMARTSProps(MolAtom) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Tests whether it is a SMARTS query atom.

hasSMARTSPropsExcluding(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Tests whether it is a SMARTS query atom.

hasSMARTSPropsExcluding(String) - Method in class chemaxon.struc.MolAtom

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

As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)

hasTautomers(Molecule) - Static method in class chemaxon.marvin.calculations.TautomerizationPlugin

Returns if a molecule has tautomers.

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

Gets whether searcher has user defined comparators.

hasValenceError() - Method in class chemaxon.struc.MolAtom

Returns previously set valence error.

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

Determines if this molecule has a valence error on any of its atoms.

hasValenceError() - Method in class chemaxon.struc.sgroup.SgroupAtom

Checks if any atom of the Sgroup has a valence error.

hasValidConformer() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Returns true if the input molecule has a valid conformer (has a valid structure in 3D space).

hasWedgedBond() - Method in class chemaxon.struc.MolAtom

Tests whether the atom has a wedged bond.

hasWiggly(MolAtom) - Static method in class chemaxon.marvin.util.CleanUtil

Check if at least one wiggly bond starts from this atom.

haveEqualProperties(MolAtom) - Method in class chemaxon.struc.MolAtom

Tests if two atoms have the same properties.

haveEqualProperties(MolBond) - Method in class chemaxon.struc.MolBond

Tests whether two bonds have the same properties.

haveEqualProperties(MolBond) - Method in class chemaxon.struc.QueryBond

Checks if two bonds have the same properties.

haveSimilarBonds(MolAtom) - Method in class chemaxon.struc.MolAtom

Checks if two atoms have similar bonds.

HBD - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Number of hydrogen-bond donors.

HBDA - Enum constant in enum class chemaxon.calculator.CalculatorTag

HBDA_MICROSPECIES - Enum constant in enum class chemaxon.calculator.CalculatorTag

HBDAPlugin - Class in chemaxon.marvin.calculations

Plugin class for H bond acceptor/donor calculation.

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

Constructor.

HBONDED_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom wtih a MolBond.HYDROGEN bond on it.

HBParameters - Class in chemaxon.descriptors.scalars

Manages parameters for the HDon and HAcc scalar descriptor classes.

HBParameters() - Constructor for class chemaxon.descriptors.scalars.HBParameters

Creates an empty object.

HBParameters(File) - Constructor for class chemaxon.descriptors.scalars.HBParameters

Creates a new object based on a given configuration file.

HBParameters(String) - Constructor for class chemaxon.descriptors.scalars.HBParameters

Creates a new object based on a given configuration string.

HCONNECTED_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom(s) connected to another hydrogen only.

HCOUNT_MATCHING_AUTO - Static variable in interface chemaxon.sss.SearchConstants

Default option for H count matching (setHCountMatching).

HCOUNT_MATCHING_EQUAL - Static variable in interface chemaxon.sss.SearchConstants

Option for H count matching.

HCOUNT_MATCHING_GREATER_OR_EQUAL - Static variable in interface chemaxon.sss.SearchConstants

Option for H count matching.

HDon - Class in chemaxon.descriptors.scalars

Implements hidrogen bond donor atom count as a scalar descriptor.

HDon() - Constructor for class chemaxon.descriptors.scalars.HDon

Creates a new, empty HDon descriptor.

HDon(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.HDon

Copy constructor.

HDon(HBParameters) - Constructor for class chemaxon.descriptors.scalars.HDon

Creates a new instance according to the parameters given.

HDon(String) - Constructor for class chemaxon.descriptors.scalars.HDon

Creates a new instance according to the parameters given.

He - Static variable in class chemaxon.core.ChemConst

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

Arrow head.

HEADER_MAP - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for header type: header with any atoms mapped by Rgroup indexes.

HEADER_NONE - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for header type: no header.

HEADER_RGROUP - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for header type: header with Rgroup atoms (cannot be exported to SMILES).

Heavy - Class in chemaxon.descriptors.scalars

Implements HeavyAtomCount (number of non-hydrogen atoms) as a scalar descriptor.

Heavy() - Constructor for class chemaxon.descriptors.scalars.Heavy

Creates a new, empty logD descriptor.

Heavy(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.Heavy

Copy constructor.

Heavy(SDParameters) - Constructor for class chemaxon.descriptors.scalars.Heavy

Creates a new instance according to the parameters given.

Heavy(String) - Constructor for class chemaxon.descriptors.scalars.Heavy

Creates a new instance according to the parameters given.

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

Heavy atom count of the molecule

heavyAtomLimit(int) - Static method in interface chemaxon.calculator.CalculatorInputChecker

Creates a new input checker that only accepts molecules with at most the given number of heavy atoms.

help - Variable in class chemaxon.checkers.StructureCheckOptions

Help needs to be printed.

HELP_TEXT - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

help text for checker

HELP_TEXT - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

help text for action

helpCheckerAction - Variable in class chemaxon.checkers.StructureCheckOptions

Checker action help needs to be printed.

helpFixerAction - Variable in class chemaxon.checkers.StructureCheckOptions

Fixer action help needs to be printed.

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

Returns the help text of the checker

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

Returns the help text of the action

HergActivityPredictor - Class in com.chemaxon.calculations.admet

hERG activity predictor.

HergClass - Enum Class in com.chemaxon.calculations.admet

The possible values of hERG class prediction.

HergClassPredictor - Class in com.chemaxon.calculations.admet

hERG class predictor.

HETERO - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the hetero any atom Q.

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

Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).

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

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

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

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

Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).

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

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

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

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

Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).

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

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

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

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

Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).

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

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

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

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

Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing non-carbon atoms).

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

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

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

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

Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).

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

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

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

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

Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).

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

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

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

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

Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).

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

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

as of release 5.5, replaced by Ring.heteroaromaticRings(int)

heteroRingCount() - Method in class chemaxon.calculations.Ring

Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

heteroRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.heteroRingCount()

heteroRingCount(int) - Method in class chemaxon.calculations.Ring

Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

heteroRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.heteroRingCount(int)

heteroRings() - Method in class chemaxon.calculations.Ring

Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).

heteroRings() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.heteroRings()

heteroRings(int) - Method in class chemaxon.calculations.Ring

Indentifies hetero rings in the molecule having a given size (number of atoms).

heteroRings(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.heteroRings(int)

Hf - Static variable in class chemaxon.core.ChemConst

Hg - Static variable in class chemaxon.core.ChemConst

HIDDEN - Static variable in class chemaxon.struc.sgroup.DataSgroup

Specifies that the data sgroup is hidden.

hierarchize() - Method in class chemaxon.struc.MPropertyContainer

Converts hierarchically specified RDF properties to MListProp and MHashProp objects.

HIGH - Enum constant in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

High solubility.

HIGH_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor

high priority value

HIGHEST_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor

the highest priority value

highestEigenvalues - Variable in class chemaxon.descriptors.BCUT

highlight(MObject) - Method in class chemaxon.struc.MDocument

Highlight an object.

HIT_EXCLUDEDQ - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting excluded query atom.

HIT_LP - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting isolated lone-pair match.

HIT_MULTICENTER - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting multicenter atoms in query.

HIT_NON_R - Static variable in interface chemaxon.sss.SearchConstants

Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.

HIT_ORDERING_NONE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

HIT_R - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting R-node matches in case of R-group search.

HIT_R_EMPTY_MATCH - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting R-node empty match.

HIT_UNMAPABLE - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting unmapable atoms in query (e.g.

HlbPlugin - Interface in chemaxon.marvin.calculations

Calculates hydrophilic-lipophilic balance (HLB) of a molecule.

HlbPlugin.Builder - Class in chemaxon.marvin.calculations

Builder class for HlbPlugin.

Ho - Static variable in class chemaxon.core.ChemConst

HomologyTranslationOption - Enum Class in chemaxon.sss.search.options

Option type describing the scope of homology matching.

Hs - Static variable in class chemaxon.core.ChemConst

HS_S - Static variable in interface chemaxon.struc.HybridizationStateConsts

S hybridization state.

HS_S - Static variable in class chemaxon.struc.MolAtom

S hybridization state.

HS_SP - Static variable in interface chemaxon.struc.HybridizationStateConsts

SP hybridization state.

HS_SP - Static variable in class chemaxon.struc.MolAtom

SP hybridization state.

HS_SP2 - Static variable in interface chemaxon.struc.HybridizationStateConsts

SP2 hybridization state.

HS_SP2 - Static variable in class chemaxon.struc.MolAtom

SP2 hybridization state.

HS_SP3 - Static variable in interface chemaxon.struc.HybridizationStateConsts

SP3 hybridization state.

HS_SP3 - Static variable in class chemaxon.struc.MolAtom

SP3 hybridization state.

HS_UNKNOWN - Static variable in interface chemaxon.struc.HybridizationStateConsts

Unknown hybridization state.

HS_UNKNOWN - Static variable in class chemaxon.struc.MolAtom

Unknown hybridization state.

HTML - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

HTML - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Property display type: display in html text.

HTTPServiceDescriptor - Class in chemaxon.marvin.services.httpservice

HTTP Request based ServiceDescriptor implementation for HTTP POST/GET based services

HTTPServiceDescriptor() - Constructor for class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor

Constructs a HTTPServiceDescriptor

HTTPServiceHandler - Class in chemaxon.marvin.services.httpservice

ServiceHandler implementation for HTTP Services

HTTPServiceHandler() - Constructor for class chemaxon.marvin.services.httpservice.HTTPServiceHandler

HuckelAnalysisPlugin - Class in chemaxon.marvin.calculations

Plugin class for Huckel Analysis calculation.

HuckelAnalysisPlugin() - Constructor for class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Constructor.

HybridizationStateConsts - Interface in chemaxon.struc

Hybridization state constants.

HYDR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

HYDROGEN - Enum constant in enum class chemaxon.struc.BondType

Hydrogen bond type.

HYDROGEN - Static variable in class chemaxon.struc.MolBond

Hydrogen bond type.

HydrogenData(MolAtom, int, int, int) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

hydrogenize - Variable in class chemaxon.marvin.io.MolExportModule

Add Hydrogen atoms if 1, remove if -1, do nothing if 0.

hydrogenize(boolean) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph) and Hydrogenize.convertExplicitHToImplicit(MoleculeGraph).

hydrogenize(int, String, boolean, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Hydrogenize molecule in the specified cell.

hydrogenize(GeneralExportOptions.HydrogenizeOption) - Method in class chemaxon.formats.GeneralExportOptions.Builder

Sets the need for adding/removing explicit hydrogens.

Hydrogenize - Class in chemaxon.calculations.hydrogenize

Addition and removal of explicit hydrogens or lone pairs.

Hydrogenize() - Constructor for class chemaxon.calculations.hydrogenize.Hydrogenize

hydrogenizeAll(boolean, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Hydrogenize molecules in all cells.

hyperWienerIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the hyper Wiener index of the molecule.

Hz - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit

Hz unit

I

I - Static variable in class chemaxon.core.ChemConst

icell - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The viewer cell index (0 for sketcher).

ICON_PATH - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

icon path of checker

ICON_PATH - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

icon path of action

iconPath() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the path of the icon for the checker

iconPath() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the path of the icon for the action

id - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

id - Variable in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

id() - Method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Returns the ID of this result type.

ID - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

id property of action

ID_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction

The key of the ID parameter of the abstract action.

IDENTIFIER - Static variable in class chemaxon.naming.document.DocumentToStructure

IDENTITY - Static variable in enum class com.chemaxon.search.transformation.transformers.Aromatizer

Identity transformer.

ids - Variable in class chemaxon.descriptors.ECFP

Identifier list storage of the fingerprint

IGNORE - Enum constant in enum class com.chemaxon.search.mcs.RingHandlingMode

This option ignores the ring/chain topology of bonds, which is the default behavior.

IGNORE_CHARGE - Enum constant in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Ignore charges in the generated molecular formula.
For example: [O-]N[O+] -> NO2

IGNORE_MASS_NUMBERS - Enum constant in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

The generated molecular formula will not contain isotopic information.
For example: C5[13C]H6 -> C6H6

ignoreAtomCharges(Set<FormulaGenerationRule>) - Static method in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Returns true if the charge of each atom should be ignored in the formula based on the given rules.

ignoreConfigurationErrors - Variable in class chemaxon.checkers.StructureCheckOptions

Ignores configuration errors - errors found in input files does not cause the execution to stop on the input file, just skips the actual structure and tries the next - printing error message on the standard error

ignoreErrors - Variable in class chemaxon.checkers.StructureCheckOptions

Ignores errors - errors found in input files does not cause the execution to stop on the input file, just skips the actual structure and tries the next - printing error message on the standard error

IMAGE_IMPORT_SERVICE_URL - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier for parameter: "imageImportServiceURL" See Parameters and Events documentation.

IMAGE_SAVE_FORMAT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "imageSaveFormat".

IMAGE_SAVE_URL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "imageSaveURL".

IMAGE_SHOW_URL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "imageShowURL".

ImageExportUtil - Class in chemaxon.util

Extends ImageExportBaseUtil with additional methods.

IMPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "implicitH".

IMPLICIT_H_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for default mode.

IMPLICIT_H_MATCHING_DISABLED - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen.

IMPLICIT_H_MATCHING_ENABLED - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for indicate matching between implicit and explicit hydrogens.

IMPLICIT_H_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching.

IMPLICITIZE - Enum constant in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption

Remove explicit hydrogen atoms.

implicitizeHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int).
Usage:

             Hydrogenize.convertExplicitHToImplicit(molecule, f);
             

implicitizeHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int).
Usage:

             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
             

implicitizeHydrogens(int, MolAtom[], boolean) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:

             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             

implicitizeHydrogens0(int, MolAtom[], boolean) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:

             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             

implicitizeHydrogens0(int, MolAtom[], boolean) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:

             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             

IMPORT_CONVERSION - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "importConv".

IMPORT_ENABLED - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "importEnabled".

importDoc(byte[]) - Static method in class chemaxon.formats.MolImporter

Reads a document from a byte array.

importDoc(byte[], String, String) - Static method in class chemaxon.formats.MolImporter

Reads a document from a byte array.

importer - Variable in class chemaxon.marvin.io.formats.MoleculeImporter

The wrapped importer.

importMol(byte[]) - Static method in class chemaxon.formats.MolImporter

Read a molecule from a byte array.

importMol(byte[], Molecule) - Static method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

As of 23.15, use MolImporter.importMol(byte[]) instead

importMol(byte[], String, String) - Static method in class chemaxon.formats.MolImporter

Read a molecule from a byte array.

importMol(byte[], String, String, Molecule) - Static method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

As of 23.15, use MolImporter.importMol(byte[], String, String) instead

importMol(String) - Static method in class chemaxon.formats.MolImporter

Read a molecule from a string.

importMol(String, ImportOptions) - Static method in class chemaxon.formats.MolImporter

Read a molecule from a string with the given options.

importMol(String, Molecule) - Static method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

As of 23.15, use MolImporter.importMol(String) instead

importMol(String, String) - Static method in class chemaxon.formats.MolImporter

Read a molecule from a string.

importMol(String, String, String) - Static method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call MolImporter.importMol(String, String); if you have a byte array, call MolImporter.importMol(byte[], String, String).

importMol(String, String, String, Molecule) - Static method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

(Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call MolImporter.importMol(String, String); if you have a byte array, call MolImporter.importMol(byte[], String, String, Molecule).

importMolAndClose(InputStream) - Method in interface chemaxon.formats.ImportOptions

Imports a molecule from the given stream and closes the stream.

importNodes(Document, boolean) - Method in class chemaxon.descriptors.MDParameters

Imports nodes from the specified Document into the current (main) Document.

importNodes(Document, boolean) - Method in class chemaxon.descriptors.PFParameters

ImportOptions - Interface in chemaxon.formats

Common interface for ImportOptions classes to use in ServiceLoader.

In - Static variable in class chemaxon.core.ChemConst

IN_POPUP - Static variable in class chemaxon.marvin.swing.MAction

Popup menu item.

inc(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Increments the content of the specified hitogram bin by one.

inc(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Increments the histogram corresponding to two features ('fa'-'fb') and a distance, 'dist'.

inc(int, int, int, float[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

The fuzzy version of inc( int fa, int fb, int dist ).

inc(int, int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

The fuzzy version of inc( int fa, int fb, int dist ).

incGrinvCC() - Method in class chemaxon.struc.MoleculeGraph

Increases the graph invariant change count and sets grinv to null.

incGrinvCC(boolean) - Method in class chemaxon.struc.MoleculeGraph

incGrinvCCOnly() - Method in class chemaxon.struc.MoleculeGraph

Increases the graph invariant change count, but does not change grinv.

INCHI - Static variable in class chemaxon.formats.MFileFormat

IUPAC InChI files.

INCHIKEY - Static variable in class chemaxon.formats.MFileFormat

IUPAC InChIKey.

INCLUDE_ALL_ATOMS - Static variable in class chemaxon.util.iterator.IteratorFactory

Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.

INCLUDE_ALL_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory

Include all bonds: covalent and coordinate bonds in bond iteration.

INCLUDE_CHEMICAL_ATOMS - Static variable in class chemaxon.util.iterator.IteratorFactory

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY instead.

INCLUDE_CHEMICAL_ATOMS_ONLY - Static variable in class chemaxon.util.iterator.IteratorFactory

Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.

INCORRECT_AROMATIC_NITROGEN_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Incorrect aromatic nitrogen remark.

INCORRECT_TETRAHEDRAL_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Represents incorrect/impossible arrangement of wedge bond around chiral centers.

IncorrectTetrahedralStereoChecker - Class in chemaxon.checkers

Incorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.

IncorrectTetrahedralStereoChecker() - Constructor for class chemaxon.checkers.IncorrectTetrahedralStereoChecker

Default constructor

incQProp(String) - Method in class chemaxon.struc.MolAtom

Increments the value of a query property.

incQueryAromaticity() - Method in class chemaxon.struc.MolAtom

Increments the value of the query aromaticity property.

incValenceProp() - Method in class chemaxon.struc.MolAtom

Increments the value of the valence property.

index(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Calculates the index of the bin specified by the arguments.

indexOf(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

indexOf(MObject) - Method in class chemaxon.struc.MDocument

Searches for an object in the document or in the chemical structure that belongs to the document.

indexOf(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Gets the index of the specified atom.

indexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule

Gets the index of the specified node in the graph union.

indexOf(MolAtom) - Method in class chemaxon.struc.RxnMolecule

Gets the index of the specified node in the graph union.

indexOf(MolAtom) - Method in class chemaxon.struc.Sgroup

Gets the atom index in the S-group graph.

indexOf(MolBond) - Method in class chemaxon.struc.MolAtom

Returns the index of the specified bond in this atom.

indexOf(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Gets the index of the specified bond.

indexOf(MolBond) - Method in class chemaxon.struc.RgMolecule

Gets the index of the specified edge in the graph union.

indexOf(MolBond) - Method in class chemaxon.struc.RxnMolecule

Gets the index of the specified edge in the graph union.

indexOf(MolBond) - Method in class chemaxon.struc.Sgroup

Gets the bond index in the S-group graph.

indexOf(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom

Returns the index of the specified bond in this atom.

indexOf(Sgroup) - Method in class chemaxon.struc.Molecule

Gets the array index of an S-group.

indexOfButtonB(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane

Gets the index of the button on the visible area of the viewer.

indexOfButtonC(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane

Gets the index of the checkbox in the visible area of the viewer.

indexOfReferenced(MolBond) - Method in class chemaxon.struc.MolAtom

Returns the index of the referenced bond in this atom.

indicesOf(String) - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Gets the level and the index of the specified format.

INFO - Enum constant in enum class chemaxon.checkers.CheckerSeverity

This severity level should used for StructureChecker implementations which search for standard informations in a Molecule

init() - Method in class chemaxon.descriptors.CDParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.CFParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.ECFPParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.PFParameters

Initializes the object.

init() - Method in class chemaxon.descriptors.RFParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.SDParameters

This method is called by the constructors before processing the XML configuration.

init(MolPanel) - Method in class chemaxon.marvin.beans.MarvinPane

Initializes the content pane.

init(MolPanel, boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Initializes the content pane.

initAccelerators(JComponent) - Method in class chemaxon.marvin.swing.MAction

Initializes this action's accelerator keys for the specified component.

initAccelerators(KeyStroke[], JComponent) - Method in class chemaxon.marvin.swing.MAction

initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.3.1, replaced by SwingUtil.initAction

initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.util.SwingUtil

Initializes an action from information in a resource.

initBrackets() - Method in class chemaxon.struc.Sgroup

Initializes the list of brackets in this S-group.

initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.3.1, replaced by SwingUtil.initButton

initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil

Utility method to initialize a button from information in a resource.

initButton(AbstractButton, ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Utility method to initialize a button from information in a resource.

initCtrlShortcutForMac(JMenuItem) - Static method in class chemaxon.marvin.util.SwingUtil

Deprecated, for removal: This API element is subject to removal in a future version.

does nothing.

initEmbeddedMD() - Method in class chemaxon.descriptors.ShapeParameters

This method is called by the constructors before processing the XML configuration.

initFields() - Method in class chemaxon.marvin.view.swing.TableOptions

Initialize field information before update.

initFunTab() - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The function table will become unmodifiable. Configure the Evaluator instead before creating the ChemJEP.

initGenerator() - Method in class chemaxon.descriptors.CDParameters

This method is void in this class as custom descriptors are opaque, their internal structure is not known.

initGenerator() - Method in class chemaxon.descriptors.CFParameters

Initializes the fingerprint generator.

initGenerator() - Method in class chemaxon.descriptors.ECFPParameters

Initializes the fingerprint generator.

initGenerator() - Method in class chemaxon.descriptors.PFParameters

Creates and initializes a PFGenerator instance.

initGenerator() - Method in class chemaxon.descriptors.RFParameters

Initializes the reaction fingerprint generator.

initGenerator() - Method in class chemaxon.descriptors.ShapeParameters

INITIAL_CAPACITY - Static variable in class chemaxon.struc.MoleculeGraph

Initial capacity of the atoms and bonds vectors.

initialize() - Method in class chemaxon.checkers.ComponentChecker

Empty default implementation

initializeReader(String) - Static method in class chemaxon.standardizer.StandardizerUtil

Initializes a configuration reader based on a configuration string

initInApplet() - Static method in class chemaxon.marvin.util.SwingUtil

Deprecated, for removal: This API element is subject to removal in a future version.

does nothing.

initMolImport(MolInputStream) - Method in class chemaxon.marvin.io.formats.mdl.MolImport

Initializes the import module.

initMolImport(MolInputStream) - Method in class chemaxon.marvin.io.MolImportModule

Initializes the import module.

initMolImport(MRecord, String) - Method in class chemaxon.marvin.io.MolImportModule

Initializes the import module.

initParameters() - Method in class chemaxon.descriptors.BCUTParameters

initParameters() - Method in class chemaxon.descriptors.CDParameters

Initializes data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.CFParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.ECFPParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.MDParameters

Initializes object after configuration parameters are loaded.

initParameters() - Method in class chemaxon.descriptors.PFParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.RFParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.scalars.HBParameters

initParameters() - Method in class chemaxon.descriptors.scalars.LDParameters

initParameters() - Method in class chemaxon.descriptors.SDParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initProgressMonitor(String, int, int) - Method in interface chemaxon.common.util.MProgressMonitor

Create a progress monitor.

initSymTab() - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.

initVariables(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule

insert(int, MTextDocument) - Method in class chemaxon.struc.graphics.MTextDocument

insert(int, String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument

Inserts a string.

insertAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolAtom).

insertBond(int, MolBond) - Method in class chemaxon.struc.MolAtom

Inserts a bond at a specified index.

insertBond(int, MolBond) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolBond).

insertBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom

insertBondInOrder(MolBond, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Insert a bond in the order specified as the second argument.

insertDocument(MTextDocument) - Method in class chemaxon.struc.graphics.MTextBox

Inserts document at the current cursor position.

insertNullAtoms(int, int) - Method in class chemaxon.struc.MoleculeGraph

Insert nulls into the atom array.

insertNullAtoms(int, int) - Method in class chemaxon.struc.RgMolecule

Insert nulls into the atom array.

insertNullBonds(int, int) - Method in class chemaxon.struc.MoleculeGraph

Insert nulls into the bond array.

insertNullBonds(int, int) - Method in class chemaxon.struc.RgMolecule

Insert nulls into the bond array.

insertTo(Container, int, int) - Method in class chemaxon.marvin.swing.MAction

Insert menu item into the specified menu.

insideLabel(double, double) - Method in class chemaxon.struc.MolAtom

Tests whether the specified point is inside the atom label.

INSTABLE_TAUTOMERIC_FORM_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Instable tautomeric form remark.

intDescr - Variable in class chemaxon.descriptors.CustomDescriptor

storage for the integer or binary descriptors

INTEGER_ARRAY - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation

INTEGER_ARRAY_BIT_REPR - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation

INTEGER_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters

internalSize - Variable in class chemaxon.descriptors.MDParameters

required memory size of one descriptor instance

internalsToString() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Print state to a String.

IntMapper - Interface in com.chemaxon.search.transformation.util

Maps int values of a range [0..size-1] to other int values.

intValue() - Method in class chemaxon.struc.prop.MIntegerProp

Gets the integer value.

INVALID_CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that stereo center with no enhanced stereo property had found in the molecule

INVALID_COORD_SYSTEM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that invalid coordination system had found in the molecule

INVALID_LINKNODE_MESSAGE - Static variable in class chemaxon.struc.MoleculeGraph

INVALID_REACTION_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that invalid mapping had found in the molecule (represents a reaction)

INVALID_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule with invalid rgroup had found

INVALID_WEDGE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Deprecated.

InvalidChecker - Class in chemaxon.checkers

An extremal checker implementation indicating error in the configuration imported from XML or action string

InvalidChecker(String) - Constructor for class chemaxon.checkers.InvalidChecker

Initializes an invalid structure checker instance

InvalidStandardizerAction - Class in chemaxon.standardizer.actions

Implementation of StandardizerAction representing an invalid instance of a standardizer action.

InvalidStandardizerAction(String) - Constructor for class chemaxon.standardizer.actions.InvalidStandardizerAction

Initializes an invalid standardizer instance

InvalidStandardizerAction(String, String, Map<String, String>) - Constructor for class chemaxon.standardizer.actions.InvalidStandardizerAction

Initializes an invalid standardizer instance

invert() - Method in class chemaxon.struc.CTransform3D

Inverts the matrix.

INVISIBLE_SETS - Static variable in class chemaxon.marvin.common.ParameterConstants

invokeAndWait(Runnable) - Method in interface chemaxon.marvin.view.TaskScheduler

Enqueues a task on the scheduler's thread and waits for its completion.

invokeAndWait(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil

Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object, blocks until it is finished and returns the result (calling FutureTask.get()).

invokeLater(Runnable, int) - Method in interface chemaxon.marvin.view.TaskScheduler

Enqueues a task on the scheduler's thread.

invokeLater(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil

Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object.

IO_ERROR - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult

ionChargeOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the ion charge.

IonChargePlugin - Class in chemaxon.marvin.calculations

Plugin class for charge calculation on ionized microspecies.

IonChargePlugin() - Constructor for class chemaxon.marvin.calculations.IonChargePlugin

Constructor.

ionizer - Variable in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Ir - Static variable in class chemaxon.core.ChemConst

is3d() - Method in class chemaxon.struc.CTransform3D

Tests whether the transformation is 3D.

isAbsoluteLabelsVisible() - Method in class chemaxon.marvin.MolPrinter

Is 'Absolute' label visible?.

isAbsolutePlacement() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets whether the placement of this attached data is absolute or relative to the objects it is attached.

isAbsStereo() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Gets the absolute value of the action

isAbsStereo() - Method in class chemaxon.struc.MoleculeGraph

Gets the absolute stereoconfiguration flag.

isAbsStereo() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Gets the absolute stereoconfiguration flag.

isAcceptableGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.MultipleSgroup

Decides whether the given molecule graph can be the graph of a multiple s-group.

isAcceptablePolymerGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Checks if the given molecular graph can be the graph of a polymer SRU

isAcceptableRSRUGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Checks if the given molecular graph can be the graph of an RSRU

isAcceptableSru(String) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

isAcceptedSpecialLigand(AtomReference) - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence

Check if the ligand is a special atom which changes the ring atom column number with -1

isAcceptedSpecialLigand(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Check if the ligand is a special atom which changes the ring atom column number with -1

isAcceptor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isActinideMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is an actinide metal Actinium is included.

isActive() - Method in class chemaxon.standardizer.AbstractStandardizerAction

isActive() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

isActive() - Method in interface chemaxon.standardizer.StandardizerAction

Returns true if the action is active, and can be used

isAdvancedSave() - Method in class chemaxon.marvin.common.UserSettings

Gets wether the useres uses advanced save or not.

isAliphaticAtom(int) - Method in class chemaxon.calculations.Ring

Determines if an atom is not a member of an aromatic ring.

isAliphaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.isAliphaticAtom(int)

isAliphaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if aliphatic atom.

isAliphaticRC(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isAlkaliMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is an alkali (group I.) metal.

isAlkalineEarthMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is an alkaline earth (group II.) metal.

isAllowTraditionalNitrogen() - Method in class chemaxon.checkers.ValenceErrorChecker

Gets whether the checker allows traditional N representation

isAllowValenceError() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Gets whether replace should be applied even in case of invalid valence in the result

isAmbiguousStereo() - Method in class chemaxon.struc.MolAtom

Check if the atom has ambiguous stereo wedge configuration.

isAminoAcid() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Gets whether the group represents an amino-acid

isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.common.UserSettings

Gets wether the user uses peptide bridge coloring or not.

isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.MolPrinter

Is peptide bridge coloring enabled?

isAnchor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isAnimated(int) - Method in class chemaxon.marvin.beans.MViewPane

Selected cell is animated or not.

isAnimSync() - Method in class chemaxon.marvin.beans.MViewPane

Gets the animation synchronization.

isAnnotationSupported() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Checks whether annotation is supported for the current document type.

isApproximateCount() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns true if count is approximate due to multiple position bonds with multicenters of variable size, false otherwise.

isAromatic(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isAromaticAtom(int) - Method in class chemaxon.calculations.Ring

Determines if an atom is a member of an aromatic ring.

isAromaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.isAromaticAtom(int)

isAromaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if aromatic atom.

isAromaticBond(int) - Method in class chemaxon.calculations.Ring

Determines if a bond is a member of an aromatic ring.

isAromaticityChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects aromaticity atom query properties or not.

isAromaticRC(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isAromaticSMILESSubset(int) - Static method in class chemaxon.struc.MolAtom

Is the atom can be aromatic according to the daylight specification: Only atoms on the following list can be considered aromatic: C, N, O, P, S, As, Se, and * (wildcard).

isAromatize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated, for removal: This API element is subject to removal in a future version.

isArrow() - Method in class chemaxon.struc.graphics.MPolyline

Checks if it is an arrow.

isAssociatedWith(Molecule) - Method in class chemaxon.struc.NoStructure

Verifies the reference equality of molecule and the component associated with this instance.

isAsymmetric() - Method in class chemaxon.descriptors.MDParameters

Returns whether current parametrized metric is asymmetric or not.

isAsymmetricAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if asymmetric atom.

isAtom() - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isAtom() - Method in class chemaxon.struc.RgMolecule

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isAtom() - Method in class chemaxon.struc.RxnMolecule

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets whether the arrow's terminus is at an atom.

isAtomicSymbol(String) - Static method in class chemaxon.struc.PeriodicSystem

Returns whether the given string corresponds to an atomic number of an element in the periodic system specified by its symbol.

isAtomInRing(AtomReference) - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence

Checks whether the atom is in ring.

isAtomInRing(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Checks whether the atom is in ring.

isAtomMapMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether atom map numbers are considered in search.

isAtomMappingVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Determines the visibility of the atom mapping.

isAtomMappingVisible() - Method in class chemaxon.marvin.MolPrinter

Returns true if atom mapping is visible.

isAtomNumbersVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

in 6.2.0. Use getAtomNumberingType() instead.

isAtomNumbersVisible() - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

in 6.2.0. Use getAtomNumberingType instead.

isAtomPropertiesVisible() - Method in class chemaxon.marvin.common.UserSettings

Tells wheter the atom properties are visible or not if exist.

isAtomPropertiesVisible() - Method in class chemaxon.marvin.MolPrinter

Get the atom properties visibility

isAtomSetColorModeSet() - Method in class chemaxon.struc.MDocument

Decides whether the atomset coloring mode is set.

isAtomSymbolsVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Tests the visibility of the atom symbols in 3D.

isAtomSymbolsVisible() - Method in class chemaxon.marvin.MolPrinter

Returns the atom symbol visibility of 3D mode.

isAtomTypeMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether atom types are considered in search.

isAttachmentAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Checks whether the given atom is an attachment atom or not.

isAutoAlign() - Method in class chemaxon.struc.graphics.MNameTextBox

Returns if the text-box is in automatic alignment mode.

isAutoCheckStructure() - Method in class chemaxon.marvin.common.UserSettings

Tells whether the automatic structure checking is enabled or not

isAutoHeight() - Method in class chemaxon.struc.graphics.MTextBox

Gets if it is autoHeight.

isAutomaticFogEnabled() - Method in class chemaxon.marvin.common.UserSettings

Gets the state of automatic fog calculation mode.

isAutomaticReactionEnabled() - Method in class chemaxon.marvin.common.UserSettings

Gets the state of automatic reaction calculation mode.

isAutoResize() - Method in class chemaxon.struc.graphics.MNameTextBox

Returns if the text-box is in automatic resize mode.

isAutoSize() - Method in class chemaxon.struc.graphics.MTextBox

isAvailable() - Method in class chemaxon.checkers.AbstractStructureChecker

isAvailable() - Method in class chemaxon.checkers.InvalidChecker

isAvailable() - Method in interface chemaxon.checkers.StructureChecker

Returns true if the checker is available, and can be used

isAvailable() - Method in class chemaxon.checkers.SubstructureChecker

isAvailable() - Method in class chemaxon.marvin.services.ServiceDescriptor

Returns true if service is available.

isAvailable() - Method in class chemaxon.standardizer.AbstractStandardizerAction

isAvailable() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

isAvailable() - Method in interface chemaxon.standardizer.StandardizerAction

Returns true if the action is available, and can be used

isBarredAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Determines if an atom is is part of a certain functional group with high rotational barrier (amides, thioamides, sulphonamides).

isBold() - Method in class chemaxon.struc.graphics.MFont

Tests whether the font is bold.

isBold() - Method in class chemaxon.struc.MolBond

Decides whether this bond is bold or not.

isBond() - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isBond() - Method in class chemaxon.struc.RgMolecule

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isBond() - Method in class chemaxon.struc.RxnMolecule

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets whether the arrow's terminus is at a bond.

isBondDraggedAlong() - Method in class chemaxon.marvin.beans.MSketchPane

Is the currently used bond shown at the mouse cursor?

isBondDraggedAlong() - Method in class chemaxon.marvin.common.UserSettings

Is the currently used bond shown at the mouse cursor?

isBondLengthVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Gets the bond length display option.

isBondLengthVisible() - Method in class chemaxon.marvin.MolPrinter

Return whether the bond length is visible or not.

isBondParallelWith(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Checks if there is a bond parallel (having same endpoints) with the given bond in this MoleculeGraph.

isBondTypeMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether bond types are considered in search.

isBoundTo(MolAtom) - Method in class chemaxon.struc.MolAtom

Checks if this MolAtom is connected to another one or not.

isBracketCrossingBond(MolBond) - Method in class chemaxon.struc.Sgroup

isBracketVisible() - Method in class chemaxon.struc.Sgroup

Tests whether the bracket is visible.

isBracketVisible() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Tests whether the bracket is visible.

isBracketVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Tests whether the bracket is visible.

isBridgehead() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing bridgehead H

isBridgeHeadAtom(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.11.1, replaced by TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)

isBridgingRAllowed() - Method in class chemaxon.sss.search.SearchOptions

Returns true if different undefined R-atoms can match the same group of atoms.

isCanceled() - Method in interface chemaxon.common.util.MProgressMonitor

Tests whether the user canceled the dialog.

isCanceled() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Returns whether the process is cancelled

isCancelled() - Method in interface chemaxon.util.progress.ProgressObserver

Returns whether cancellation of current task has been requested.

isCancelledOrError() - Method in enum class chemaxon.common.swing.io.output.FileSaveResult

isCanonical() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

isCellwiseWeights() - Method in class chemaxon.descriptors.MDParameters

Gets boolean telling whether cell weights are to be generated for current parametrized metric.

isChainAtom(int) - Method in class chemaxon.calculations.Ring

Determines if an atom a ring bond or a chain bond.

isChainAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.isChainAtom(int)

isChainAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if chain atom.

isChainBond(int) - Method in class chemaxon.calculations.Ring

Determines if a bond is a ring bond or a chain bond.

isChainBond(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.isChainBond(int)

isChainBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines if a bond is a ring bond or a chain bond.

isChargeAngleSet() - Method in class chemaxon.struc.MolAtom

isChargeCalc() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns true if pH-Charge calculation.

isCharged() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing charged H

isChargeMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether formal charges are considered in search.

isChargeWithCircle() - Method in class chemaxon.marvin.MolPrinter

Get the visibility of Charge with Circle

isChecking() - Method in interface chemaxon.checkers.runner.CheckerRunner

This function identifies the state of the checker thread

isChildOf(MObject) - Method in class chemaxon.struc.graphics.MMidPoint

Is this object a children of another one?

isChildOf(MObject) - Method in class chemaxon.struc.graphics.MRectanglePoint

Is this object a children of another one?

isChildOf(MObject) - Method in class chemaxon.struc.MObject

Is this object a children of another one?

isChildOf(MObject) - Method in class chemaxon.struc.MPoint

Is this object a children of another one?

isChiral() - Method in class chemaxon.calculations.stereo.Stereochemistry

Determines if the molecule contains an atom with R or S stereo configuration.

isChiral() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.isChiral()

isChiralCenter(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines if an atom can be a tetrahedral stereogenic center.

isChirality() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the chirality value of absolute stereo action

isCleanable() - Method in class chemaxon.formats.MolExporter

Tests whether cleaning is meaningful for the chosen output format.

isCleanable() - Method in class chemaxon.marvin.io.MolExportModule

Tests whether 2D or 3D cleaning is meaningful for this output format.

isCleanHOptionEnabled() - Method in class chemaxon.marvin.common.UserSettings

Returns true if the H option for cleaning is enabled.

isCleanNeeded() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns true if clean is needed for GUI display.

isCloseEnabled() - Method in class chemaxon.marvin.beans.MSketchPane

Determines if the File->Close menu item is enabled or not.

isCollinear(DPoint3, DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3

Checks whether three 3D points can be connected with a line.

isCollinear(MolAtom) - Method in class chemaxon.struc.MolBond

Returns whether atom is collinear with the bond or not.

isComment(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

isCompatible(MTextAttributes, MTextAttributes, MFont) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether two attribute sets are compatible.

isCompleted() - Method in enum class chemaxon.common.swing.io.output.FileSaveResult

isConfirmExit() - Method in class chemaxon.marvin.beans.MSketchPane

Gets whether the confirmation dialog will be appear or not by exit.

isConjugated() - Method in class chemaxon.struc.MolBond

Gets the conjugation state of the bond set by the conjugation modul.

isConnected() - Method in class chemaxon.calculations.TopologyAnalyser

Determines if the molecule is a connected graph or not.

isConnected(int, int) - Method in class chemaxon.calculations.TopologyAnalyser

Determines if two atoms are members of a connected graph or not.

isConnected(int, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if two atoms are in the same connected component, false for atoms of disconnected structures.

isConnectedGraph() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines if the molecule is a connected graph or not.

isConnectedMode() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether the common substructures should be connected or they can consist of multiple fragments.

isConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects connection count atom query properties or not.

isContainerFree() - Method in class chemaxon.struc.graphics.MElectronContainer

isContainerFull() - Method in class chemaxon.struc.graphics.MElectronContainer

isContracted() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Is this S-group contracted?

isContracted() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Decides whether this S-group is contracted or not.

isCoordDependent() - Method in class chemaxon.struc.MProp

Tests whether the property depends on the molecular coordinates.

isCoordinate() - Method in class chemaxon.struc.MolBond

Tests whether the bond is coordinate.

isCopolymerMatching() - Method in class chemaxon.sss.search.SearchOptions

Specifies whether matching mode is copolymer.

isCopyAsTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Determines whether the MTransferable is appearing as an option in the Copy As dialog.

isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionChecker

This method determines if a component of the reaction correct or not.

isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionMapErrorChecker

isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Tells whether the spectrum is coupled.

isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator

Coupled/decoupled spectrum.

isCouplingNeeded() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns whether spin-spin couplings are taken into account.

isCreateRingCenters() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

isCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether the bond is a crossing bond in a ladder-type polymer bracket.

isCubeLine(String, int) - Static method in class chemaxon.formats.recognizer.CubeRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

isCumulatedDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectCummulatedDoubleBonds

isCurrentFontDefault() - Method in class chemaxon.struc.graphics.MTextBox

Deprecated, for removal: This API element is subject to removal in a future version.

isCurrentFontRegular() - Method in class chemaxon.struc.graphics.MTextBox

Deprecated, for removal: This API element is subject to removal in a future version.

isCxSMILESLine(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

isDataDetached() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets whether the data should be displayed close to the objects or separately (detached).

isDataFlavorSupported(DataFlavor) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Checks whether the MarvinTransferable.flavor equals with the given parameter.

isDefault() - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether all attributes have default values.

isDefaultSelected() - Method in class chemaxon.marvin.util.OptionDescriptor

Tests whether the option is selected by default.

isDefaultTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Determines whether the MTransferable instance should be used by the default copy operation.

isDehidrogenize() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated, for removal: This API element is subject to removal in a future version.

The explicit Hydrogens are not removed from the original input structure. No need to use.

isDescendantOf(Sgroup) - Method in class chemaxon.struc.Sgroup

Decides whether this is a descendant of another sgroup.

isDetachable() - Method in class chemaxon.marvin.beans.MViewPane

Gets the detachable property.

isDetectCumulatedDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectCummulatedDoubleBonds

isDetectTransDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTransDoubleBonds

isDetectTripleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTripleBonds

isDialogVisible() - Method in interface chemaxon.common.util.MProgressMonitor

Tests whether the dialog is visible.

isDirty() - Method in class chemaxon.sss.search.SearchOptions

Returns the dirty flag.

isDisplayChargeWithCircle() - Method in class chemaxon.marvin.common.UserSettings

isDisplayLonePairsAsLine() - Method in class chemaxon.marvin.common.UserSettings

isDistancerangeSet() - Method in enum class chemaxon.marvin.alignment.AlignmentProperties

isDistinctFirstAtomMatching() - Method in class chemaxon.sss.search.MolSearchOptions

Get option ensuring that upon the findNext() call the first atom must be stepped as well.

isDndTransferable() - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

isDocumentExport() - Method in class chemaxon.marvin.io.MolExportModule

Tests if this export module is document export instead of a simple molecule export.

isDocumentImporter() - Method in class chemaxon.marvin.io.MolImportModule

Tests whether this module is a document importer or not.

isDonor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isDontRemoveLastComponent() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

isDoubleBond() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the double bond value of absolute stereo action

isDraggable() - Method in class chemaxon.marvin.beans.MViewPane

Determines whether mouse dragged evens are allowed or not.

isEditable() - Method in class chemaxon.standardizer.advancedactions.TransformAction

Returns if this action is editable.

isEditable() - Method in class chemaxon.struc.graphics.MAnalysisBox

isEditable() - Method in class chemaxon.struc.graphics.MNameTextBox

isEditable() - Method in class chemaxon.struc.graphics.MTextBox

Determines if this text box's content can be edited by the user.

isEditable(int, Molecule, String) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Tests whether a field is editable or not.

isEmpty() - Method in class chemaxon.jep.context.ReactionContext

Returns true if the context is empty.

isEmpty() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets whether the configuration contains actions

isEmpty() - Method in class chemaxon.struc.graphics.MChemicalStruct

A chemical structure object is empty if the molecule graph is empty.

isEmpty() - Method in class chemaxon.struc.graphics.MMoleculeMovie

A chemical structure object is empty if the molecule graph is empty.

isEmpty() - Method in class chemaxon.struc.graphics.MPolyline

A polyline becomes empty if it has less than 2 points.

isEmpty() - Method in class chemaxon.struc.graphics.MTextBox

A text box is empty if the string contains only whitespace.

isEmpty() - Method in class chemaxon.struc.MDocument

Tests whether the document is empty: the main molecule object in the document is empty no graphic object is included (neither simple nor extra)

isEmpty() - Method in class chemaxon.struc.MObject

An object may become empty if all the children are removed.

isEmpty() - Method in class chemaxon.struc.Molecule

Tests whether the molecule is empty.

isEmpty() - Method in class chemaxon.struc.MoleculeGraph

Tests whether the molecule graph is empty.

isEmpty() - Method in class chemaxon.struc.RgMolecule

Ask if the molecule is empty or not.

isEmpty() - Method in class chemaxon.struc.RxnMolecule

Ask if the reaction is empty or not.

isEmpty() - Method in class chemaxon.struc.Sgroup

Is it an empty S-group?

isEmpty() - Method in class com.chemaxon.search.mcs.McsSearchResult

Checks whether the common substructure contains any bonds or is empty.

isEnabled() - Method in class chemaxon.struc.PageSettings

isEnabledT(int, int) - Method in class chemaxon.marvin.view.MDocStorage

Tests whether a text field is enabled.

isEnableTranslateAndRotate() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

isEndgroupMatching() - Method in class chemaxon.sss.search.SearchOptions

Get whether polymers end groups must match.

isEndReached() - Method in class chemaxon.formats.MolImporter

Tests whether the end of input is already reached.

isEndReached() - Method in class chemaxon.marvin.io.ArrayMDocSource

Tests whether the end of input is already reached.

isEndReached() - Method in class chemaxon.marvin.io.MDocSource

Tests whether the end of input is already reached.

isEndReached() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Tests whether the end of input is already reached.

isEndReached() - Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException

Tests whether the end of storage is reached.

isEnforceAbsStereo() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

isEnumerationNeeded() - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

isExact() - Method in class chemaxon.standardizer.advancedactions.TransformAction

Gets the exact value of the action

isExactBondMatching() - Method in class chemaxon.sss.search.SearchOptions

Indicates whether bond types should match exactly - looking for query bonds target.

isExactBondMatchingAlwaysOn() - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

isExactQueryAtomMatching() - Method in class chemaxon.sss.search.SearchOptions

Returns whether exact matching of query atom information is set.

isExactQueryAtomMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether query atoms are matched only to query atoms of exactly the same type.

isExactQueryBondMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether query bonds are matched only to query bonds of exactly the same type.

isExceptionOccurred() - Method in class chemaxon.standardizer.concurrent.StandardizerResult

Gets whether an exception occurred during standardization

isExcludedAtom(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory

By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more atoms, than it would normally.

isExcludedBond(MolBond) - Method in class chemaxon.util.iterator.IteratorFactory

By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more bonds, than it would normally.

isExclusionRegexp() - Method in class chemaxon.checkers.AttachedDataChecker

Tells how to interpret the AtomLabels: A comma separated list or a regular expression.

isExitCanceled() - Method in class chemaxon.marvin.beans.MarvinPane

Check whether exiting is allowed or not.

isExpandable(int) - Method in class chemaxon.struc.Molecule

Tests if the molecule is expandable with the specified options.

isExpanded() - Method in interface chemaxon.struc.sgroup.Expandable

Is this S-group expanded?

isExpanded() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Is this S-group expanded?

isExpanded() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Is this S-group expanded?

isExperimentalEnabled() - Method in class chemaxon.marvin.beans.MarvinPane

Tests whether experimental features are enabled.

isExperimentalFeaturesAreAllowed() - Method in class chemaxon.marvin.common.UserSettings

isExplicitConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects explicit connection count atom query properties or not.

isExplicitHVisible() - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.5.1 this method always returns true. This method will be removed in a future release.

isExtraObject(MObject) - Method in class chemaxon.struc.MDocument

Decides whether a graphic object belongs to the main chemical structure of the document.

isEZLabelsVisible() - Method in class chemaxon.marvin.MolPrinter

Returns the visibility state of absolute double bond stereo configuration labels.

isEzVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Gets the E/Z display option.

isEzVisible() - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.2.2, replaced by MolPrinter.isEZLabelsVisible()

isEZVisible() - Method in class chemaxon.marvin.common.UserSettings

Are E/Z labels visible?

isFallBackToBasic() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

Returns true if runner should fall back to basic runner when preferred fix failed.

isFiltered() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Return true if molecule filter is set.

isFixed(int) - Method in class chemaxon.marvin.view.MDocStorage

Tests whether a record is fixed.

isFlagSet(long) - Method in class chemaxon.formats.MFileFormat

Checks whether the format has a given (set of) flag(s) set.

isFlipped() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether this sgroup is flipped.

isFontDefault(MFont) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether the default font is used.

isFontDefaultInRange(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Deprecated, for removal: This API element is subject to removal in a future version.

isFontRegular() - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether the default font is used.

isFontRegularInRange(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Deprecated, for removal: This API element is subject to removal in a future version.

isFractionQuicklyAvailable(double) - Method in class chemaxon.marvin.view.MDocStorage

Tests whether the specified fraction of the total (estimated) number of records is quickly available.

isFree() - Method in class chemaxon.struc.sgroup.AttachmentPoint

Decides whether the attachment point is free or not.

isFree(int) - Method in class chemaxon.struc.graphics.MElectronContainer

True if MElectron referenced by the index is not occupied.

isFree(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

isFreeAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Checks whether the specified atom has free attachment point.

isFreeLegalAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.0, replaced by SuperatomSgroup.isFreeAttachAtom(MolAtom a).

isFuzzyFingerprint() - Method in class chemaxon.descriptors.PFParameters

Gets whether the fuzzy fingerprints are used or not.

isGaussianSmoothing() - Method in class chemaxon.descriptors.PFParameters

Gets if fuzzy smmoothing is based on normal distribution.

isGenerateDistanceRanges() - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

isGeneric() - Method in class chemaxon.struc.MolAtom

Tests whether the atom is a generic atom.

isGenNameShown() - Method in class chemaxon.marvin.view.swing.TableOptions

Are IUPAC names shown in the table?

isGrabbingEnabled() - Method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.2. It has no effect on the code.

isGraphInvariantVisible() - Method in class chemaxon.marvin.MolPrinter

Return whether the graph invariant is visible or not.

isGridVisible() - Method in class chemaxon.marvin.common.UserSettings

isGrinv() - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.5, use isGrinvVisible() instead

isGrinvCCValid() - Method in class chemaxon.struc.MoleculeGraph

Tests whether the graph invariant change count is valid.

isGrinvCCValid() - Method in class chemaxon.struc.SelectionMolecule

Tests whether the graph invariant change count is valid.

isGrinvVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Gets the visibility of the graph invariants.

isGUIContracted() - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()

isH(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isHalogen(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is a halogen (F, Cl, Br, I, At, Ts).

isHashed() - Method in class chemaxon.struc.MolBond

Decides whether this bond is hashed or not.

isHconnected() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing H connected H

isHierarchic() - Method in class chemaxon.struc.MPropertyContainer

Tests whether the property list contains subcollections like MListProp and MHashProp.

isHighlighted(MObject) - Method in class chemaxon.struc.MDocument

Is the specified object currently highlighted?

isHinderedBiarylBridgeBond(int) - Method in class chemaxon.calculations.TopologyAnalyser

Determines if a bond bridges two aryl systems having more than two ortho substituents.

isHomologyEnumerated() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Indicates if homology groups are enumerated or not.

isHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects hydrogen count atom query properties or not.

isHydrophobic(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isIdentity() - Method in class chemaxon.struc.CTransform3D

isIgnoreAxialStereo() - Method in class chemaxon.sss.search.SearchOptions

Retrieves if axial stereo is ignored during searching.

isIgnoreCumuleneOrRingCisTransStereo() - Method in class chemaxon.sss.search.SearchOptions

Retrieves if cumulene cis-trans stereo is ignored during searching.

isIgnoreDoubleBondStereo() - Method in class chemaxon.sss.search.SearchOptions

Retrieves if double bond stereo is ignored during searching.

isIgnoreSynAntiStereo() - Method in class chemaxon.sss.search.SearchOptions

Retrieves if syn-anti stereo is ignored during searching.

isIgnoreTetrahedralStereo() - Method in class chemaxon.sss.search.SearchOptions

Retrieves if tetrahedral stereo is ignored during searching.

isImplicitHcountImportant(MolAtom) - Static method in class chemaxon.marvin.io.MolExportModule

Checks whether the number of implicit hydrogens is important information for an atom or not.

isImplicitHcountImportant(MoleculeGraph) - Method in class chemaxon.marvin.io.MolExportModule

Checks whether the number of implicit hydrogens is important information for the atoms of mol or not.

isImplicitHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects implicit hydrogen count atom query properties or not.

isImplicitHydrogenMode() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns implicit hydrogen mode.

isImplicitizableH(int) - Method in class chemaxon.struc.MolAtom

Tests whether the hydrogen atom is implicitizable or not.

isIn3D() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Returns true if structures are returned in 3D.

isIncipBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets whether the arrow's sink is at an incipient bond.

isIncompleteReaction() - Method in class chemaxon.struc.RgMolecule

Check whether the reaction is incomplete or not.

isIncompleteReaction() - Method in class chemaxon.struc.RxnMolecule

Check whether the reaction is incomplete or not.

isInputAvailable() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Checks that the implementation supports input from clipboard.

isInputAvailable() - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable

Checks that the implementation supports input from clipboard.

isInputMoleculeAromatized() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if the input molecule has aromatic bond.

isInternalSelectable() - Method in class chemaxon.struc.graphics.MElectronContainer

isInternalSelectable() - Method in class chemaxon.struc.MObject

Is it a selection only internal object?

isInternalSelectable() - Method in class chemaxon.struc.MPoint

Is it a selection only internal object?

isIsotopeMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether isotopes are considered in search.

isIsotopic() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing isotopic H

isItalic() - Method in class chemaxon.struc.graphics.MFont

Tests whether the font is italic.

isKeepMapping() - Method in class chemaxon.standardizer.actions.MapAction

Returns if underlying mapper keeps existing maps should be kept when mapping.

isKeepMapping() - Method in class chemaxon.standardizer.actions.MapReactionAction

Returns if underlying mapper keeps existing maps should be kept when mapping.

isKeepMapping() - Method in class com.chemaxon.mapper.AutoMapper

Returns if the mapper will keep the initial mapping or not.

isKeepMapping() - Method in class com.chemaxon.mapper.AutoMapper.Options

isKeepQueryOrder() - Method in class chemaxon.sss.search.SearchOptions

Get options for rearranging query atoms for better search performance.

isLanthanideMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is a lanthanide metal Lanthanum is included.

isLargeMolecule() - Method in class chemaxon.struc.MoleculeGraph

Returns true if large molecule (number of atoms exceeds 1000).

isLastLine() - Method in class chemaxon.formats.recognizer.Recognizer

Tests whether it is the last line of file.

isLastTaskClean(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil

Deprecated, for removal: This API element is subject to removal in a future version.

isLegalAttachment(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.0, replaced by SuperatomSgroup.isAttachmentAtom(MolAtom).

isLicensed() - Method in class chemaxon.calculations.Ring

This method is for internal use only.

isLicensed() - Method in class chemaxon.calculations.TopologyAnalyser

isLicensed() - Method in class chemaxon.checkers.AbstractStructureChecker

isLicensed() - Method in class chemaxon.descriptors.BCUT

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.descriptors.ECFP

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.descriptors.ECFPGenerator

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.descriptors.ShapeDescriptor

isLicensed() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

isLicensed() - Method in class chemaxon.marvin.alignment.AlignRigidEasy

isLicensed() - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

isLicensed() - Method in class chemaxon.marvin.calculations.ChargePlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

isLicensed() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

isLicensed() - Method in class chemaxon.marvin.calculations.MSAPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.sss.search.MolSearch

isLicensed() - Method in class chemaxon.sss.search.RGroupDecomposition

isLicensed() - Method in class chemaxon.standardizer.AbstractStandardizerAction

isLicensed() - Method in class chemaxon.standardizer.Standardizer

Gets whether the standardizer is licensed

isLicensed() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Returns true if this action can be used in current license environment.

isLicensed() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Returns information about the licensing of the product.

isLigandErrorVisible() - Method in class chemaxon.marvin.common.UserSettings

Tells wheter the bond's ligand error is visible or not.

isLigandErrorVisible() - Method in class chemaxon.marvin.MolPrinter

Gets the bond's ligand error visibility

isLinkNode() - Method in class chemaxon.struc.MolAtom

The atom is a link node if the maximum number of repetitions is nonzero.

isLoadedMolModified() - Method in class chemaxon.marvin.beans.MSketchPane

Determines whether the original molecule that is loaded in is modified or not.

isLocalAromatic() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

Do not calculate valence for ambiguous aromatic atoms behaving like aromatic Nitrogens (e.g.

isLonely() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing lonely H

isLonePair() - Method in class chemaxon.struc.graphics.MElectronContainer

isLonePairAsLine() - Method in class chemaxon.marvin.MolPrinter

Get the visibility of Lone Pairs: dots/line

isLonePairAutoCalc() - Method in class chemaxon.marvin.common.UserSettings

Returns the state of the automatic lone pair calculation.

isLonePairsAsLines() - Method in class chemaxon.struc.graphics.MElectronContainer

isLonePairsAutoCalculated() - Method in class chemaxon.marvin.MolPrinter

Returns the state of the automatic calculation of lone pairs.

isLonePairsVisible() - Method in class chemaxon.marvin.MolPrinter

Returns the visibility state of lone pairs.

isLP(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isMappable() - Method in class chemaxon.struc.MolAtom

Checks if this atom it a mappable.

isMapped() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing mapped H

isMarkBonds() - Method in class chemaxon.standardizer.actions.MapAction

Returns if bonds are marked while mapping.

isMarkBonds() - Method in class chemaxon.standardizer.actions.MapReactionAction

Returns if bonds are marked while mapping.

isMarkBonds() - Method in class com.chemaxon.mapper.AutoMapper

Returns if the mapper marks the reaction center bonds or not.

isMarkBonds() - Method in class com.chemaxon.mapper.AutoMapper.Options

isMarkush() - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

isMarkushEnabled() - Method in class chemaxon.sss.search.MolSearchOptions

Specifies whether a target containing Markush features should be treated as a Markush library.

isMarkushQuery() - Method in class chemaxon.sss.search.RGroupDecomposition

Returns true if query contains Markush features which will be enumerated (all features except defined R-rgroups and homologies).

isMarvinCompMode() - Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Marvin compatibility mode.

isMatchCountBetween(int, boolean, int, boolean) - Method in class chemaxon.sss.search.Search

Decides questions like "does the query match the target between 2 and 5 times (inclusively)" Makes this efficiently, which means it only searches for the number of hits necessary to decide the question.

isMatchCountInRelation(String, int) - Method in class chemaxon.sss.search.Search

Decides questions like "does the query match the target at least 3 times", "[] up to 5 times", "[] exactly once".

isMatchCountInRelation(String, int, int) - Static method in class chemaxon.sss.search.Search

isMatching() - Method in class chemaxon.sss.formula.FormulaSearch

Checks if the query formula matches the target formula according to the formula search type.

isMatching() - Method in class chemaxon.sss.search.MolSearch

isMatching() - Method in class chemaxon.sss.search.Search

Checks if the query structure matches the target structure with respect to the search options.

isMatching() - Method in interface com.chemaxon.search.SimpleSearcher

Determines if there is a matching between the specified query and target.

isMergedComponent(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Check whether given molecule is reaction component with a set of intentionally merged fragments or not.

isMetadataMol(Molecule) - Static method in class chemaxon.naming.document.DocumentToStructure

isMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Decides whether the element is a metal.

isMetalconnected() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing metal connected H

isMetalloid(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is a metalloid (B, Si, Ge, As, Sb, Te, Po).

isMinimumHeightSet() - Method in class chemaxon.struc.graphics.MTextBox

Gets if it is minimumHeightSet.

isMixSgroupMatching() - Method in class chemaxon.sss.search.SearchOptions

Get option whether search should consider consider COM, MIX and FOR sgroups during search.

isModified() - Method in class chemaxon.standardizer.Changes

Gets whether any modifications were applied on the molecule.

isMolecular() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns true if molecule output.

isMolecule() - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 14.7.7, no replacement.
Usage:

 use myObject instanceof Molecule instead
             

isMolMovie() - Method in class chemaxon.formats.MolImporter

Are the imported molecules merged into one multi-set molecule?

isMolNameShown() - Method in class chemaxon.marvin.view.swing.TableOptions

Are molecule names shown in the table?

isMPLabelsVisible() - Method in class chemaxon.marvin.MolPrinter

Returns the visibility state of M/P labels.

isMPVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Gets the M/P display option.

isMPVisible() - Method in class chemaxon.marvin.common.UserSettings

isMsCalc() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns true if microspecies calculation.

isMsCalc() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns true if microspecies calculation.

isMsCalc() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if microspecies calculation.

isMSpaceDisplayLabelOnlyOnHeavyAtoms() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Returns if mspace should display label only on heavy atoms.

isMultiChiral() - Method in class chemaxon.struc.MoleculeGraph

Returns the multiple chirality flag.

isMultiPageEnabled() - Method in class chemaxon.struc.PageSettings

isMultipleDisplay() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Returns true if results for more molecules can be displayed in a single component, false if each molecule should be displayed in a separate component.

isMultiSet() - Method in class chemaxon.formats.MolImporter

Are the imported molecules merged into one multi-set molecule?

isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.GeometryPlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.MSAPlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.ResonancePlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

For internal use only.

isNegative(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isNegligible(double[]) - Method in class chemaxon.marvin.calculations.pKaPlugin

isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Returns whether the result can be ignored.

isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns whether the result can be ignored.

isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns whether the result can be ignored.

isNobleGas(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is a noble gas.

isNonAromaticCovalentBond() - Method in enum class chemaxon.struc.BondType

Determines whether this bond is a non-aromatic covalent bond.

isNonAssociated() - Method in class chemaxon.struc.NoStructure

isNonPreferredStereoAtom(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Check if the atoms in the molecule is in SP2 hybridization state and has wedge whose getAtom1 is the specified atom, but wiggly bonds next to double bonds are allowed.

isNormal() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

isNormalized() - Method in class chemaxon.descriptors.MDParameters

Returns whether current parametrized metric is normalized or not.

isOccupied(int) - Method in class chemaxon.struc.graphics.MElectronContainer

True if the MElectron referenced by the index is occupied.

isOccupied(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

ISOELECTRICPOINT - Enum constant in enum class chemaxon.calculator.CalculatorTag

IsoelectricPointPlugin - Class in chemaxon.marvin.calculations

Plugin class for isoelectric point and pH - charge distribution calculation.

IsoelectricPointPlugin() - Constructor for class chemaxon.marvin.calculations.IsoelectricPointPlugin

Constructor.

isOK() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if no calculation error, false on error.

isOK() - Method in class com.chemaxon.calculations.cli.CalculatorPluginCachedResults

Returns true if the calculation has run without error.

isOK() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns true if the calculation has run without error.

isOK() - Method in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns true if the calculation has run without error.

isOkActionEnabled() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

isOkActionEnabled() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Returns true if "OK" button is enabled.

isolate(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Isolates atom: a more efficient way of removing an atom than MoleculeGraph.removeAtom(chemaxon.struc.MolAtom), especially for large molecule graphs.

isolate(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Isolates bond: a more efficient way of removing a bond than MoleculeGraph.removeBond(chemaxon.struc.MolBond), especially for large molecule graphs.

isOneLetterPeptideDisplay() - Method in class chemaxon.marvin.MolPrinter

Decides whether the Peptide display settings set to one letter.

isOnlyExpanded() - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

isOnlyFirstAtomInStereoCalculation() - Method in class chemaxon.struc.MoleculeGraph

Get how parity module interpret wedges.

isOptionsPaneLoaded(int) - Method in class com.chemaxon.calculations.gui.PluginFactory

Returns true is options pane is loaded for plugin, false otherwise.

isOrderedComponentSgroup() - Method in class chemaxon.struc.Sgroup

Returns if the Sgroup is ordered component Sgroup.

isOrderSensitiveSearch() - Method in class chemaxon.sss.search.SearchOptions

Indicates whether the search is order sensitive

isOrderSensitiveSearch() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether search is sensitive to the order of the matched atoms and bonds when searching for multiple hits.

isOrigTargetMayBeMarkush - Variable in class chemaxon.sss.search.MolSearch

FS#9166 Should be set to 'false' to indicate that any bonds (Markush components) occurred only after generating generic tautomer of target.

isOtherMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is an "other metal", group IIIa-Va metal.

ISOTOPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that isotpoe atom had found in the molecule

ISOTOPE_2H3H - Enum constant in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

2H/3H isotope symbol

ISOTOPE_COMPOSITION - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "isotopecomposition".

ISOTOPE_DT - Enum constant in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

D/T isotope symbol

ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "isotopeformalchargeformula".

ISOTOPE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "isotopeformula".

ISOTOPE_H - Static variable in class chemaxon.struc.MolAtom

Include Hydrogen isotope(s).

ISOTOPE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).

ISOTOPE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).

ISOTOPE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for ignore isotope searching (isotope information is ignored during searching).

IsotopeChecker - Class in chemaxon.checkers

IsotopeChecker detects isotopes (non-elemental atoms).

IsotopeChecker() - Constructor for class chemaxon.checkers.IsotopeChecker

Default constructor

isotopeComposition(int) - Method in class chemaxon.calculations.ElementalAnalyser

Gets the molecular composition (w/w%).

isotopeComposition(int, boolean) - Method in class chemaxon.calculations.ElementalAnalyser

Gets the molecular composition (w/w%).

isotopeDistribution() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the isotopic distributions for the molecule.

IsotopeFixer - Class in chemaxon.fixers

Deprecated, for removal: This API element is subject to removal in a future version.

use ConvertToElementalFormFixer

IsotopeFixer() - Constructor for class chemaxon.fixers.IsotopeFixer

Deprecated.

isotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the molecular formula (isotopes are separated).

isotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the molecular formula (isotopes are separated).

isotopeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether isotopes of atoms should be considered in search.

isotopeType(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the type of an isotope.

isOuterAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether an atom is part of this repeating unit.

isOutputCleanable(String) - Static method in class chemaxon.formats.MFileFormatUtil

Tests whether the specified output format is cleanable.

isOverflowCalculation() - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns true if overflow calculation: maximum number of ionizable atoms exceeded and protein ionization invoked.

isPartSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup

Decides if part of the sgroup is selected or not.

isPassed() - Method in enum class com.chemaxon.common.annotations.RemovalDate

isPhaseShiftedMatching() - Method in class chemaxon.sss.search.SearchOptions

Get option whether phase shifted polymer matches on the original.

isPlainHydrogen() - Method in class chemaxon.struc.MolAtom

isPointed() - Method in class chemaxon.struc.graphics.MElectron

isPolymerendgroup() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing polymer end group H

isPolymerMatching() - Method in class chemaxon.sss.search.SearchOptions

Get option whether to search consider polymer sgroups during search.

isPositionVariation() - Method in class chemaxon.struc.MolBond

Decides whether this bond is a position variation bond.

isPositive(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

isPrefixModeSupported() - Method in interface chemaxon.naming.NameConverter

Returns true if prefix mode is supported.

isPrintEnabled() - Method in class chemaxon.marvin.beans.MarvinPane

Determines if the File->Print menu item is enabled or not.

isPropertyRecord() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

isPropertyRecord() - Method in interface chemaxon.marvin.io.MRecordReader

isPseudo() - Method in class chemaxon.struc.MolAtom

Tests whether if the atom is a pseudo atom.

isQProp() - Method in class chemaxon.struc.MolAtom

Tests whether this object represents a query property.

isQuery() - Method in class chemaxon.struc.MolAtom

Tests whether it is a query atom.

isQuery() - Method in class chemaxon.struc.MolBond

Tests whether it is query bond or has query property: any single or double single or aromatic double or aromatic smarts bond ring or chain topology For more information on smarts bond and query bonds, see The JChem Query Guide

isQuery() - Method in class chemaxon.struc.MoleculeGraph

Indicates if the molecule has query features: query atoms or query bonds.

isQuery() - Method in class chemaxon.struc.RgMolecule

Indicates if the molecule has query features.

isQuery() - Method in class chemaxon.struc.RxnMolecule

Indicates if the molecule has query features: query atoms or query bonds.

isQueryAbsoluteStereo() - Method in class chemaxon.sss.search.MolSearchOptions

Returns whether the chiral flag is ignored or not for the query molecule.

isQueryBond() - Method in enum class chemaxon.struc.BondType

Determines whether this bond is a query bond.

isRadical() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing radical H

isRadical() - Method in class chemaxon.struc.graphics.MElectronContainer

isRadicalMatching() - Method in class com.chemaxon.search.mcs.McsSearchOptions

Returns whether radicals are considered in search.

isRandomEnumeration() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns true if random enumeration is requested.

isReaction() - Method in class chemaxon.struc.Molecule

Checks if the structure represents a reaction or not.

isReaction() - Method in class chemaxon.struc.RgMolecule

Checks if the structure represents a reaction or not.

isReaction() - Method in class chemaxon.struc.RxnMolecule

Checks if the structure represents a reaction or not.

isReactionArrow(MoleculeGraph) - Method in class chemaxon.struc.MObject

isReactionErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.

Are reaction errors highlighted?

isReactionMappingIncomplete() - Method in class chemaxon.descriptors.ReactionFingerprint

Returns true if reaction molecule was not mapped completely during reaction fingerprint generation.

isReactionUnpairedMapMatching() - Method in class chemaxon.sss.search.SearchOptions

Get whether unpaired(orphan or widow) atom maps can match any atom.

isRealAtom(MolAtom) - Static method in class chemaxon.checkers.StructureCheckerUtility

Gets whether the provided atom represents an atom (and not something that should not be an atom)

isRealAtomParent() - Method in class chemaxon.struc.MoleculeGraph

Can it be a real atom parent?

isRealAtomParent() - Method in class chemaxon.struc.RgMolecule

R-group molecule objects cannot be real node parents.

isRealAtomParent() - Method in class chemaxon.struc.RxnMolecule

Reaction molecules cannot be real node parents.

isRealAtomParent() - Method in class chemaxon.struc.SelectionMolecule

Selection molecules are not real atom parents.

isRegionalizedMatchingCompatible() - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

isRemovable() - Method in class chemaxon.struc.Sgroup

Decides whether an S-group should be ungrouped if its structure changes.

isRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Checks if the specified atom object is in the paradigmatic repeating unit or not.

isRestH(int) - Method in class chemaxon.struc.RgMolecule

Informs whether the restH condition is set to the referenced R-group definition.

isRewindable() - Method in class chemaxon.formats.MolImporter

Tests whether rewinding (seeking backwards) is possible in the underlying input stream.

isRewindable() - Method in class chemaxon.marvin.io.ArrayMDocSource

Tests whether rewinding (seeking backwards) is possible.

isRewindable() - Method in class chemaxon.marvin.io.MDocSource

Tests whether rewinding (seeking backwards) is possible.

isRewindable() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Tests whether rewinding (seeking backwards) is possible.

isRewindable() - Method in class chemaxon.marvin.view.MDocStorage

Tests whether the document storage is rewindable.

isRgrouped(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if molecule with R-groups.

isRgroupsVisible() - Method in class chemaxon.marvin.beans.MarvinPane

Determines the visibility of R-group defintions.

isRgroupsVisible() - Method in class chemaxon.marvin.MolPrinter

Decides whether the R-group definitions are visible.

isRing() - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isRingAtom(int) - Method in class chemaxon.calculations.Ring

Determines if an atom a ring bond or a chain bond.

isRingAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.isRingAtom(int)

isRingAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Returns true if ring atom.

isRingBond(int) - Method in class chemaxon.calculations.Ring

Determines if a bond is a ring bond or a chain bond.

isRingBond(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.isRingBond(int)

isRingBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines if a bond is a ring bond or a chain bond.

isRingBond(int) - Method in class chemaxon.struc.MoleculeGraph

Is this bond in ring?

isRingBondCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects ring bond count atom query properties or not.

isRingCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects ring count atom query properties or not.

isRLogicVisible() - Method in class chemaxon.marvin.MolPrinter

Is R-logic visible?.

isRotatableBond(int) - Method in class chemaxon.calculations.TopologyAnalyser

Determines if a bond is a rotatable or not

isRotatableBond(int) - Method in class chemaxon.marvin.alignment.RotatableBondDetector

Not flexible if:
double, aromatic, triple bond single bond neighboring a triple like at cyanide chain end bonds amide thioamide: -C(=S)-NR2 sulphonamide R-S(=O)2-NR2 aniline N : C(aromatic)-N(sp3) aromatic amidine : C(aromatic)-C(=NH)-NH2 aromatic nitroso : C(aromatic)-N=O aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable) C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature: Ring bonds may be rotatable also.

isRotatableBond(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Determines if a bond is a rotatable or not

isRunning() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

isRunning() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

This function identifies the state of the standardizer thread

isSafeHtmlElement(String) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter

isSameParityClass(int, int, int, int, int, int, int, int) - Static method in class chemaxon.struc.MolAtom

Calculates if chirality centers in the structure and the query belong to the same parity class.

isSaveBOM() - Method in class chemaxon.marvin.common.UserSettings

isSaveIniEnabled() - Method in class chemaxon.marvin.beans.MarvinPane

Automatically saves user settings to an initialization file.

isScaled() - Method in class chemaxon.descriptors.MDParameters

Returns whether current parametrized metric is scaled or not.

isSearchAll() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects all R-atoms or not.

isSearchBridgehead() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for bridgehead explicit hydrogens

isSearchCharged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for charged explicit hydrogens

isSearchContracted() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Returns if the checker is searching for contracted SGroups or not

isSearchDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker

Returns if the checker detects valence properties with the default valence of the current atom type.

isSearchDisconnected() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms not connected to any other atoms or not.

isSearchExpanded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Returns if the checker is searching for expanded SGroups or not

isSearchGeneric() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms without identifier numbers or not.

isSearchHConnected() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for H connected explicit hydrogens

isSearchIsotopic() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for isotopic explicit hydrogens

isSearchLinker() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms with more than one connection or not.

isSearchLonely() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for lonely explicit hydrogens

isSearchMapped() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for mapped explicit hydrogens

isSearchNested() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms within R-groups or not.

isSearchNonDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker

Returns if the checker detects valence properties with a non-default valence of the current atom type.

isSearchPolymerEndGroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for polymer end group explicit hydrogens

isSearchRadical() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for radical explicit hydrogens

isSearchSgroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for S-group explicit hydrogens

isSearchSgroupEnd() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for S-group end explicit hydrogens

isSearchValenceError() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for valence errored explicit hydrogens

isSearchWedged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for wedged explicit hydrogens

isSeekable() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Tests whether the record reader is seekable.

isSeekable() - Method in class chemaxon.marvin.io.MRecordImporter

Tests whether the record reader is seekable.

isSeekable() - Method in interface chemaxon.marvin.io.MRecordReader

Tests whether the record reader is seekable.

isSeekable() - Method in class chemaxon.marvin.io.PositionedInputStream

Tests whether the stream is seekable.

isSelectable() - Method in class chemaxon.marvin.beans.MViewPane

Are the cells selectable?

isSelectableNow() - Method in class chemaxon.struc.graphics.MMidPoint

isSelectableNow() - Method in class chemaxon.struc.graphics.MReactionSign

isSelectableNow() - Method in class chemaxon.struc.graphics.MRectanglePoint

isSelectableNow() - Method in class chemaxon.struc.MObject

Is the object selectable now?

isSelected() - Method in class chemaxon.struc.graphics.MElectron

isSelected() - Method in class chemaxon.struc.graphics.MElectronContainer

isSelected() - Method in class chemaxon.struc.MObject

Is the object selected?

isSelected() - Method in class chemaxon.struc.MolAtom

Tests whether this atom is selected.

isSelected() - Method in class chemaxon.struc.NoStructure

isSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup

Is the sgroup or part of the sgroup selected?

isSelfReference(MProp) - Method in class chemaxon.struc.MoleculeGraph

Tests whether the specified property is a self reference to the molecule.

isSelfReference(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether a property is a self reference to the containing molecule.

isSelfReference(MProp) - Method in class chemaxon.struc.RgMolecule

Tests whether the specified property is a self reference to the molecule.

isSetColoringEnabled() - Method in class chemaxon.marvin.beans.MarvinPane

Is the atom/bond set coloring enabled?

isSetColoringEnabled() - Method in class chemaxon.marvin.MolPrinter

Returns true if atoms and bonds are colored according to the color of the pre-defined set they belong to.

isSgroup() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing s-group H

isSgroup() - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 14.7.7, no replacement.
Not supported feature.

isSgroupDataFormatted() - Method in class chemaxon.marvin.beans.MarvinPane

Returns whether the Sgroup data is formatted.

isSgroupDataFormatted() - Method in class chemaxon.marvin.MolPrinter

Returns whether the Sgroup data is formatted.

isSgroupend() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing s-group end H

isShowMultiMoleculeOnEditSource() - Method in class chemaxon.marvin.common.UserSettings

isSimilarTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Tests if the molecule graph is similar to another graph.

isSimpleMolecule() - Method in class chemaxon.struc.MDocument

Tests whether the document is equivalent to a simple molecule.

isSingleCellLabelShown() - Method in class chemaxon.marvin.view.swing.TableOptions

Tests whether label should be shown for a single cell.

isSingleStepReaction() - Method in class chemaxon.struc.RxnMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

isSingleUpOrDownBond() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the single wedge value of absolute stereo action

isSizeFinal() - Method in class chemaxon.marvin.view.MDocStorage

Tests whether the storage size is final.

isSketchWindowOpened(int) - Method in class chemaxon.marvin.beans.MViewPane

Checks whether the molecule from the specified cell is opened in a sketcher window or not.

isSmallestRingSizeChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects smallest ring size atom query properties or not.

isSmartsQueryChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects SMARTS query properties or not.

isSMILESShown() - Method in class chemaxon.marvin.view.swing.TableOptions

Are SMILES strings shown in the table?

isSpecBeilsteinGeneric(String) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Tests whether the specified symbol is a Beilstein Generic except A, Q and X.

isSpecialAtom(MolAtom) - Static method in class chemaxon.checkers.StructureCheckerUtility

Gets whether the provided atom is special

isSpecIsotopeSymbolPreferred() - Method in class chemaxon.struc.MolAtom

Tests whether special symbol is used.

isSpecIsotopeSymbolUsed() - Method in class chemaxon.struc.MolAtom

Tests whether special symbol is used.

isStandardizationMandatory() - Method in class chemaxon.descriptors.MDParameters

Checks is Standardization of molecules is mandatory for the corresponding MolecularDescriptor before descriptor generation.

isStarAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether an atom is a star atom in this S-group.

isStartupSelectorShown() - Method in class chemaxon.marvin.common.UserSettings

isStereo(Molecule) - Static method in class chemaxon.checkers.StereoCheckUtility

Deprecated.

Gets whether the molecule is stereo

isStereoFix() - Method in class chemaxon.standardizer.Standardizer

Gets whether last stereo fix should be applied

isStreamOutput() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Returns true if stream output.

isSubFormatOf(String, String) - Static method in class chemaxon.formats.MFileFormatUtil

Tests whether a format is a sub-format of another format.

isSubsetChangable() - Method in class chemaxon.marvin.view.swing.TableOptions

Returns whether startAt and maxSize can be changed.

isSubsetOf(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.

isSubSetOf(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.

isSubSetOf(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.

isSubstitutionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects substitution count atom query properties or not.

isSwitchOffAllProtectsForTDF() - Method in class chemaxon.sss.search.MolSearchOptions

Deprecated, for removal: This API element is subject to removal in a future version.

Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.

isSymmetric() - Method in class chemaxon.struc.MoleculeGraph

Tests whether the molecule graph is symmetric.

isSymmetricalFuzzy() - Method in class chemaxon.descriptors.PFParameters

isTargetAbsoluteStereo() - Method in class chemaxon.sss.search.MolSearchOptions

Returns whether the chiral flag is ignored or not for the target molecule.

isTerminalAtom() - Method in class chemaxon.struc.MolAtom

Determines whether it is a terminal atom or not.

isThicknessSet() - Method in class chemaxon.struc.graphics.MPolyline

Checks if the line thickness is set.

isThreeLetterPeptideDisplay() - Method in class chemaxon.marvin.MolPrinter

Decides whether the Peptide display settings set to three letter.

isThrowExceptionOnTimeout() - Method in class chemaxon.sss.search.SearchOptions

Is search should throw exception upon timeout.

isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup

Decides if the whole sgroup is selected or not.

isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Decides if the whole superatom sgroup is selected or not.

isTraditionalNitrogensAllowed() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

Returns if the traditional way of the ylidene and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O, CN(=C)=O and c1ccccn1=O is accepted if false they are marked as valence error.

isTransDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTransDoubleBonds

isTransformable() - Method in class chemaxon.struc.graphics.MAtomSetPoint

Is it a transformable object?

isTransformable() - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Is it a transformable object?

isTransformable() - Method in class chemaxon.struc.graphics.MRectanglePoint

isTransformable() - Method in class chemaxon.struc.MObject

Is it a transformable object?

isTransformationEnabled() - Method in class chemaxon.marvin.common.UserSettings

Gets the transformation enabled/disabled.

isTransitionMetal(int) - Static method in class chemaxon.struc.PeriodicSystem

Checks if the given atom is a transition metal, IB-VIIIB.

isTransparent() - Method in class chemaxon.marvin.MolPrinter

Returns the transparency state of the painting.

isTripleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTripleBonds

isUndecided(Object) - Static method in class chemaxon.jep.ChemJEP

Returns whether the result object is undecided.

isUndefinedRAtomMatchingGroup() - Method in class chemaxon.sss.search.SearchOptions

Gets whether undefined R atom matches group of atoms.

isUnitDisplayed() - Method in class chemaxon.struc.sgroup.DataSgroup

Gets whether the units string should be displayed.

isUnsaturationChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects unsaturation atom query properties or not.

isURLOrFileName(String) - Static method in class chemaxon.formats.MFileFormatUtil

Tests whether the specified string is an URL (absolute or relative) or file name.

isUseDefaultSalts() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Gets whether default salt dictionary should be used

isUseDefaultSolvents() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Gets whether default solvent dictionary should be used

isUsefulForQuery() - Method in class chemaxon.sss.search.MolComparator

Decides based on the query and the search object if the comparator should be used or not.

isUsefulForTarget() - Method in class chemaxon.sss.search.MolComparator

Decides based on the query, target and the search object if the comparator should be used or not.

isValenceCheckEnabled() - Method in class chemaxon.struc.MoleculeGraph

Determines whether valence check is enabled on this molecule graph.

isValenceerror() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing valence error H

isValenceErrorvisible() - Method in class chemaxon.marvin.MolPrinter

Returns the visibility state of valence errors.

isValenceErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane

Are valence errors highlighted?

isValenceErrorVisible() - Method in class chemaxon.marvin.common.UserSettings

Are valence errors visible?

isValenceErrorVisibleInView() - Method in class chemaxon.marvin.beans.MViewPane

Are valence errors highlighted?

isValenceErrorVisibleInView() - Method in class chemaxon.marvin.common.UserSettings

Are valence errors visible in MarvinView?

isValenceMatching() - Method in class chemaxon.sss.search.SearchOptions

Get the valence matching option

isValencePropertyVisible() - Method in class chemaxon.marvin.common.UserSettings

Tells wheter the atom valence property is visible or not.

isValencePropertyVisible() - Method in class chemaxon.marvin.MolPrinter

Gets the atom valence property visibility

isValid() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Excluded object is initialized.

isValid() - Method in class chemaxon.checkers.AbstractStructureChecker

isValid() - Method in class chemaxon.checkers.AttachedDataChecker

isValid() - Method in class chemaxon.checkers.InvalidChecker

isValid() - Method in class chemaxon.checkers.PseudoAtomChecker

isValid() - Method in interface chemaxon.checkers.StructureChecker

Returns true if the checker's configuration is valid, false otherwise

isValid() - Method in class chemaxon.checkers.SubstructureChecker

isValid() - Method in class chemaxon.marvin.services.DynamicArgument

isValid() - Method in class chemaxon.marvin.services.ServiceArgument

Returns true if service argument is valid

isValid() - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor

Returns true if editor represents a valid descriptor in current state

isValid() - Method in class chemaxon.standardizer.AbstractStandardizerAction

isValid() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

isValid() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Gets whether the configuration contains only valid elements

isValid() - Method in interface chemaxon.standardizer.StandardizerAction

Returns true if the action's parameters are valid, false otherwise

isValid(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether a coordinate dependent property is still valid.

isValid(InputStream) - Static method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader

Checks whether the contents of the provided input stream is a valid configuration XML

isvalidateSgroupsAtCreation() - Method in class chemaxon.marvin.common.UserSettings

Is the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.

isValidLinkNode(int, int, int) - Method in class chemaxon.struc.MoleculeGraph

Checks whether the specified link atom is valid or not.

isValidList() - Method in class chemaxon.checkers.util.DataExclusionList

isValidQuery(String) - Static method in class chemaxon.sss.formula.FormulaSearch

Checks the given formula whether it is a valid query formula

isValidSourceAndSinkForMolecule(Object, Object, Molecule) - Static method in class chemaxon.struc.graphics.MEFlow

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule) or one of the other implementations instead.

isValidSourceForMolecule(Object, Molecule) - Static method in class chemaxon.struc.graphics.MEFlow

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidSource(MolAtom, Molecule) or EFlowPlacementValidators.isValidSource(MolAtom[], Molecule) or EFlowPlacementValidators.isValidSource(MolBond, Molecule) .

isValidTarget(String) - Static method in class chemaxon.sss.formula.FormulaSearch

Checks the given formula whether it is a valid target formula

isValidXMLConfiguration(InputStream) - Static method in class chemaxon.standardizer.configuration.reader.StandardizerXMLReader

Checks whether the contents of the provided input stream is a valid configuration XML

isVerbose() - Method in class chemaxon.sss.search.Search

For debugging purposes only.

isVerbose() - Method in class chemaxon.sss.search.SearchOptions

For debugging purposes only.

isViewAtomMarkEnabled() - Method in class chemaxon.marvin.common.UserSettings

Returns true if atom mark and highlight is enabled in View.

isViewWindowOpened(int) - Method in class chemaxon.marvin.beans.MViewPane

Checks whether the view canvas of the specified cell is detached into a separate window or not.

isVisible() - Method in class chemaxon.struc.Sgroup

Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.

isWedged() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing wedged H

isWeighted() - Method in class chemaxon.descriptors.MDParameters

Returns whether current parametrized metric is weighted or not.

isZoomToScaffoldOnLoad() - Method in class chemaxon.marvin.common.UserSettings

ITALIC - Static variable in class chemaxon.struc.graphics.MFont

Italic font style.

items - Variable in class chemaxon.marvin.plugin.gui.ParameterPanel

itemStateChanged(ItemEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

The ItemListener interface: invoked when a legend image is selected or deselected.

iterator() - Method in class chemaxon.marvin.io.MDocSource

Gets a molecule iterator for this document source.

iterator(Iterator<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper

Deprecated.

use AutoMapper.closeableIterator(Iterator) instead

iterator(Iterator<Molecule>, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Deprecated.

use StandardizerRunner.closeableIterator(Iterator, StandardizerConfiguration, int, ErrorHandlingPolicy, String) instead

iterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper

Deprecated.

use AutoMapper.closeableIterator(Iterator, Options) instead

iterator(Iterator<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper

Deprecated.

use AutoMapper.closeableIterator(Iterator, Mapper[])

IteratorFactory - Class in chemaxon.util.iterator

The IteratorFactory class provides implementations of Iterator to ease the handling of atoms and bonds used in Molecule objects and its descendants.

IteratorFactory(Molecule) - Constructor for class chemaxon.util.iterator.IteratorFactory

Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.

IteratorFactory(MoleculeGraph) - Constructor for class chemaxon.util.iterator.IteratorFactory

Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.

IteratorFactory(Molecule, int, int) - Constructor for class chemaxon.util.iterator.IteratorFactory

Constructs an iterator factory for the specified molecule with a specified atom and bond related behavior.

IteratorFactory.AtomIterator - Class in chemaxon.util.iterator

The AtomIterator class provides an iterator for the atoms of the specified molecule of the factory according to the atom related behavior set in the factory.

IteratorFactory.AtomNeighbourIterator - Class in chemaxon.util.iterator

The AtomNeighbourIterator class provides an iterator to process the atoms connecting to a specified atom according to the atom and bond related behavior of this factory.

IteratorFactory.BondIterator - Class in chemaxon.util.iterator

The BondIterator class provides an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.

IteratorFactory.BondNeighbourIterator - Class in chemaxon.util.iterator

The BondNeighbourIterator class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory.

IteratorFactory.NeighbourIterator<E> - Class in chemaxon.util.iterator

The NeighbourIterator class provides an iterator to process the bonds connecting to the specified atom according to the atom and bond related behavior of this factory.

IteratorFactory.RgComponentIterator - Class in chemaxon.util.iterator

The RgComponentIterator class provides an iterator to process the rgroup definition components in the specified molecule of the factory.

IteratorFactory.RxnComponentIterator - Class in chemaxon.util.iterator

The RxnComponentIterator class provides an iterator to process the components (reactant, product and agent components) in the reaction molecule of the factory.

IteratorFactory.SgroupIterator - Class in chemaxon.util.iterator

The SgroupIterator class provides an iterator for the s-groups of the specified molecule of the factory.

IUPACNamingPlugin - Class in chemaxon.marvin.calculations

IUPAC name generator plugin.

IUPACNamingPlugin() - Constructor for class chemaxon.marvin.calculations.IUPACNamingPlugin

J

JAN_01_2025 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate

JAN_01_2026 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate

jar - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

jar - Variable in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

JepException - Exception in chemaxon.jep

Exception thrown during the compilation or evaluation of Chemical Terms exceptions.

JepException() - Constructor for exception chemaxon.jep.JepException

JepException(String) - Constructor for exception chemaxon.jep.JepException

JepException(String, Throwable) - Constructor for exception chemaxon.jep.JepException

JepException(Throwable) - Constructor for exception chemaxon.jep.JepException

JPEG - Static variable in class chemaxon.formats.MFileFormat

JPEG format.

JsonServiceDescriptor - Class in chemaxon.marvin.services.json

Service descriptor of JSON type requests.

JsonServiceDescriptor() - Constructor for class chemaxon.marvin.services.json.JsonServiceDescriptor

JsonServiceDescriptor.Method - Enum Class in chemaxon.marvin.services.json

request method

JsonServiceHandler - Class in chemaxon.marvin.services.json

Service handler for JSON type requests.

JsonServiceHandler() - Constructor for class chemaxon.marvin.services.json.JsonServiceHandler

JUL_01_2025 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate

JUL_01_2026 - Enum constant in enum class com.chemaxon.common.annotations.RemovalDate

K

K - Static variable in class chemaxon.core.ChemConst

keep - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

KEEP_BOTH_FLEXIBLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

Keep both structures flexible during the alignment.

KEEP_BOTH_RIGID - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

Keep both structures conformationally rigid during the alignment.

KEEP_FIRST_RIGID_SECOND_FLEXIBLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

Keep the first reference structure rigid, and the second as flexible during the alignment.

KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

As of AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).

KEEP_HYDROGENS - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

KEEP_MAPPING - Static variable in class chemaxon.standardizer.actions.MapAction

keep mapping property

KEEP_MAPPING - Static variable in class chemaxon.standardizer.actions.MapReactionAction

keep mapping property

KEEP_RINGS - Enum constant in enum class com.chemaxon.search.mcs.RingHandlingMode

This option specifies that rings should not be broken.

keepHydrogens - Variable in class chemaxon.marvin.plugin.CalculatorPlugin

KEEPLARGEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Keep largest fragment

keepLargestFragment(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

keeporiginalLineEnding - Variable in class chemaxon.marvin.io.PositionedInputStream

KEEPSMALLEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Keep largest fragment

KEKULE_MATCH_AMBIG - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

Ambiguous aromatic parts are not aromatized in the target Markush structures.

KEY_VALUE_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Parameter key and value separator token of the action string

KLOPMAN - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod

Calculation method based on Klopman's model.

KNOWN_TETRAHEDRAL_STEREO - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter

Known tetrahedral stereo centers (even, odd).

KnownAtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop

Filter for known atrop stereo centers.

KnownAtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter

knownAtropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the KNOWN atrop stereocenters.

KnownAxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial

Filter for known axial centers.

KnownAxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter

knownAxialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the KNOWN axial stereocenters.

KnownDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans

Filter for known (CIS or TRANS) double bonds.

KnownDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter

knownResolvedStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the known, resolved tetrahedral stereogenic centers.

knownResolvedStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the known, resolved tetrahedral stereogenic centers (with attached data).

KnownResolvedTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral

Filter for known, resolved tetrahedral centers.

KnownResolvedTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter

Kr - Static variable in class chemaxon.core.ChemConst

L

La - Static variable in class chemaxon.core.ChemConst

LABEL - Static variable in class chemaxon.struc.NoStructure

Label for NoStructure.

LABEL - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Property display type: display in label.

LABEL_AUTO - Static variable in class chemaxon.struc.sgroup.SgroupAtom

LABEL_DEFAULT - Static variable in class chemaxon.struc.sgroup.SgroupAtom

labelAsAnchor(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

largestring - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

largestRing() - Method in class chemaxon.calculations.Ring

Identifies the atoms of the largest ring (number of atoms) in the molecule.

largestRing() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.largestRing()

largestRingSize() - Method in class chemaxon.calculations.Ring

Calculates the size of the largest ring in the molecule (SSSR based).

largestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.largestRingSize()

largestRingSizeOfAtom(int) - Method in class chemaxon.calculations.Ring

Calculates the size of the largest ring an atom is a member of (SSSR based).

largestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.largestRingSizeOfAtom(int)

largestringsystem - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

largestRingSystem() - Method in class chemaxon.calculations.Ring

Identifies the atoms of the largest ring system (number of rings) in the molecule.

largestRingSystem() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.largestRingSystem()

largestRingSystemSize() - Method in class chemaxon.calculations.Ring

Calculates the size of the largest ring system (number of rings) in the molecule.

largestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.largestRingSystemSize()

LAST_LICENSE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

lastPage - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

The last page of the document that should be annotated.

lastPage(Integer) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

LAYOUT - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "layout".

LAYOUT_HEADER - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "layoutH".

LDIR_ABOVE - Static variable in class chemaxon.struc.MolAtom

Implicit Hydrogen(s) are above the element symbol.

LDIR_BELOW - Static variable in class chemaxon.struc.MolAtom

Implicit Hydrogen(s) are below the element symbol.

LDIR_LEFT - Static variable in class chemaxon.struc.MolAtom

Implicit Hydrogen(s) are left to element symbol.

LDIR_RIGHT - Static variable in class chemaxon.struc.MolAtom

Implicit Hydrogen(s) are right to element symbol.

LDParameters - Class in chemaxon.descriptors.scalars

Manages parameters for the LogD scalar descriptor class.

LDParameters() - Constructor for class chemaxon.descriptors.scalars.LDParameters

Creates an empty object.

LDParameters(File) - Constructor for class chemaxon.descriptors.scalars.LDParameters

Creates a new object based on a given configuration file.

LDParameters(String) - Constructor for class chemaxon.descriptors.scalars.LDParameters

Creates a new object based on a given configuration string.

LEAVE_COORDS_UNCHANGED - Static variable in interface chemaxon.struc.sgroup.Expandable

Coordinates are not calculated during expand or contract.

leftMul(CTransform3D) - Method in class chemaxon.struc.CTransform3D

Multiplies by another matrix from left.

length - Variable in class chemaxon.descriptors.MDParameters

the length of the descriptor: the number of cells

length() - Method in class chemaxon.marvin.io.MRecordImporter

Gets the length of the input file.

length() - Method in class chemaxon.marvin.io.PositionedInputStream

Gets the file length.

length() - Method in class chemaxon.struc.graphics.MTextDocument

Gets the length of the document.

length() - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the number of characters.

length() - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets text length.

lengthSquare() - Method in class chemaxon.struc.DPoint3

Calculates the square of the length of the vector defining the point.

Li - Static variable in class chemaxon.core.ChemConst

license() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the license required for this action.

LICENSE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "license".

LICENSE_FILE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "licenseFile".

LicenseDialog - Class in chemaxon.marvin.uif.dialog

LicenseDialog(Window) - Constructor for class chemaxon.marvin.uif.dialog.LicenseDialog

licenseEnvironment - Variable in class chemaxon.marvin.plugin.CalculatorPlugin

Member storing license environment.

LicenseException - Exception in chemaxon.license

LicenseException(String) - Constructor for exception chemaxon.license.LicenseException

Constructs an instance of LicenseException with the specified detail message.

LicenseException(String, String) - Constructor for exception chemaxon.license.LicenseException

LIGAND_ERROR_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "ligandErrorVisible".

ligands() - Method in class chemaxon.struc.MolAtom

Provides an unmodifiable list view of the ligands of the atom.

limitRecordCount(int) - Method in class chemaxon.marvin.plugin.PluginMDocSource

Limits the number of result docs.

lineByteBuffer - Variable in class chemaxon.marvin.io.PositionedInputStream

Lines are read into this buffer.

lineCurrentColumn - Variable in class chemaxon.marvin.io.PositionedInputStream

Column position of the next character to read.

LINKNODE - Static variable in class chemaxon.sss.search.MarkushFeature

Deprecated.

Expansion type: link node.

LIST - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the inclusive atom list.

LISTEN_MOUSE_EVENT - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "listenmouseevent".

LISTEN_PROPERTY_CHANGE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "listenpropertychange".

listener - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

A listener that will be notified of the progress of the annotation.

load() - Static method in class com.chemaxon.calculations.admet.HergActivityPredictor

Initializes the default hERG activity model.

load() - Static method in class com.chemaxon.calculations.admet.HergClassPredictor

Initializes the default hERG classification model.

load() - Method in class com.chemaxon.calculations.gui.PluginFactory

Loads default property file.

load(String, String) - Method in class com.chemaxon.calculations.gui.PluginFactory

Loads plugin data from property file.

load(Properties) - Method in class com.chemaxon.calculations.gui.PluginFactory

Loads plugin data from properties.

LOAD_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "loadMols".

loadClass(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

An instance-specific class loader is no longer used by this method. Use Class.forName(String) instead.

loadPluginClass(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Loads a plugin class, first tries to load it from CLASSPATH, then from JAR.

loadPluginClass(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.loadPluginClass(String) instead.

LOCAL_MENU_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

local menu name property of checker

localMenuName() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the local menu name of the checker

LocalServiceDescriptor - Class in chemaxon.marvin.services.localservice

Service Descriptor for java based local services.

LocalServiceDescriptor() - Constructor for class chemaxon.marvin.services.localservice.LocalServiceDescriptor

LocalServiceHandler - Class in chemaxon.marvin.services.localservice

ServiceHandler implementation for LocalServiceDescriptor

LocalServiceHandler() - Constructor for class chemaxon.marvin.services.localservice.LocalServiceHandler

LOG - Static variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Logger object.

LogD - Class in chemaxon.descriptors.scalars

Implements logD value as a scalar descriptor.

LogD() - Constructor for class chemaxon.descriptors.scalars.LogD

Creates a new, empty logD descriptor.

LogD(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.LogD

Copy constructor.

LogD(LDParameters) - Constructor for class chemaxon.descriptors.scalars.LogD

Creates a new instance according to the parameters given.

LogD(String) - Constructor for class chemaxon.descriptors.scalars.LogD

Creates a new instance according to the parameters given.

LOGD - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Calculated distribution coefficient az pH 7.4.

LOGDCALCULATOR - Enum constant in enum class chemaxon.calculator.CalculatorTag

logDPlugin - Class in chemaxon.marvin.calculations

Plugin class for logD calculation.

logDPlugin() - Constructor for class chemaxon.marvin.calculations.logDPlugin

Constructor.

logger - Variable in class chemaxon.checkers.runner.AdvancedCheckerRunner

LogP - Class in chemaxon.descriptors.scalars

Implements LogP value as a scalar descriptor.

LogP() - Constructor for class chemaxon.descriptors.scalars.LogP

Creates a new, empty logP descriptor.

LogP(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.LogP

Copy constructor.

LogP(SDParameters) - Constructor for class chemaxon.descriptors.scalars.LogP

Creates a new instance according to the parameters given.

LogP(String) - Constructor for class chemaxon.descriptors.scalars.LogP

Creates a new instance according to the parameters given.

LOGP - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Lipophilicity, calculated partition coefficient.

logPath - Variable in class chemaxon.checkers.StructureCheckOptions

The path of the program error log file.

LogPMethod - Enum Class in chemaxon.marvin.calculations

logP calculation method.

logPPlugin - Class in chemaxon.marvin.calculations

Plugin class for logP calculation.

logPPlugin() - Constructor for class chemaxon.marvin.calculations.logPPlugin

Constructor.

LOGS - Enum constant in enum class chemaxon.calculator.CalculatorTag

LOGS - Enum constant in enum class com.chemaxon.calculations.solubility.SolubilityUnit

Solubility is expressed in base-10 logarithm unit.

logToDebug(System.Logger, System.Logger.Level, String, boolean) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult

Append to log.

LONE_PAIRS_AS_LINE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "lonePairsAsLine".

LONE_PAIRS_AUTO_CALCULATION - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "lonePairsAutoCalc".

LONE_PAIRS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "lonePairsVisible".

LONELY_H - Static variable in class chemaxon.struc.MolAtom

Include lonely Hydrogen atom(s).

lonePairCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint

lonePairRealCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint

lonePairState - Static variable in class chemaxon.struc.graphics.MEFlow

LOOSE - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type

Loose aromatization

LOOSE - Enum constant in enum class com.chemaxon.search.AromatizationMethod

Loose aromatization.

LOOSE - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer

LOW - Enum constant in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

Low solubility.

LOW_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor

low priority value

LOWEST_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor

the lowest priority value

lowestEigenvalues - Variable in class chemaxon.descriptors.BCUT

LP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

LP - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the lone pair.

Lr - Static variable in class chemaxon.core.ChemConst

Lu - Static variable in class chemaxon.core.ChemConst

Lv - Static variable in class chemaxon.core.ChemConst

M

m - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

m - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

M - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

M - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

m00 - Variable in class chemaxon.struc.CTransform3D

The m00 element of the matrix.

m01 - Variable in class chemaxon.struc.CTransform3D

The m01 element of the matrix.

m02 - Variable in class chemaxon.struc.CTransform3D

The m02 element of the matrix.

m03 - Variable in class chemaxon.struc.CTransform3D

The m03 element of the matrix.

m10 - Variable in class chemaxon.struc.CTransform3D

The m10 element of the matrix.

m11 - Variable in class chemaxon.struc.CTransform3D

The m11 element of the matrix.

m12 - Variable in class chemaxon.struc.CTransform3D

The m12 element of the matrix.

m13 - Variable in class chemaxon.struc.CTransform3D

The m13 element of the matrix.

m20 - Variable in class chemaxon.struc.CTransform3D

The m20 element of the matrix.

m21 - Variable in class chemaxon.struc.CTransform3D

The m21 element of the matrix.

m22 - Variable in class chemaxon.struc.CTransform3D

The m22 element of the matrix.

m23 - Variable in class chemaxon.struc.CTransform3D

The m23 element of the matrix.

m30 - Variable in class chemaxon.struc.CTransform3D

The m30 element of the matrix.

m31 - Variable in class chemaxon.struc.CTransform3D

The m31 element of the matrix.

m32 - Variable in class chemaxon.struc.CTransform3D

The m32 element of the matrix.

m33 - Variable in class chemaxon.struc.CTransform3D

The m33 element of the matrix.

MAction - Class in chemaxon.marvin.swing

Comman base class for Marvin actions.

MAction(String, String) - Constructor for class chemaxon.marvin.swing.MAction

Creates an action.

MAction(String, String, KeyStroke) - Constructor for class chemaxon.marvin.swing.MAction

Creates an action.

MAction(String, String, KeyStroke[]) - Constructor for class chemaxon.marvin.swing.MAction

Creates an action.

main(String[]) - Static method in class chemaxon.checkers.StructureCheck

Standard JAVA Main function which delegates the run mechanism to the StructureCheck.run(String[]) method.

main(String[]) - Static method in class chemaxon.descriptors.MolecularDescriptor

Deprecated, for removal: This API element is subject to removal in a future version.

Will be removed, no replacement.

main(String[]) - Static method in class chemaxon.descriptors.ReactionFingerprint

Deprecated, for removal: This API element is subject to removal in a future version.

Will be removed, no replacement.

main(String[]) - Static method in class chemaxon.formats.MdlCompressor

Main program.

main(String[]) - Static method in class chemaxon.formats.MolConverter

Main method.

main(String[]) - Static method in class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

This main method will be removed, CLI interfaces should not be used directly from Java code.

main(String[]) - Static method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Deprecated, for removal: This API element is subject to removal in a future version.

Will be removed, no replacement.

main(String[]) - Static method in class com.chemaxon.version.VersionInfo

Main method that prints out the version information into the standard output.

mainMChemicalStruct - Variable in class chemaxon.struc.MDocument

mainMMoleculeMovie - Variable in class chemaxon.struc.MDocument

mainWithoutExit(String[]) - Static method in class chemaxon.formats.MolConverter

Same as main(), but never calls System.exit().

MajorMicrospeciesAccessorPlugin - Class in chemaxon.marvin.calculations

Common base class for all plugins with possible major microspecies input.

MajorMicrospeciesAccessorPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Constructor.

MajorMicrospeciesPlugin - Class in chemaxon.marvin.calculations

Plugin class that calculates the major microspecies on a given pH.

MajorMicrospeciesPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Constructor.

makeColor(String) - Static method in class chemaxon.struc.MObject

makeEditMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane

Adds menu items to the specified Edit menu.

makeHelpMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 3.4, MarvinPane.addHelpMenu(java.awt.Container) should be used.

makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.Molecule

Copies some properties of this molecule to the other one specified as argument.

makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Copies some properties of this molecule to the other one specified as argument.

makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Copies some properties of this molecule to the other one specified as argument.

makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Copies some properties of this molecule to the other one specified as argument.

makeRecentFileListMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane

Read the recent file list from marvin.properties, and add it to the specified parent menu.

makeSaveAsMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane

Creates the "Save As" menu and adds it to the specified parent menu.

makeStructureMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane

makeTableMenu(Container) - Method in class chemaxon.marvin.view.swing.TableSupport

Creates Table menu items.

makeToolsMenu() - Method in class chemaxon.marvin.beans.MViewPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 3.4, MarvinPane.addToolsMenu(java.awt.Container) should be used.

makeViewMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane

Adds menu items to the specified View menu.

MAnalysisBox - Class in chemaxon.struc.graphics

MAnalysisBox(Molecule, List<MAnalysisBoxTerm>) - Constructor for class chemaxon.struc.graphics.MAnalysisBox

Constructor.

map(int) - Method in interface com.chemaxon.search.transformation.util.IntMapper

Maps an int to another int.

map(RxnMolecule) - Method in class com.chemaxon.mapper.AutoMapper

Maps the reaction.

map(T) - Method in interface com.chemaxon.mapper.Mapper

Marks the matching parts of item with the same identifier.

MapAction - Class in chemaxon.standardizer.actions

Map standardizer action

MapAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MapAction

Initializes the action

MapMoleculeFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which maps the atoms of the molecule incrementally

MapMoleculeFixer() - Constructor for class chemaxon.fixers.MapMoleculeFixer

MAPPED_H - Static variable in class chemaxon.struc.MolAtom

Mapped Hydrogen atom(s).

Mapper<T> - Interface in com.chemaxon.mapper

Provides support for mapping parts of <T> instances by finding the matching parts and mark them with the same identifier.

Mapper.MappingStyle - Enum Class in com.chemaxon.mapper

Available mapping styles by Mapper

MAPPING_STYLE - Static variable in class chemaxon.standardizer.actions.MapAction

mapping style property

MAPPING_STYLE - Static variable in class chemaxon.standardizer.actions.MapReactionAction

mapping style property

mapReaction(MolImporter, MolExporter) - Static method in class com.chemaxon.mapper.AutoMapper

Reads the reactions from the importer, maps them, and writes to the exporter.

mapReaction(MolImporter, MolExporter, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper

Reads the reactions from the importer, maps them, and writes to the exporter.

mapReaction(MolImporter, MolExporter, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper

Reads the reactions from the importer, maps them, and writes to the exporter.

mapReaction(Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper

Maps the reactions in the specified collection using multiple threads if possible.

mapReaction(AutoMapper.Options, Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper

Maps the reactions in the specified collection using the specified options.

mapReaction(Mapper<RxnMolecule>[], Molecule...) - Static method in class com.chemaxon.mapper.AutoMapper

Maps the reactions in the specified collection using the specified mappers in multiple threads.

mapReaction(Collection<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper

Maps the reactions in the specified collection using multiple threads if possible.

mapReaction(Collection<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper

Maps the reactions in the specified collection using the specified options.

mapReaction(Collection<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper

Maps the reactions in the specified collection using the specified mappers in multiple threads.

MapReactionAction - Class in chemaxon.standardizer.actions

Map reaction standardizer action

MapReactionAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MapReactionAction

Initializes the action

MapReactionFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which maps the reaction with AutoMapper.

MapReactionFixer() - Constructor for class chemaxon.fixers.MapReactionFixer

Default constructor

MARGIN_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "marginSize".

MARK_BONDS - Static variable in class chemaxon.standardizer.actions.MapAction

mark bonds property

MARK_BONDS - Static variable in class chemaxon.standardizer.actions.MapReactionAction

mark bonds property

MARKUSH_HIT_INNER - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for returning hit indices of the inner, compiled representation of a Markush target.

MARKUSH_HIT_ORIGINAL - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for returning hit indices of the original Markush target.

MarkushAromaticityHandlingOption - Enum Class in chemaxon.sss.search.options

Option type describing the way aromaticity is handled in Markush structures.

MarkushEnumerationPlugin - Class in chemaxon.marvin.calculations

Plugin class for enumerating Markush molecules.

MarkushEnumerationPlugin() - Constructor for class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Constructor.

MarkushFeature - Class in chemaxon.sss.search

Deprecated, for removal: This API element is subject to removal in a future version.

MarkushFeature(int...) - Constructor for class chemaxon.sss.search.MarkushFeature

Deprecated.

Constructor.

MarkushFeature(int, int[]) - Constructor for class chemaxon.sss.search.MarkushFeature

Deprecated.

Constructor.

MarkushGenerator - Class in chemaxon.sss.search

Generates RgMolecule output that covers the specified targets with the specified scaffold.

MarkushGenerator() - Constructor for class chemaxon.sss.search.MarkushGenerator

Constructor.

MARVIN_CONFIG_DEFAULT_PATH - Static variable in class chemaxon.marvin.common.UserSettings

The default configuration file path inside the chemaxon settings directory in user home.

MarvinPane - Class in chemaxon.marvin.beans

Ancestor of the Marvin Beans.

MarvinPane() - Constructor for class chemaxon.marvin.beans.MarvinPane

Constructor.

MarvinPaneBeanInfo - Class in chemaxon.marvin.beans

Ancestor of Marvin's BeanInfo classes that are needed by GUI builders.

MarvinPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MarvinPaneBeanInfo

MarvinTransferable - Class in chemaxon.marvin.modules.datatransfer

Abstract Adapter implementation of the MTransferable interface used by Marvin.

MarvinTransferable() - Constructor for class chemaxon.marvin.modules.datatransfer.MarvinTransferable

mass() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the molecular weight of the molecule.

mass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the molecular weight of the molecule.

Mass - Class in chemaxon.descriptors.scalars

Implements Mass (total mass of molecule) value as a scalar descriptor.

Mass() - Constructor for class chemaxon.descriptors.scalars.Mass

Creates a new, empty logD descriptor.

Mass(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.Mass

Copy constructor.

Mass(SDParameters) - Constructor for class chemaxon.descriptors.scalars.Mass

Creates a new instance according to the parameters given.

Mass(String) - Constructor for class chemaxon.descriptors.scalars.Mass

Creates a new instance according to the parameters given.

MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "mass".

MASS_SPECTRUM - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "massspectrum".

MAssigner - Class in chemaxon.struc.graphics

Atom assigner to connect two atoms.

MAssigner() - Constructor for class chemaxon.struc.graphics.MAssigner

Contructs an assigner.

MAssigner(MAssigner) - Constructor for class chemaxon.struc.graphics.MAssigner

Copy constructor.

MAssigner(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MAssigner

Contructs an assigner with the specified endpoints.

massPrecision() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the precision of the molecular weight (number of decimal digits).

match(MolAtom, MolAtom) - Method in interface com.chemaxon.search.mcs.McsCustomMatcher

Returns true if the given atoms are matchable according to some custom matching criteria.

match(MolBond, MolBond) - Method in interface com.chemaxon.search.mcs.McsCustomMatcher

Returns true if the given bonds are matchable according to some custom matching criteria.

MATCH_AMBIG_IF_POSSIBLE - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

Ambiguous aromatic parts can be matched by a query if it has the same aromaticity as the target Markush structure considering its reduction (enumeration) according to the hit candidate.

MATCH_COUNT_BETWEEN - Static variable in interface chemaxon.sss.SearchConstants

MATCH_COUNT_RELATION - Static variable in interface chemaxon.sss.SearchConstants

MATCH_RING_BONDS - Enum constant in enum class com.chemaxon.search.mcs.RingHandlingMode

This option allows the algorithm to match a query and a target bond only if both are in rings or both are in chains.

matcher - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

The matcher object containing the preprocessed query and target molecules.

matches(MolAtom, MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Matches 2 atoms

matches(String, long, long) - Method in class chemaxon.formats.MFileFormat

Tests whether the format matches the specified pattern.

MATCHING - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle

Only matching atoms will be mapped

MAtomSetPoint - Class in chemaxon.struc.graphics

Point fixed to the location of one or more atoms.

MAtomSetPoint() - Constructor for class chemaxon.struc.graphics.MAtomSetPoint

Contructs an empty point object.

MAtomSetPoint(MAtomSetPoint) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint

Copy constructor.

MAtomSetPoint(MolAtom[]) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint

Contructs a point object.

Matrix - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView

MAX_LINE_LENGTH - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Maximum desired line length used to form multi-line text.

MAX_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings

The maximum size of sketchRecentFileList

MAX_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "maxscale".

maxAbsOxStateOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the oxidation state that has the maximum absolute value

MaxCliqueMcs - Class in com.chemaxon.search.mcs.maxclique

Implements a heuristic MCS algorithm based on maximum clique detection.

MaxCliqueMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.maxclique.MaxCliqueMcs

Creates a MaxCliqueMcs object with the specified search options.

MaxCommonSubstructure - Class in com.chemaxon.search.mcs

Abstract base class of the algorithms for finding the maximum common substructure (MCS) of two molecules.

MaxCommonSubstructure(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.MaxCommonSubstructure

maxConsideredRingSize(int) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets the maximum size of rings considered for ring matching purposes.

maxNonEmptyId - Variable in class chemaxon.descriptors.MDGenerator

maxNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator

maxParameterCount() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunction

The higher end of the allowed parameter count range (inclusive), or ChemContext.VARARG to signal that there is no maximum.

maxParameterCount() - Method in interface chemaxon.jep.CustomFunction

Returns the maximum parameter count of this function, or CustomFunction.VARARG if there is no maximum.

maxScale(Dimension) - Method in class chemaxon.marvin.MolPrinter

Calculates the maximum scaling factor for fitting the image in a rectangle of the specified size.

maxScale(Rectangle) - Method in class chemaxon.marvin.MolPrinter

Calculates the maximum scaling factor for fitting the image in the specified rectangle.

maxStereoisomerCount() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Returns the adjusted maximum number of generated stereoisomers or Optional#absent().

MAYBE_USEFUL - Static variable in class chemaxon.sss.search.MolComparator

Describes that the MolComparator may be needed with the current search object and the current query, depending on the target.

MBooleanProp - Class in chemaxon.struc.prop

String property.

MBooleanProp(boolean) - Constructor for class chemaxon.struc.prop.MBooleanProp

Constructs a property.

MBooleanProp(String) - Constructor for class chemaxon.struc.prop.MBooleanProp

Constructs a property.

MBracket - Class in chemaxon.struc.graphics

Bracket object.

MBracket() - Constructor for class chemaxon.struc.graphics.MBracket

Constructs a bracket.

MBracket(MBracket) - Constructor for class chemaxon.struc.graphics.MBracket

Copy constructor.

MBracket(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MBracket

Constructs a bracket with the specified corner points.

MBracket(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MBracket

Constructs a bracket with the specified corner points and color.

Mc - Static variable in class chemaxon.core.ChemConst

MChart - Class in com.chemaxon.calculations.gui

Wrapper for the EasyChart module.

MChart() - Constructor for class com.chemaxon.calculations.gui.MChart

Constructor.

MChemicalStruct - Class in chemaxon.struc.graphics

Molecule graph object.

MChemicalStruct(MChemicalStruct) - Constructor for class chemaxon.struc.graphics.MChemicalStruct

Copy constructor.

MChemicalStruct(MoleculeGraph) - Constructor for class chemaxon.struc.graphics.MChemicalStruct

Contructs a molecule graph object.

MCollectionProp - Class in chemaxon.struc.prop

Collection of properties.

MCollectionProp() - Constructor for class chemaxon.struc.prop.MCollectionProp

mcs - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

MCS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType

Deprecated.

MCSAlignment - Interface in chemaxon.marvin.alignment

Align molecules using the maximum common substructure (MCS) of the given molecules.
Usage examples:

MCSAlignment.Factory - Class in chemaxon.marvin.alignment

Factory class for ConformationAlignment.

MCSAlignmentResult - Interface in chemaxon.marvin.alignment

Result class for MCS alignment calculation.

McsCustomMatcher - Interface in com.chemaxon.search.mcs

Interface for custom matching of atoms and bonds for MaxCommonSubstructure search.

McsCustomMatcherFactory - Interface in com.chemaxon.search.mcs

Factory interface for creating McsCustomMatcher objects.

McsSearchOptions - Class in com.chemaxon.search.mcs

Options class for MaxCommonSubstructure (MCS) search.

McsSearchOptions.Builder - Class in com.chemaxon.search.mcs

Builder class for creating immutable instances of the enclosing McsSearchOptions class.

McsSearchResult - Class in com.chemaxon.search.mcs

Class for representing the result of a MaxCommonSubstructure (MCS) search.

McsSearchResult(Molecule, int[], int[], int) - Constructor for class com.chemaxon.search.mcs.McsSearchResult

Creates a SearchResult object representing a common substructure of two molecules.

md - Variable in class chemaxon.descriptors.MDParameters

this object is needed to access default dissimilarity functions

Md - Static variable in class chemaxon.core.ChemConst

MDGenerator - Class in chemaxon.descriptors

Base class for all kinds of MolecularDescriptor generators.

MDGenerator() - Constructor for class chemaxon.descriptors.MDGenerator

Created an object.

MDGeneratorException - Exception in chemaxon.descriptors

Exception definition for the MolecularDescriptor.generate() interface.

MDGeneratorException() - Constructor for exception chemaxon.descriptors.MDGeneratorException

Creates new MDGeneratorException without detailed explanation.

MDGeneratorException(String) - Constructor for exception chemaxon.descriptors.MDGeneratorException

Constructs a MDGeneratorException with the specified detailed message.

MDGeneratorException(String, Throwable) - Constructor for exception chemaxon.descriptors.MDGeneratorException

Constructs a MDGeneratorException with the specified detail message and cause.

MDGeneratorException(Throwable) - Constructor for exception chemaxon.descriptors.MDGeneratorException

Constructs a MDGeneratorException with the specified cause.

MDL_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable

MDL like multiple group expansion flag.

MdlCompressor - Class in chemaxon.formats

Molfile compression.

MdlCompressor(InputStream, OutputStream, int) - Constructor for class chemaxon.formats.MdlCompressor

Create a(n un)compressor for the specified input and output streams.

MDLCT2MDL(byte[]) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Converts an MDLCT data to MDL.

MDocSource - Class in chemaxon.marvin.io

Marvin document source.

MDocSource() - Constructor for class chemaxon.marvin.io.MDocSource

MDocStorage - Class in chemaxon.marvin.view

Sparse dynamic document storage and reader.

MDocStorage() - Constructor for class chemaxon.marvin.view.MDocStorage

Constructs a document storage.

MDocStorage(int) - Constructor for class chemaxon.marvin.view.MDocStorage

Constructs a document storage.

MDocStorage.CancellationException - Exception in chemaxon.marvin.view

Exception indicating that records are not available because the user cancelled file reading.

MDocStorage.Listener - Interface in chemaxon.marvin.view

Document production listener.

MDocStorage.RecordUnavailableException - Exception in chemaxon.marvin.view

Requested record is not available in the source.

MDocument - Class in chemaxon.struc

Marvin document.

MDocument(MDocument) - Constructor for class chemaxon.struc.MDocument

Copy constructor.

MDocument(MDocument, boolean) - Constructor for class chemaxon.struc.MDocument

Copy constructor.

MDocument(Molecule[]) - Constructor for class chemaxon.struc.MDocument

Creates a document for the specified molecule animation.

MDocument(MoleculeGraph) - Constructor for class chemaxon.struc.MDocument

Creates a document for the specified molecule graph.

MDocument.CheckerMark - Class in chemaxon.struc

Provides informations for Structure Checker higlight

MDocument.Prop - Class in chemaxon.struc

Property that stores an MDocument.

MDoubleArrayProp - Class in chemaxon.struc.prop

Double array property.

MDoubleArrayProp(double[]) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp

Constructs a property object from a double array.

MDoubleArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp

Constructs a double array property from a string value.

MDoubleProp - Class in chemaxon.struc.prop

Double floating point property.

MDoubleProp(double) - Constructor for class chemaxon.struc.prop.MDoubleProp

Constructs a property object from a double floating point value.

MDoubleProp(String) - Constructor for class chemaxon.struc.prop.MDoubleProp

Constructs a double floating point property from a string value.

MDParameters - Class in chemaxon.descriptors

MolecularDescriptor parameter settings.

MDParameters() - Constructor for class chemaxon.descriptors.MDParameters

Creates and initializes an empty object.

MDParametersException - Exception in chemaxon.descriptors

MDParametersException reports all kinds of parametrization related failures.

MDParametersException() - Constructor for exception chemaxon.descriptors.MDParametersException

Creates an exception object with a default message.

MDParametersException(String) - Constructor for exception chemaxon.descriptors.MDParametersException

Creates an exception object with a given message.

MDParametersException(String, Throwable) - Constructor for exception chemaxon.descriptors.MDParametersException

Creates an exception object with a given message and cause.

MEASUREMENT_KEY - Static variable in class chemaxon.standardizer.actions.RemoveFragmentAction

Key of measurement for parsing and property change

MEFlow - Class in chemaxon.struc.graphics

Electron flow arrow.
Representing the movement of one or two electrons in a reaction as a curved arrow.
Electron flow can start from any atom or bond, but not from any atom pairs that has no connection bond.
The logic of the electron flows: If the source is an Atom, the sink can be: any Atom Bond connected to this Atom an atom pair from this atom and any other atom (incipient bond) If the source is a Bond, the sink can be: one of the Atoms on the end of this Bond a Bond connected to this Bond (has common ending Atom) an atom pair from one of the Atoms on the end of this Bond and any other atom (incipient bond) If only the sink/source is in an sgroup, the sink/source must be the attachment point.

MEFlow() - Constructor for class chemaxon.struc.graphics.MEFlow

Contructs an empty 2 electron flow arrow.

MEFlow(int) - Constructor for class chemaxon.struc.graphics.MEFlow

Contructs an empty electron flow arrow.

MEFlow(MEFlow) - Constructor for class chemaxon.struc.graphics.MEFlow

Copy constructor.

MEFlow(MPoint, MPoint, int) - Constructor for class chemaxon.struc.graphics.MEFlow

Contructs an electron flow arrow with the specified endpoints.

MEFlowBasePoint - Class in chemaxon.struc.graphics

Electron flow arrow base point.

MEFlowBasePoint() - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint

Contructs an empty point object.

MEFlowBasePoint(MEFlowBasePoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint

Copy constructor.

MEFlowBasePoint(MolAtom, MPoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint

Contructs a point object.

MElectron - Class in chemaxon.struc.graphics

MElectron() - Constructor for class chemaxon.struc.graphics.MElectron

MElectron(DPoint3, MolAtom) - Constructor for class chemaxon.struc.graphics.MElectron

MElectronContainer - Class in chemaxon.struc.graphics

MElectronContainer() - Constructor for class chemaxon.struc.graphics.MElectronContainer

This constructor is only available for MRVImport

MElectronContainer(MElectron) - Constructor for class chemaxon.struc.graphics.MElectronContainer

Creates a Radical from one MElectron

MElectronContainer(MElectron, MElectron) - Constructor for class chemaxon.struc.graphics.MElectronContainer

Creates a LonePair by the clones of the MElectrons.

MElectronContainer(MElectron, MElectron, boolean) - Constructor for class chemaxon.struc.graphics.MElectronContainer

Creates a LonePair which can represent radicals or lonepairs by the clones of the MElectrons.

MEllipse - Class in chemaxon.struc.graphics

Ellipse object.

MEllipse() - Constructor for class chemaxon.struc.graphics.MEllipse

Constructs an ellipse.

MEllipse(MEllipse) - Constructor for class chemaxon.struc.graphics.MEllipse

Copy constructor.

MEllipse(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MEllipse

Constructs a ellipse with the specified corner points.

MEllipse(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MEllipse

Constructs a ellipse with the specified corner points and color.

MENU_CUSTOMIZATION_FILE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "menuconfig".

MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "menubar".

MER - Enum constant in enum class chemaxon.struc.SgroupType

merge(CheckerFixerFactory) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder

Adds all checkers, fixers and properties registered in the given other factory instance.

MERGE_DISTANCE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "mergedst".

mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.

mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.

mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.RgMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.

mergeAtoms(MolAtom, MolAtom) - Method in class chemaxon.struc.RxnMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.

mergeBrackets(MolBond, MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the crossing bonds of this sgroup so that they will share a common bracket.

mergeComponentParts(MoleculeGraph, int, boolean) - Method in class chemaxon.struc.RxnMolecule

Finds those component parts that are contained in the molecule graph m and creates a new component containing all atoms of m, splitting them from the previous merges.

mergeFrags(int, int, int) - Method in class chemaxon.struc.MoleculeGraph

Merges two connected components of the given fragmentation type.

mergeProperties(UserSettings, MPropertyContainer, Rectangle) - Static method in class chemaxon.util.ImageExportUtil

Merge the properties of UserSettings with the GUI properties.
If both has a value for a given key, the value stored in GUI properties will be used.

MesomerizeAction - Class in chemaxon.standardizer.actions

Mesomerize standardizer action

MesomerizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MesomerizeAction

Initializes the action

message - Variable in class chemaxon.naming.document.annotate.DocumentAnnotator.ProgressInfo

A message about the current state of the annotation.

METALCONNECTED_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom(s) connected to metal.

METALLOCENE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that incorrectly drawn metallocene had found in the molecule

METALLOCENE_AMBIGUOUS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that incorrectly drawn metallocenes had found in the molecule

MetalloceneCheckerResult - Class in chemaxon.checkers.result

MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult

Deprecated.

use MetalloceneCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List, List, int) instead

MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>, int) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult

Constructor which initialize all the properties.

MetalloceneErrorChecker - Class in chemaxon.checkers

MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats, that are not coordinate multicenters.

MetalloceneErrorChecker() - Constructor for class chemaxon.checkers.MetalloceneErrorChecker

Default constructor

MetalloceneFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts a single incorrectly drawn metallocene into multicenter based coordinate bond representation.

MetalloceneFixer() - Constructor for class chemaxon.fixers.MetalloceneFixer

METHOD - Static variable in class chemaxon.marvin.services.ServiceDescriptor

Property key for Method name to call as String

METHOD_KEY - Static variable in class chemaxon.standardizer.actions.RemoveFragmentAction

Key of method for parsing and property change

METHOD_KLOP - Static variable in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

This field will not be available from May 2016. Use LogPMethod instead.

METHOD_KLOP - Static variable in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

This field will not be available from May 2016. Use LogPMethod instead.

METHOD_PHYS - Static variable in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

This field will not be available from May 2016. Use LogPMethod instead.

METHOD_PHYS - Static variable in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

This field will not be available from May 2016. Use LogPMethod instead.

METHOD_USER_DEFINED - Static variable in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use LogPMethod.USER_DEFINED instead.

METHOD_USER_DEFINED - Static variable in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use LogPMethod.USER_DEFINED instead.

METHOD_VG - Static variable in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use LogPMethod.CHEMAXON instead.

METHOD_VG - Static variable in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use LogPMethod.CHEMAXON instead.

METHOD_WEIGHTED - Static variable in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use LogPMethod.CONSENSUS instead.

METHOD_WEIGHTED - Static variable in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use LogPMethod.CONSENSUS instead.

metricIndexes - Variable in class chemaxon.descriptors.MDParameters

convert parameterized indexes to MolecularDescriptor metric indexes

Metrics - Class in chemaxon.descriptors

The Metrics class implements dissimilarity metrics for MolecularDescriptors.

Metrics() - Constructor for class chemaxon.descriptors.Metrics

MetricsType - Enum Class in chemaxon.descriptors

MFieldAccessor - Class in chemaxon.marvin.io.fieldaccess

Abstract class for extracting fields (properties) from input and storing them.

MFieldAccessor() - Constructor for class chemaxon.marvin.io.fieldaccess.MFieldAccessor

MFileFormat - Class in chemaxon.formats

File format descriptor class.

MFileFormat(String, String, String, String, String, String, String, String, long) - Constructor for class chemaxon.formats.MFileFormat

Deprecated, for removal: This API element is subject to removal in a future version.

Use one of the MFileFormat.createUserDefined(java.lang.String, java.lang.String, java.lang.String, chemaxon.formats.factory.MRecordReaderFactory, chemaxon.formats.factory.MolImportModuleFactory, chemaxon.formats.factory.MolExportModuleFactory, chemaxon.formats.factory.RecognizerFactory, java.lang.String, long) factory methods.

MFileFormatUtil - Class in chemaxon.formats

File format related utility functions.

MFileFormatUtil() - Constructor for class chemaxon.formats.MFileFormatUtil

MFont - Class in chemaxon.struc.graphics

Font wrapper class that does not require an X server.

MFont(MFont) - Constructor for class chemaxon.struc.graphics.MFont

Copy constructor.

MFont(Font) - Constructor for class chemaxon.struc.graphics.MFont

Create a wrapper for the specified AWT font.

MFont(String) - Constructor for class chemaxon.struc.graphics.MFont

Parses a font from a string.

MFont(String, int, double) - Constructor for class chemaxon.struc.graphics.MFont

Contructs a font.

MFontProp - Class in chemaxon.struc.prop

Font property to store in PropertyContainer

MFontProp(MFont) - Constructor for class chemaxon.struc.prop.MFontProp

MFontProp(Font) - Constructor for class chemaxon.struc.prop.MFontProp

MFontProp(String) - Constructor for class chemaxon.struc.prop.MFontProp

Mg - Static variable in class chemaxon.core.ChemConst

MGPERML - Enum constant in enum class com.chemaxon.calculations.solubility.SolubilityUnit

Solubility is expressed in mg/ml unit.

MHashProp - Class in chemaxon.struc.prop

Linked hash map of properties.

MHashProp() - Constructor for class chemaxon.struc.prop.MHashProp

Constructs a property object from an integer value.

MHashProp(MHashProp, Set) - Constructor for class chemaxon.struc.prop.MHashProp

Copy constructor.

MHCoords3DProp - Class in chemaxon.struc.prop

3D coordinates array property.

MHCoords3DProp(String) - Constructor for class chemaxon.struc.prop.MHCoords3DProp

Constructs a point array property from a string value.

MHCoords3DProp(Map<MolAtom, DPoint3[]>, MoleculeGraph) - Constructor for class chemaxon.struc.prop.MHCoords3DProp

Constructs a property object from a map.

MHCoords3DProp(Map<Integer, DPoint3[]>, long) - Constructor for class chemaxon.struc.prop.MHCoords3DProp

Constructs a property object from a map.

MICROSPECIES_MAJORMS2 - Enum constant in enum class chemaxon.calculator.CalculatorTag

MICROSPECIES_MSDISTR2 - Enum constant in enum class chemaxon.calculator.CalculatorTag

MIN_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings

The minimum size of sketchRecentFileList

MIN_RING_SIZE_FOR_TRANS_DB - Static variable in class chemaxon.struc.MoleculeGraph

The minimal size of the ring for the existence of TRANS double bond.

minFragmentSize(int) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets the minimum required size of the fragments of MCS.

MinMaxDistance - Class in chemaxon.marvin.alignment

Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.

MinMaxDistance() - Constructor for class chemaxon.marvin.alignment.MinMaxDistance

minNonEmptyId - Variable in class chemaxon.descriptors.MDGenerator

minNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator

minParameterCount() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunction

The lower end of the allowed parameter count range (inclusive).

minParameterCount() - Method in interface chemaxon.jep.CustomFunction

Returns the minimum parameter count of this function.

MIntegerArrayProp - Class in chemaxon.struc.prop

Integer array property.

MIntegerArrayProp(int[]) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp

Constructs a property object from an integer value.

MIntegerArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp

Constructs an integer array property from a string value.

MIntegerProp - Class in chemaxon.struc.prop

Integer property.

MIntegerProp(int) - Constructor for class chemaxon.struc.prop.MIntegerProp

Constructs a property object from an integer value.

MIntegerProp(String) - Constructor for class chemaxon.struc.prop.MIntegerProp

Constructs an integer property from a string value.

MISSING_ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom with no atom map had found in the molecule

MISSING_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule with missing R-group definition found

MissingAtomMapChecker - Class in chemaxon.checkers

MissingAtomMapChecker detects unmapped atoms.

MissingAtomMapChecker() - Constructor for class chemaxon.checkers.MissingAtomMapChecker

Default constructor

MissingRGroupChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting missing R-group definition errors.

MissingRGroupChecker() - Constructor for class chemaxon.checkers.MissingRGroupChecker

Initializes the checker

MIXTURE - Enum constant in enum class chemaxon.struc.SgroupType

MListProp - Class in chemaxon.struc.prop

Property list property.

MListProp() - Constructor for class chemaxon.struc.prop.MListProp

Constructs a property object from a list.

MListProp(MListProp, Set) - Constructor for class chemaxon.struc.prop.MListProp

Copy constructor.

MMF_FIELD - Static variable in class chemaxon.marvin.view.swing.TableOptions

Main molecule is a field in at least one record.

MMF_NOT_FIELD - Static variable in class chemaxon.marvin.view.swing.TableOptions

Main molecule is not a field in at least one record.

MMF_UNSET - Static variable in class chemaxon.marvin.view.swing.TableOptions

Not yet decided whether the main molecule is a field or not.

MMidPoint - Class in chemaxon.struc.graphics

Middle point in a line.

MMidPoint(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint

Copy constructor.

MMidPoint(MPolyline, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MMidPoint

Contructs a middle point object.

MMidPoint.Sticky - Class in chemaxon.struc.graphics

Fixed middle point that can be a point of a polyline.

MMoleculeMovie - Class in chemaxon.struc.graphics

Molecule animation.

MMoleculeMovie(MMoleculeMovie) - Constructor for class chemaxon.struc.graphics.MMoleculeMovie

Copy constructor.

MMoleculeMovie(Molecule[]) - Constructor for class chemaxon.struc.graphics.MMoleculeMovie

Contructs a molecule animation.

MMoleculeProp - Class in chemaxon.struc.prop

Molecule property.

MMoleculeProp(Molecule) - Constructor for class chemaxon.struc.prop.MMoleculeProp

Constructs a property object from a molecule.

MMoleculeStringProp - Class in chemaxon.struc.prop

Molecule string property.

MMoleculeStringProp(String, String, String) - Constructor for class chemaxon.struc.prop.MMoleculeStringProp

Constructs a property.

MMPAlignment - Class in chemaxon.marvin.alignment

3D Molecular alignment that uses the maximum common substructure to align a pair of structures.

MMPAlignment(Molecule, Molecule) - Constructor for class chemaxon.marvin.alignment.MMPAlignment

Constructs an MMPAlignment object for later alignment of two structures.

MMPAlignment(Molecule, Molecule, MMPAlignmentProperties) - Constructor for class chemaxon.marvin.alignment.MMPAlignment

Constructs an MMPAlignment object for later alignment of two structures.

MMPAlignmentProperties - Class in chemaxon.marvin.alignment

Input property settings for MMPAlignment.

MMPAlignmentProperties() - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties

Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3

MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties

Constructs a MMPAlignmentProperties object.

MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties

Constructs a MMPAlignmentProperties object.

MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean, int) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties

Constructs a MMPAlignmentProperties object.

MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, int) - Constructor for class chemaxon.marvin.alignment.MMPAlignmentProperties

Constructs a MMPAlignmentProperties object.

MMPAlignmentResult - Class in chemaxon.marvin.alignment

Results of the MMPAlignment process.

Mn - Static variable in class chemaxon.core.ChemConst

MNameTextBox - Class in chemaxon.struc.graphics

Name Text box object to display IUPAC name.

MNameTextBox() - Constructor for class chemaxon.struc.graphics.MNameTextBox

Constructs an empty name text box.

MNameTextBox(MNameTextBox) - Constructor for class chemaxon.struc.graphics.MNameTextBox

Copy constructor.

Mo - Static variable in class chemaxon.core.ChemConst

MObject - Class in chemaxon.struc

Paintable object.

MObject(MObject) - Constructor for class chemaxon.struc.MObject

Copy constructor.

MObject(Color, Color, Color) - Constructor for class chemaxon.struc.MObject

Contructs a paintable object with the specified color.

MObjectProp - Class in chemaxon.struc.prop

Property that stores any object.

MObjectProp(Object) - Constructor for class chemaxon.struc.prop.MObjectProp

Constructs a property object.

MObjectProp(String) - Constructor for class chemaxon.struc.prop.MObjectProp

Constructs a property from a string value.

mode - Variable in class chemaxon.checkers.StructureCheckOptions

The mode of the structure check (only check or fixes too)

ModeConverter() - Constructor for class chemaxon.checkers.StructureCheckOptions.ModeConverter

MODEL_LARGE - Static variable in class chemaxon.marvin.calculations.pKaPlugin

Calculation model: large (always precise, can take more time).

MODEL_SMALL - Static variable in class chemaxon.marvin.calculations.pKaPlugin

Calculation model: small (precise up to the specified number of ionizable atoms).

MODERATE - Enum constant in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

Moderate solubility.

MODIFICATION - Enum constant in enum class chemaxon.struc.SgroupType

modifyAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes

Adds atoms to the "modified atom" list.

modifyAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes

Adds atoms to the "modified atom" list.

modifyAtom(MolAtom) - Method in class chemaxon.standardizer.Changes

Adds an atom to the "modified atom" list.

modifyAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes

Adds an atom to the "modified atom" list.

MOL - Static variable in class chemaxon.formats.MFileFormat

MDL Molfiles and Rgfiles.

MOL - Static variable in class chemaxon.jep.context.MolContext

MOL_LOADER_FINISHED_EVENT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "molLoaderFinishedEvent".

MOL_UID_PROPERTY - Static variable in class chemaxon.naming.document.annotate.DocumentAnnotator

MOL_V2_OUT - Static variable in class chemaxon.formats.MFileFormat

MOL_V3_OUT - Static variable in class chemaxon.formats.MFileFormat

MDL Extended Molfiles and Rgfiles.

MOL2 - Static variable in class chemaxon.formats.MFileFormat

Tripos Mol2 files.

MolAligner - Class in chemaxon.marvin.alignment

Tool for aligning a target molecule to a pattern molecule.

MolAligner() - Constructor for class chemaxon.marvin.alignment.MolAligner

Creates a new MolAligner object.

MolAligner(Molecule, Molecule) - Constructor for class chemaxon.marvin.alignment.MolAligner

Creates a new MolAligner object while setting the pattern and target molecules

MolAtom - Class in chemaxon.struc

Atom object and the properties of the elements.

MolAtom(double, double) - Constructor for class chemaxon.struc.MolAtom

Construct a carbon atom at the specified location.

MolAtom(int) - Constructor for class chemaxon.struc.MolAtom

Construct an atom of the specified type at the origin.

MolAtom(int, double, double, double) - Constructor for class chemaxon.struc.MolAtom

Construct an atom.

MolBond - Class in chemaxon.struc

Chemical bond.

MolBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.MolBond

Construct a single bond between two atoms.

MolBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.MolBond

Construct a bond between two atoms.

MolBond(MolAtom, MolAtom, BondType) - Constructor for class chemaxon.struc.MolBond

Construct a bond between two atoms.

MolBond(MolBond) - Constructor for class chemaxon.struc.MolBond

Copy constructor.

MolComparator - Class in chemaxon.sss.search

Interface for comparing atoms, bonds, etc.

MolComparator() - Constructor for class chemaxon.sss.search.MolComparator

MolCondition - Interface in chemaxon.jep

Deprecated, for removal: This API element is subject to removal in a future version.

Will be removed soon.

MolContext - Class in chemaxon.jep.context

Expression evaluation context containing a single molecule.

MolContext() - Constructor for class chemaxon.jep.context.MolContext

Constructor.

MolContext(Molecule) - Constructor for class chemaxon.jep.context.MolContext

Creates a MolContext with the given input molecule.

MolConverter - Class in chemaxon.formats

Converts between molecule file formats.

MolConverter(MolConverter.Builder) - Constructor for class chemaxon.formats.MolConverter

Creates a MolConverter object.

MolConverter(MolConverter.Options) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, use MolConverter.Builder.build() instead.

MolConverter(InputStream, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter

Creates a MolConverter object.

MolConverter(InputStream, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter

Use this constructor if you do not need output buffering but want to determine output file positions.

MolConverter(List<Object>, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, replaced by MolConverter(Builder)

MolConverter(List<Object>, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, replaced by MolConverter(Builder)

MolConverter(List<Object>, List<String>, OutputStream, String, boolean) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, replaced by MolConverter(Builder)

MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, replaced by MolConverter(Builder)

MolConverter(List<Object>, List<String>, OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, replaced by MolConverter(Builder)

MolConverter(List<Object>, List<String>, String, String, boolean) - Constructor for class chemaxon.formats.MolConverter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, replaced by MolConverter(Builder)

MolConverter.Builder - Class in chemaxon.formats

MolConverter builder.

MolConverter.Options - Class in chemaxon.formats

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 5.2.3, use MolConverter.Builder instead.

molCount - Variable in class chemaxon.descriptors.MDGenerator

variables to collect statistical data in

MolecularDescriptor - Class in chemaxon.descriptors

Generic definition of molecular descriptors.

MolecularDescriptor() - Constructor for class chemaxon.descriptors.MolecularDescriptor

Default constructor, creates an empty object.

MolecularDescriptor(MDParameters) - Constructor for class chemaxon.descriptors.MolecularDescriptor

Creates a new MolecularDescriptor with the given parameters.

MolecularDescriptor(MolecularDescriptor) - Constructor for class chemaxon.descriptors.MolecularDescriptor

Copy constructor, creates am identical copy of the MolecularDescriptor passed as a parameter.

MolecularDescriptorGenerator - Interface in chemaxon.descriptors

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

MolecularDynamicsPlugin - Class in chemaxon.marvin.calculations

Molecular Dynamics plugin.

MolecularDynamicsPlugin() - Constructor for class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Creates a new instance of MolecularDynamicsPlugin

MolecularFormulas - Class in com.chemaxon.calculations.elemanal.factory

Static utility methods related to molecular formula calculations.

MolecularFormulas - Class in com.chemaxon.calculations.elemanal

Deprecated, for removal: This API element is subject to removal in a future version.

Moved to MolecularFormulas.

molecule - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

The Molecule which will be transferred to the clipboard.

molecule - Variable in class chemaxon.standardizer.runner.BasicStandardizerRunner

The Molecule instance to standardize

Molecule - Class in chemaxon.struc

Molecule class.

Molecule() - Constructor for class chemaxon.struc.Molecule

Construct a 2 dimensional molecule.

Molecule(Molecule, int, int) - Constructor for class chemaxon.struc.Molecule

Construct a molecule or fragment with the specified number of atoms and bonds.

Molecule(Molecule, MolAtom) - Constructor for class chemaxon.struc.Molecule

Construct a molecule consisting of a single atom (node).

Molecule(Molecule, MolBond) - Constructor for class chemaxon.struc.Molecule

Construct a molecule consisting of a single bond (edge).

MOLECULE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "mol".

MOLECULE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Calculation domain type: calculation refers to the molecule.

MOLECULE_BACKGROUND - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "molbg".

MOLECULE_CHANGED - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "molChanged".

MOLECULE_CHARGE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that the sum charge of the molecule wasn't zero

MOLECULE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "molFormat".

MoleculeChargeChecker - Class in chemaxon.checkers

MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.

MoleculeChargeChecker() - Constructor for class chemaxon.checkers.MoleculeChargeChecker

Default constructor

MoleculeGraph - Class in chemaxon.struc

A graph consisting of MolAtom nodes and MolBond edges.

MoleculeGraph() - Constructor for class chemaxon.struc.MoleculeGraph

Construct a 2 dimensional molecule.

MoleculeGraph(MoleculeGraph, int, int) - Constructor for class chemaxon.struc.MoleculeGraph

Construct a molecule or fragment with the specified number of atoms and bonds.

MoleculeGraph.ValenceCheckState - Enum Class in chemaxon.struc

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and ValenceCheckOptions.

MoleculeImporter - Class in chemaxon.marvin.io.formats

Molecule importer.

MoleculeImporter(File) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the file.

MoleculeImporter(File, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the file.

MoleculeImporter(InputStream) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the input stream.

MoleculeImporter(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the stream.

MoleculeImporter(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the stream.

MoleculeImporter(String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the file.

MoleculeImporter(String, String) - Constructor for class chemaxon.marvin.io.formats.MoleculeImporter

Constructs a new importer for the file.

MoleculeImporterIface - Interface in chemaxon.marvin.io.formats

Interface for molecule importer classes.

MoleculeIterator - Interface in chemaxon.util.iterator

Molecule iterator.

MoleculeIteratorFactory - Class in chemaxon.util.iterator

Molecule iterator factory.

MoleculeIteratorFactory() - Constructor for class chemaxon.util.iterator.MoleculeIteratorFactory

MOLECULES - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Calculation domain type: calculation refers to multiple molecule output.

MoleculeWithValence<AtomReference> - Interface in chemaxon.core.calculations.valencecheck

Interface for molecule object for which valence calculations can be performed.

MolExport - Class in chemaxon.marvin.io.formats.mdl

Exports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.

MolExport() - Constructor for class chemaxon.marvin.io.formats.mdl.MolExport

Constructor.

MolExporter - Class in chemaxon.formats

Molecule exporter class.

MolExporter(OutputStream, String) - Constructor for class chemaxon.formats.MolExporter

Creates a molecule exporter.

MolExporter(OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolExporter

Creates a molecule exporter.

MolExporter(OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolExporter

Creates a molecule exporter.

MolExporter(OutputStream, String, String) - Constructor for class chemaxon.formats.MolExporter

Creates a molecule exporter.

MolExporter(String, String) - Constructor for class chemaxon.formats.MolExporter

Creates a molecule exporter.

MolExporter(String, String, int, String[], String) - Constructor for class chemaxon.formats.MolExporter

Creates a molecule exporter.

MolExportException - Exception in chemaxon.marvin.io

Molecule export exception.

MolExportException(String) - Constructor for exception chemaxon.marvin.io.MolExportException

Creates a molecule export exception with the specified message.

MolExportException(String, Throwable) - Constructor for exception chemaxon.marvin.io.MolExportException

Creates a molecule export exception with the specified message and cause.

MolExportException(Throwable) - Constructor for exception chemaxon.marvin.io.MolExportException

Creates a molecule export exception with the specified cause.

MolExportModule - Class in chemaxon.marvin.io

Abstract base class of molecule export modules.

MolExportModule() - Constructor for class chemaxon.marvin.io.MolExportModule

MolExportModuleFactory - Interface in chemaxon.formats.factory

Factory interface for MolExportModules.

MolfileUtil - Class in chemaxon.marvin.io.formats.mdl

MDL molfile related utility methods.

MolfileUtil() - Constructor for class chemaxon.marvin.io.formats.mdl.MolfileUtil

MolFilter - Interface in chemaxon.util

Molecule filter.

MolFormatException - Exception in chemaxon.formats

Something's wrong with a molecule file format.

MolFormatException() - Constructor for exception chemaxon.formats.MolFormatException

Creates a molecule format exception.

MolFormatException(String) - Constructor for exception chemaxon.formats.MolFormatException

Creates a molecule format exception with the specified message.

MolFormatException(String, Throwable) - Constructor for exception chemaxon.formats.MolFormatException

Creates a molecule format exception with the specified message and cause.

MolFormatException(Throwable) - Constructor for exception chemaxon.formats.MolFormatException

Creates a molecule format exception with the specified cause.

molID - Variable in class chemaxon.marvin.alignment.AlignmentMolecule

MolImport - Class in chemaxon.marvin.io.formats.mdl

Imports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.

MolImport() - Constructor for class chemaxon.marvin.io.formats.mdl.MolImport

MolImporter - Class in chemaxon.formats

Molecule file importer.

MolImporter(File) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for a file.

MolImporter(File, String) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for a file.

MolImporter(InputStream) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for an input stream.

MolImporter(InputStream, String) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for an input stream.

MolImporter(InputStream, String, String) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for an input stream.

MolImporter(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for an input stream.

MolImporter(String) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer for a file.

MolImporter(String, Component, String) - Constructor for class chemaxon.formats.MolImporter

Create a molecule importer with a progress monitor.

MolImporter(String, Object, String) - Constructor for class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

Use MolImporter(String, Component, String) instead.

MolImportModule - Class in chemaxon.marvin.io

Base class of Molecule import modules.

MolImportModule() - Constructor for class chemaxon.marvin.io.MolImportModule

MolImportModule.PreferredView - Enum Class in chemaxon.marvin.io

MolImportModuleFactory - Interface in chemaxon.formats.factory

Factory interface for MolImportModules.

MolInputProducer - Class in chemaxon.util.concurrent.marvin

Input producer wrapping a MolImporter object.

MolInputProducer() - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer

Constructor.

MolInputProducer(MolImporter) - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer

Constructor.

MolInputProducer(MolImporter[]) - Constructor for class chemaxon.util.concurrent.marvin.MolInputProducer

Constructor.

MolInputStream - Class in chemaxon.formats

Molecule input stream that has the ability to determine the input file format.

MolInputStream(InputStream) - Constructor for class chemaxon.formats.MolInputStream

Create a molecule input stream from an ordinary one, and determine the format.

MolInputStream(InputStream, String) - Constructor for class chemaxon.formats.MolInputStream

Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.

MolInputStream(InputStream, String, String) - Constructor for class chemaxon.formats.MolInputStream

Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.

MolInputStream(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolInputStream

Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.

MOLMASS - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

Mass of the molecule

MOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil

Read multi-molecule files as movies.

molPanel - Variable in class chemaxon.marvin.beans.MarvinPane

Underlying panel.

MOLPERL - Enum constant in enum class com.chemaxon.calculations.solubility.SolubilityUnit

Solubility is expressed in mol/l unit.

MolPrinter - Class in chemaxon.marvin

Molecule renderer that can draw a molecule to a graphics context using various display settings.

MolPrinter() - Constructor for class chemaxon.marvin.MolPrinter

Constructs a molecule renderer for an empty molecule.

MolPrinter(MDocument) - Constructor for class chemaxon.marvin.MolPrinter

Constructs a molecule renderer for the specified document.

MolPrinter(MoleculeGraph) - Constructor for class chemaxon.marvin.MolPrinter

Constructs a molecule renderer for the specified molecule.

MolRenderer - Class in chemaxon.marvin.beans

MolRenderer is a simple TableCellRenderer component based on MolPrinter that can be used to render Molecule objects in JTables.

MolRenderer() - Constructor for class chemaxon.marvin.beans.MolRenderer

MolSearch - Class in chemaxon.sss.search

Atom-by-atom structure search.

MolSearch() - Constructor for class chemaxon.sss.search.MolSearch

Constructs a MolSearch object.

MolSearchOptions - Class in chemaxon.sss.search

Class to encapsulate search parameters used by Search implementations(ex: MolSearch).

MolSearchOptions(int) - Constructor for class chemaxon.sss.search.MolSearchOptions

Creates a MolSearchOptions object while setting different search options according to a predefined search type.

molToScreenCoords(DPoint3, Point2D) - Method in class chemaxon.marvin.MolPrinter

Converts molecular coordinates to 2D screen coordinates.

MONOMER - Enum constant in enum class chemaxon.struc.SgroupType

MONOVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Monovalent radical center.

MORE_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "moreEnabled".

MORE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

multiple error message for checker

moreErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the more than one error message for the checker

mouseClicked(MouseEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

mouseEntered(MouseEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

mouseExited(MouseEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

mousePressed(MouseEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Shows / hides popup.

mouseReleased(MouseEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Shows / hides popup.

moveCorners(double, double) - Method in class chemaxon.struc.MolAtom

Translates the coordinates of the atom label.

moveMainMoleculeGraphToFront() - Method in class chemaxon.struc.MDocument

Move the main molecule graph to the top of stack.

moveMoleculeMovieToFront() - Method in class chemaxon.struc.MDocument

Move the molecule movie (if exists) to the top of stack.

moveObject(MObject, int) - Method in class chemaxon.struc.MDocument

Move an object to another place in the stack.

moveTo(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Move the molecule.

MP_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "mpVisible".

MP_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "mpVisible" property.

MPoint - Class in chemaxon.struc

Point object.

MPoint(double, double) - Constructor for class chemaxon.struc.MPoint

Contructs a point object.

MPoint(double, double, double) - Constructor for class chemaxon.struc.MPoint

Contructs a point object.

MPoint(DPoint3) - Constructor for class chemaxon.struc.MPoint

Constructs a point object.

MPoint(MPoint) - Constructor for class chemaxon.struc.MPoint

Copy constructor.

MPolyline - Class in chemaxon.struc.graphics

Polyline object.

MPolyline() - Constructor for class chemaxon.struc.graphics.MPolyline

Contructs an empty line.

MPolyline(boolean, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline

Creates a closed polyline.

MPolyline(MPolyline) - Constructor for class chemaxon.struc.graphics.MPolyline

Copy constructor.

MPolyline(MPolyline, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline

Contructs a polyline from the specified starting polyline and endpoint.

MPolyline(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline

Contructs a line with the specified endpoints.

MPolyline(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline

Contructs a line with the specified endpoints.

MProgressMonitor - Interface in chemaxon.common.util

Progress monitor interface.

MProp - Class in chemaxon.struc

Property base class.

MProp() - Constructor for class chemaxon.struc.MProp

MPropertyContainer - Class in chemaxon.struc

Property container.

MPropertyContainer() - Constructor for class chemaxon.struc.MPropertyContainer

Creates an empty property container.

MPropHandler - Class in chemaxon.marvin.io

Property factory.

MPropHandler() - Constructor for class chemaxon.marvin.io.MPropHandler

MRArrow - Class in chemaxon.struc.graphics

Reaction arrow object.

MRArrow() - Constructor for class chemaxon.struc.graphics.MRArrow

Constructs an empty reaction arrow where end points are not set.

MRArrow(MRArrow) - Constructor for class chemaxon.struc.graphics.MRArrow

Copy constructor.

MRArrow(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRArrow

Constructs a graphical reaction arrow between two points.

MReactionSign - Class in chemaxon.struc.graphics

Special MTextBox desdendant for displaying Reaction signs.

MReactionSign() - Constructor for class chemaxon.struc.graphics.MReactionSign

MReactionSign(DPoint3) - Constructor for class chemaxon.struc.graphics.MReactionSign

MRecord - Class in chemaxon.marvin.io

Record in a multi-molecule file.

MRecord() - Constructor for class chemaxon.marvin.io.MRecord

Default constructor.

MRecord(long, long, int, String, MPropertyContainer, int[]) - Constructor for class chemaxon.marvin.io.MRecord

Creates a record.

MRecord(long, long, int, String, MPropertyContainer, int[], int) - Constructor for class chemaxon.marvin.io.MRecord

Creates a record.

MRecord(long, long, int, String, MPropertyContainer, int[], int, String) - Constructor for class chemaxon.marvin.io.MRecord

Creates a record.

MRecordImporter - Class in chemaxon.marvin.io

Marvin molecule file reader.

MRecordImporter(MolInputStream, String) - Constructor for class chemaxon.marvin.io.MRecordImporter

Creates a reader for the specified molecule input stream in concurrent mode.

MRecordParseException - Exception in chemaxon.marvin.io

Record reading exception.

MRecordParseException(MRecordReader.Position, String) - Constructor for exception chemaxon.marvin.io.MRecordParseException

Creates an exception with the specified message.

MRecordParseException(MRecordReader.Position, String, Throwable) - Constructor for exception chemaxon.marvin.io.MRecordParseException

Creates an exception with the specified message and cause.

MRecordParseException(MRecordReader.Position, Throwable) - Constructor for exception chemaxon.marvin.io.MRecordParseException

Creates an exception with the specified cause.

MRecordReader - Interface in chemaxon.marvin.io

Marvin record reader.

MRecordReader.Position - Class in chemaxon.marvin.io

Position in the input file.

MRecordReaderFactory - Interface in chemaxon.formats.factory

Factory interface for MRecordReaders.

MRectangle - Class in chemaxon.struc.graphics

Rectangle object.

MRectangle() - Constructor for class chemaxon.struc.graphics.MRectangle

Constructs a rectangle.

MRectangle(MRectangle) - Constructor for class chemaxon.struc.graphics.MRectangle

Copy constructor.

MRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRectangle

Constructs a rectangle with the specified corner points.

MRectangle(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MRectangle

Constructs a rectangle with the specified corner points.

MRectanglePoint - Class in chemaxon.struc.graphics

Rectangle point object.

MRectanglePoint(MRectangle, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MRectanglePoint

Contructs a rectangle corner point object.

MRectanglePoint(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint

Copy constructor.

MRectanglePoint.Sticky - Class in chemaxon.struc.graphics

Fixed rectangle point that can be a point of a polyline.

MRoundedRectangle - Class in chemaxon.struc.graphics

Rounded rectangle object.

MRoundedRectangle() - Constructor for class chemaxon.struc.graphics.MRoundedRectangle

Constructs a rounded rectangle

MRoundedRectangle(MRoundedRectangle) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle

Copy constructor.

MRoundedRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle

Constructs a rounded rectangle with the specified corner points.

MRoundedRectangle(MPoint, MPoint, double, double) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle

Constructs a rounded rectangle with the specified corner points.

MRoundedRectangle(MPoint, MPoint, double, double, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle

Constructs a rounded rectangle with the specified corner points and color.

MRoundedRectangle(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle

Constructs a rounded rectangle with the specified corner points and color.

MRV - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Marvin Document.

MRV_OUTPUT_LEVEL - Static variable in class chemaxon.sss.search.Search

MRV format of the query and target is logged at this level.

MSA - Enum constant in enum class chemaxon.calculator.CalculatorTag

MSAPlugin - Class in chemaxon.marvin.calculations

Plugin class for molecular surface area calculation.

MSAPlugin() - Constructor for class chemaxon.marvin.calculations.MSAPlugin

Constructor.

MSBMP - Static variable in class chemaxon.formats.MFileFormat

Windows Bitmap format.

MSelectionDocument - Class in chemaxon.struc

Selection document.

MSelectionDocument(MSelectionDocument) - Constructor for class chemaxon.struc.MSelectionDocument

Copy constructor.

MSelectionDocument(SelectionMolecule) - Constructor for class chemaxon.struc.MSelectionDocument

Creates a document for the specified molecule graph.

MSketch - Class in chemaxon.marvin.beans

Java independent serialization of the sketcher bean.

MSketch() - Constructor for class chemaxon.marvin.beans.MSketch

Constructor used for deserialization.

MSketch(MSketchPane) - Constructor for class chemaxon.marvin.beans.MSketch

Constructor used for serialization.

MSketchPane - Class in chemaxon.marvin.beans

The MarvinSketch Bean.

MSketchPane() - Constructor for class chemaxon.marvin.beans.MSketchPane

Constructs the sketcher.

MSketchPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MSketchPane

Constructs the sketcher with the specified user settings object.

MSketchPane(UserSettings, boolean) - Constructor for class chemaxon.marvin.beans.MSketchPane

Constructs the sketcher with the specified user settings object.

MSketchPane(UserSettings, boolean, JComponent) - Constructor for class chemaxon.marvin.beans.MSketchPane

Constructs the sketcher with the specified user settings object.

MSketchPaneBeanInfo - Class in chemaxon.marvin.beans

MarvinSketch bean information.

MSketchPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MSketchPaneBeanInfo

MStringProp - Class in chemaxon.struc.prop

String property.

MStringProp(String) - Constructor for class chemaxon.struc.prop.MStringProp

Constructs a property.

Mt - Static variable in class chemaxon.core.ChemConst

MTextAttributes - Class in chemaxon.struc.graphics

Text attributes.

MTextAttributes(int, int, Color, MFont, double, double, double) - Constructor for class chemaxon.struc.graphics.MTextAttributes

Constructs a attributes object.

MTextBox - Class in chemaxon.struc.graphics

Text box object.

MTextBox() - Constructor for class chemaxon.struc.graphics.MTextBox

Contructs an empty text box.

MTextBox(MTextBox) - Constructor for class chemaxon.struc.graphics.MTextBox

Copy constructor.

MTextBoxTransformation - Class in chemaxon.struc.graphics

MTextBoxTransformation(MTextBox, CTransform3D, double) - Constructor for class chemaxon.struc.graphics.MTextBoxTransformation

MTextDocument - Class in chemaxon.struc.graphics

Text document consisting of sections with different attributes.

MTextDocument() - Constructor for class chemaxon.struc.graphics.MTextDocument

Constructs an empty document.

MTextDocument(MTextDocument) - Constructor for class chemaxon.struc.graphics.MTextDocument

Copy constructor.

MTextDocument(String) - Constructor for class chemaxon.struc.graphics.MTextDocument

Constructs a document from the specified string.

MTextDocument.Portion - Class in chemaxon.struc.graphics

Selected text.

MTextDocument.Section - Class in chemaxon.struc.graphics

Plain text section with uniform attributes.

MTransferable - Interface in chemaxon.marvin.modules.datatransfer

The interface of Marvin transferable implementations.

MTransformable - Interface in chemaxon.struc

Interface for 3D transformable classes.

mul(CTransform3D) - Method in class chemaxon.struc.CTransform3D

Multiplies by another matrix from right.

MULTI_CENTER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing that invalid R-group definition is in the molecule

MULTI_COMPONENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule had contained multiple components

MULTIBOND - Static variable in class chemaxon.sss.search.MarkushFeature

Deprecated.

Expansion type: multiple position bond.

MULTICENTER - Enum constant in enum class chemaxon.struc.SgroupType

MULTICENTER - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of a central atom of a MulticenterSgroup.

MultiCenterChecker - Class in chemaxon.checkers

MultiCenterChecker detects structures containing multicenter atoms.

MultiCenterChecker() - Constructor for class chemaxon.checkers.MultiCenterChecker

MulticenterSgroup - Class in chemaxon.struc.sgroup

Multicenter S-group to represent complexes like markush ring structures, ferrocenes, metallocenes...

MulticenterSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup

Constructs a Multicenter S-group.

MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup

Copy constructor.

MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup

Copy constructor.

MultiComponentChecker - Class in chemaxon.checkers

MultiComponentChecker detects structures containing disconnected components/fragments.

MultiComponentChecker() - Constructor for class chemaxon.checkers.MultiComponentChecker

Default constructor

MULTIPLE - Enum constant in enum class chemaxon.struc.SgroupType

MULTIPLE - Static variable in class chemaxon.formats.MolExporter

Use this flag to produce multiple output files.

MULTIPLE_STEREO_CENTER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule contains multiple stereo centers

MultipleSgroup - Class in chemaxon.struc.sgroup

Multiple S-group.

MultipleSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup

Constructs a multiple S-group.

MultipleSgroup(MultipleSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup

Copy constructor.

MultipleStereocenterChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting molecules containing multiple stereocenters.

MultipleStereocenterChecker() - Constructor for class chemaxon.checkers.MultipleStereocenterChecker

Initializes a multiple stereo checker

Multiplet - Class in chemaxon.calculations.nmr

Class for NMR multiplets.

Multiplet(boolean) - Constructor for class chemaxon.calculations.nmr.Multiplet

Constructor.

multipliedScore() - Method in class chemaxon.calculations.bbb.BBB.Property

MULTISET - Static variable in class chemaxon.formats.MFileFormatUtil

The multi-molecule file really contains multiple atom sets of one molecule.

MView - Class in chemaxon.marvin.beans

Java independent serialization of the viewer bean.

MView() - Constructor for class chemaxon.marvin.beans.MView

Constructor used for deserialization.

MView(MViewPane) - Constructor for class chemaxon.marvin.beans.MView

Constructor used for serialization.

MViewEditor - Class in chemaxon.marvin.beans

MViewEditor is an implementation of AbstractCellEditor and TableCellEditor that can be used to assign a cell editor to Molecule objects in JTables.

MViewEditor() - Constructor for class chemaxon.marvin.beans.MViewEditor

Creates the cell editor.

MViewPane - Class in chemaxon.marvin.beans

The MarvinView Bean.

MViewPane() - Constructor for class chemaxon.marvin.beans.MViewPane

Constructs the viewer.

MViewPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MViewPane

Constructs the viewer with the specified user settings.

MViewPaneBeanInfo - Class in chemaxon.marvin.beans

MarvinView bean information.

MViewPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MViewPaneBeanInfo

MViewParams - Class in chemaxon.marvin.beans

MViewParams is a helper tool to generate parameter string to MViewPane.

MViewParams() - Constructor for class chemaxon.marvin.beans.MViewParams

For each new parameter generation a new MViewParams instance is necessary to be created.

MViewRenderer - Class in chemaxon.marvin.beans

MViewRenderer is a TableCellRenderer component that can be used to render Molecule objects in JTables.

MViewRenderer() - Constructor for class chemaxon.marvin.beans.MViewRenderer

Creates the cell renderer.

MW - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Molecular weight.

MWHBN - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction

MW^(-0.5) * (HBN), where HBN = HBA + HBD.

N

N - Static variable in class chemaxon.core.ChemConst

Na - Static variable in class chemaxon.core.ChemConst

name - Variable in class chemaxon.marvin.services.ServiceArgument

the name of the argument

name() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the name of the checker

name() - Element in annotation interface chemaxon.fixers.FixerInfo

Returns the name of the fixer.

name() - Method in class chemaxon.marvin.io.Encoding

Gets the name of the encoding.

name() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the name of the action

NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

name property of checker

NAME - Static variable in class chemaxon.fixers.StructureFixerDescriptor

name property of fixer

NAME - Static variable in class chemaxon.formats.MFileFormat

IUPAC Name files.

NAME - Static variable in class chemaxon.marvin.services.ServiceDescriptor

Property key for Service name as String

NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

name property of action

NAME_IO_WEB_SERVICE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier for parameter: "namingWebServiceURL" See Parameters and Events documentation.

NameConverter - Interface in chemaxon.naming

The interface of a converter from names to structures.

NameConverters - Class in chemaxon.naming

Maintains the list of custom and built-in name-to-structures converters.

NameFormatException - Exception in chemaxon.naming

A failure to convert a name to a structure.

NameFormatException(String) - Constructor for exception chemaxon.naming.NameFormatException

NameFormatException(String, String) - Constructor for exception chemaxon.naming.NameFormatException

NameFormatException(String, Throwable) - Constructor for exception chemaxon.naming.NameFormatException

NameFormatException(Throwable) - Constructor for exception chemaxon.naming.NameFormatException

NameFormatException.FilteredCase - Exception in chemaxon.naming

Exception signaling that the given input name should not be converted.

nameOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the name of the specified element.

NamePrefixException - Exception in chemaxon.naming

This exception should be thrown by a NameConverter to indicate that even though a name cannot be converted to a structure, it is the prefix of a valid name.

NamePrefixException() - Constructor for exception chemaxon.naming.NamePrefixException

NamePrefixException(String) - Constructor for exception chemaxon.naming.NamePrefixException

NamePrefixException(String, String) - Constructor for exception chemaxon.naming.NamePrefixException

names() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunction

The names of the functions which are registered by this annotation.

NAMESPACE - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Property key for namespace as String

nameStructureFormat - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

The structure format used to represent hits converted from names.

nameStructureFormat(String) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

NAN - Static variable in interface chemaxon.jep.CustomFunction

NAN - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Double constant for Double.NaN.

NAN - Static variable in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

naturalWeightOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the natural weight of the element.

NAVIGATION_MODE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "navmode".

Nb - Static variable in class chemaxon.core.ChemConst

NBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

Nd - Static variable in class chemaxon.core.ChemConst

Ne - Static variable in class chemaxon.core.ChemConst

needError() - Method in class chemaxon.marvin.calculations.logPPlugin

needsAnalysisBoxWarning() - Method in class chemaxon.marvin.common.UserSettings

needsConfig() - Method in class chemaxon.descriptors.MolecularDescriptor

Indicates if class takes parameters from configuration file.

needsConfig() - Method in class chemaxon.descriptors.scalars.Heavy

Indicates if class takes parameters from configuration file.

needsConfig() - Method in class chemaxon.descriptors.scalars.LogP

Indicates if class takes parameters from configuration file.

needsConfig() - Method in class chemaxon.descriptors.scalars.Mass

Indicates if class takes parameters from configuration file.

needsConfig() - Method in class chemaxon.descriptors.scalars.TPSA

Indicates if class takes parameters from configuration file.

needsMore - Variable in class chemaxon.formats.recognizer.Recognizer

needsMore() - Method in class chemaxon.formats.recognizer.Recognizer

Should we read more lines?

NEG - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

negOxOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the negative oxidation number.

NeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Constructs an iterator to process the bonds connecting to the specified atom.

NeutralizeAction - Class in chemaxon.standardizer.actions

Neutralization standardizer action

NeutralizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.NeutralizeAction

Initializes the action

NeutralizeChargeFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which neutralize the charge of the atoms of the molecule

NeutralizeChargeFixer() - Constructor for class chemaxon.fixers.NeutralizeChargeFixer

newBond(BondInfo) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener

Called when start to visit a new bond.

newCalculation(Molecule, Molecule) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener

Called when a new structure is processed.

newInstance() - Method in interface chemaxon.common.util.MProgressMonitor

Creates new monitor with same parent, message, levels.

newInstance() - Method in class chemaxon.struc.Molecule

Creates a new Molecule object.

newInstance() - Method in class chemaxon.struc.MoleculeGraph

Creates a new MoleculeGraph object.

newInstance() - Method in class chemaxon.struc.RgMolecule

Creates a new RgMolecule object.

newInstance() - Method in class chemaxon.struc.RxnMolecule

Creates a new RxnMolecule object.

newInstance() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets a new MultipleSgroup instance.

newInstance() - Static method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Creates a new instance of MCS search algorithm using the default search options.

newInstance(McsSearchOptions) - Static method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Creates a new instance of MCS search algorithm using the given search options.

newInstance(String) - Static method in class chemaxon.descriptors.MolecularDescriptor

Creates a MolecularDescriptor specified by its name.

newInstance(String, String) - Static method in class chemaxon.descriptors.MolecularDescriptor

Creates a MolecularDescriptor specified by its name and xml parameter.

newInstanceFromXML(String) - Static method in class chemaxon.descriptors.MolecularDescriptor

Creates a new MolecularDescriptor instance according to the given parameter string.

newSelectionMolecule() - Method in class chemaxon.struc.Molecule

Creates a new SelectionMolecule object appropriate for storing selection from this molecule.

newSelectionMolecule() - Method in class chemaxon.struc.RgMolecule

Creates a new SelectionMolecule object appropriate for storing selection from this molecule.

newToOld() - Method in class chemaxon.standardizer.Changes

Returns the new -> old atom index mapping.
newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.

newToOld(List<Changes>, Molecule) - Static method in class chemaxon.standardizer.Changes

Calculates the new -> old atom index mapping based on a list of changes.
newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.

next() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator

Returns the next atom in the iteration.

next() - Method in class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator

Returns the next atom in the iteration.

next() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator

Returns the next bond in the iteration.

next() - Method in class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator

Returns the next bond in the iteration.

next() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator

Returns the next component in the iteration.

next() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator

Returns the next component in the iterator.

next() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator

Returns the next s-group in the iteration.

next() - Method in interface chemaxon.util.iterator.MoleculeIterator

Gets the next molecule.

nextAtom() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.AtomIterator.next() instead.

nextAtom() - Method in class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.AtomNeighbourIterator.next() instead.

nextBond() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.BondIterator.next() instead.

nextBond() - Method in class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.BondNeighbourIterator.next() instead.

nextBondIndex(int) - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Returns the next bond index in the iteration according to the atom and bond related behavior specified in the factory.

nextComponent() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.RgComponentIterator.next() instead.

nextComponent() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.2, Use IteratorFactory.RxnComponentIterator.next() instead.

nextDoc() - Method in class chemaxon.formats.MolImporter

Reads the next document.

nextDoc() - Method in class chemaxon.marvin.io.ArrayMDocSource

Produces the next document.

nextDoc() - Method in class chemaxon.marvin.io.MDocSource

Produces the next document.

nextDoc() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Produces the next document.

nextOpt(String, int, String) - Static method in class chemaxon.marvin.io.MolExportModule

Tests whether the option string contains the specified substring at the specified position.

nextRecord() - Method in interface chemaxon.marvin.io.MRecordReader

Reads the next record.

nextResult() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Finds the next MCS search result according to the specified options.

Nh - Static variable in class chemaxon.core.ChemConst

NHAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

Ni - Static variable in class chemaxon.core.ChemConst

NMR_CNMR - Enum constant in enum class chemaxon.calculator.CalculatorTag

NMR_HNMR - Enum constant in enum class chemaxon.calculator.CalculatorTag

NMRCalculator - Class in chemaxon.calculations.nmr

Class for NMR spectrum calculation.

NMRCalculator.Builder - Class in chemaxon.calculations.nmr

Builder class for NMRCalculator.

NMRExporter - Class in chemaxon.calculations.nmr.io

Class for NMR spectrum export.

NMRExporter() - Constructor for class chemaxon.calculations.nmr.io.NMRExporter

NMRSpectrum - Class in chemaxon.calculations.nmr

Class for the representation of NMR spectra.

NMRSpectrum(Molecule) - Constructor for class chemaxon.calculations.nmr.NMRSpectrum

Constructor.

NMRSpectrum(Molecule, NMRSpectrum.Nucleus) - Constructor for class chemaxon.calculations.nmr.NMRSpectrum

Constructor.

NMRSpectrum.Nucleus - Enum Class in chemaxon.calculations.nmr

Nucleus enumeration type.

NMRSpectrum.Unit - Enum Class in chemaxon.calculations.nmr

Unit enumeration type.

No - Static variable in class chemaxon.core.ChemConst

NO - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption

Recover from record level errors if possible.

NO - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

NO - Static variable in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

NO_ABAS - Static variable in interface chemaxon.sss.SearchConstants

Substructure search that applies only screening.

NO_BOND - Enum constant in enum class chemaxon.struc.BondType

No bond type.

NO_ERROR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type for results sign no error.

NO_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

no error message for checker

NO_LICENSE_REQUIRED - Static variable in annotation interface chemaxon.standardizer.StandardizerActionInfo

no license required

NO_MNEMONIC - Static variable in class chemaxon.marvin.swing.MAction

Do not set the mnemonic.

NO_RADICAL - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Not radical center.

NO_SCREEN - Static variable in interface chemaxon.sss.SearchConstants

Substructure search that applies only atom-by-atom search.

NO_UNDEF_RGROUP - Static variable in class chemaxon.sss.search.MarkushGenerator

nodes - Variable in class chemaxon.marvin.alignment.AlignmentMolecule

noErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the no error message for the checker

NOMINAL_MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "nominalmass".

nominalMass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.

NOMOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil

Do not read multi-molecule XYZ files as movies.

NON_STANDARD_WEDGE_SCHEME - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Wedge configuration around a chiral center doesn't follow IUPAC recommendations.

NON_STEREO_WEDGE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

The wedge is connected to a non-stereo atom.

NONE - Enum constant in enum class chemaxon.marvin.collecting.Consent

NONE - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption

No atom can have translation.

NONE - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration

NONE - Enum constant in enum class com.chemaxon.search.AromatizationMethod

No aromatization.

NONE - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer

NONE - Static variable in class chemaxon.sss.formula.FormulaSearch

Constant value specifying the none search type.

NONE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Property display type: no property display.

NONNEGATIVE_REAL - Static variable in class chemaxon.marvin.util.OptionDescriptor

Positive real number.

nonPositiveToInfinite(int) - Static method in class chemaxon.sss.search.SearchOptions

NONRECURSIVE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable

Non recursive expansion of child groups.

NonStandardWedgeSchemeChecker - Class in chemaxon.checkers

Non-standard Wedge Scheme Checker detects wedge configurations not following the IUPAC recommendations.

NonStandardWedgeSchemeChecker() - Constructor for class chemaxon.checkers.NonStandardWedgeSchemeChecker

Default constructor

NonStereoWedgeBondChecker - Class in chemaxon.checkers

Non-stereo Wedge Bond Checker detects wedge bonds connected to non-stereo atoms.

NonStereoWedgeBondChecker() - Constructor for class chemaxon.checkers.NonStereoWedgeBondChecker

Default constructor

NOPARAMS - Static variable in class com.chemaxon.calculations.gui.PluginFactory

No parameter panel sign in property file: if present then no parameter panel belongs to the plugin.

noReport - Variable in class chemaxon.checkers.StructureCheckOptions

The execution does not generate report to file or property (the execution does only effect structures with fixable structure errors in fix mode.)

NORMAL - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode

Atomic contribution only, no correction terms.

NORMAL - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy

NORMAL - Enum constant in enum class com.chemaxon.search.mcs.SearchMode

Normal search mode.

NORMAL_CANONICAL - Enum constant in enum class chemaxon.sss.search.options.TautomerEqualityMode

NORMAL_CANONICAL - Enum constant in enum class chemaxon.sss.search.options.TautomerTransformationMode

NORMAL_CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

NORMAL_GENERIC - Enum constant in enum class chemaxon.sss.search.options.TautomerTransformationMode

normalized - Variable in class chemaxon.descriptors.MDParameters

flags indicating if the metric is normalized or not

NORMALIZED_EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType

normalizedEuclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the normalized Euclidean distance.

normalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the normalized Euclidean distance.

NoStructure - Class in chemaxon.struc

This class represents NoStructure labels.

NoStructureFormat - Static variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

Use this format constant to avoid exporting any structural format in the HTML output.

NOT_SAVED - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult

NOT_USEFUL - Static variable in class chemaxon.sss.search.MolComparator

Describes that the MolComparator is not needed with the current search object, the current query (and target).

NOTLIST - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the exclusive atom list.

Np - Static variable in class chemaxon.core.ChemConst

nullObserver() - Static method in interface chemaxon.util.progress.ProgressObserver

Returns an observer that ignores progress report and cannot be cancelled.

numberOfAtoms() - Method in class chemaxon.util.iterator.IteratorFactory

Returns the number of atoms iterated by AtomIterator.

numberOfBonds() - Method in class chemaxon.util.iterator.IteratorFactory

Returns the number of bonds iterated by BondIterator.

numberOfNeighbours(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory

Returns the number of atoms/bonds iterated by (Atom/Bond)NeighbourIterator (the two values are the same).

numOf(String) - Static method in class chemaxon.struc.MolAtom

Deprecated.

As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String).
The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.

numoxstatesOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the number of oxidation states for the specified element.

O

O - Static variable in class chemaxon.core.ChemConst

OBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

objectContainingSelection - Variable in class chemaxon.struc.MDocument

objects - Variable in class chemaxon.struc.MDocument

ocr - Variable in class chemaxon.checkers.StructureCheckOptions

OCR check involved

OCRErrorChecker - Class in chemaxon.checkers

OCRErrorChecker detects structures which do not look like chemical structures.

OCRErrorChecker() - Constructor for class chemaxon.checkers.OCRErrorChecker

Default constructor

ODD - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue

ODD - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue

ODD - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue

ODD - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue.P.

ODD - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue.P.

ODD - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue.R.

ODD - Static variable in class chemaxon.calculations.stereo.Stereochemistry

of(CalculatorTag...) - Static method in interface chemaxon.calculator.TaggedCalculator

Creates a TaggedCalculator that always returns the given tags.

of(String, Predicate<Molecule>) - Static method in interface chemaxon.calculator.CalculatorInputChecker

Creates a new input checker that accepts those molecules which satisfy the given lambda.

of(Collection<CalculatorTag>) - Static method in interface chemaxon.calculator.TaggedCalculator

Creates a TaggedCalculator that always returns the given tags.

OFF - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckEnabled(boolean). Usage:

             molecule.setValenceCheckEnabled(false);
             

OFFICE - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

Og - Static variable in class chemaxon.core.ChemConst

OHAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

oldToNew() - Method in class chemaxon.standardizer.Changes

Returns the old -> new atom index mapping.
oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.

oldToNew(List<Changes>, Molecule) - Static method in class chemaxon.standardizer.Changes

Calculates the old -> new atom index mapping based on a list of changes.
oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.

OMIT_POSTCLEAN - Static variable in class chemaxon.struc.MolAtom

Omit arranging process after the hydrogen addition.

OMIT_POSTCLEAN - Static variable in class chemaxon.struc.MoleculeGraph

Omit arranging process after the hydrogen addition.

ONE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

single error message for checker

oneErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the one error message for the checker

onFailure(ServiceException) - Method in interface chemaxon.marvin.services.AsyncCallback

Called when asynchronous call is failed

onSuccess(T) - Method in interface chemaxon.marvin.services.AsyncCallback

Called when asynchronous call is completed successfully

open(String) - Method in class chemaxon.marvin.io.MolExportModule

Opens the exporter stream.

open(String, MPropertyContainer) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Open the exporter stream.

open(String, MPropertyContainer) - Method in class chemaxon.marvin.io.MolExportModule

Opens the exporter stream.

openSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane

Opens the sketcher window with the molecule from the specified cell if the viewer is editable.

openWindow(int) - Method in class chemaxon.marvin.beans.MViewPane

Detaches the view canvas of the specified cell into a separate window if the viewer is detachable.

OPTIMIZATION_NORMAL - Static variable in class chemaxon.marvin.calculations.ConformerPlugin

OPTIMIZATION_STRICT - Static variable in class chemaxon.marvin.calculations.ConformerPlugin

OPTIMIZATION_VERY_LOOSE - Static variable in class chemaxon.marvin.calculations.ConformerPlugin

OPTIMIZATION_VERY_STRICT - Static variable in class chemaxon.marvin.calculations.ConformerPlugin

OPTION_NAME_STRING - Static variable in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

OPTION_NAME_STRING - Static variable in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

OptionDescriptor - Class in chemaxon.marvin.util

General option descriptor class.

OptionDescriptor(String, String, int, String, String[], String[], String[]) - Constructor for class chemaxon.marvin.util.OptionDescriptor

Creates an option.

Options() - Constructor for class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

Options() - Constructor for class com.chemaxon.mapper.AutoMapper.Options

OptionsPane - Class in chemaxon.marvin.plugin.gui

Displays plugin parameter tabbed panes.

OptionsPane(Dialog, String, String, ParameterPanelHandler, ActionListener) - Constructor for class chemaxon.marvin.plugin.gui.OptionsPane

Creates an options pane: plugin parameter panel with "Display", "OK", "Cancel" buttons.

OptionsPane(Frame, String, String, ParameterPanelHandler, ActionListener) - Constructor for class chemaxon.marvin.plugin.gui.OptionsPane

Creates an options pane: plugin parameter panel with "Display", "OK", "Cancel" buttons.

OptionsPane(String, String, ParameterPanelHandler, ActionListener) - Constructor for class chemaxon.marvin.plugin.gui.OptionsPane

Creates an options pane: plugin parameter panel with "Display", "OK", "Cancel" buttons.

OR - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

Stereogenic centers belonging to an ORn group (e.g.

OR - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

OrbitalElectronegativityPlugin - Class in chemaxon.marvin.calculations

Plugin class for orbital electronegativity calculation.

OrbitalElectronegativityPlugin() - Constructor for class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Constructor.

order() - Method in class chemaxon.marvin.io.Encoding

Gets the endianness.

orderSensitive(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.

ORIGINAL_MOLECULE - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy

In case of standardization error the original molecule is provided on the output

orix - Variable in class chemaxon.struc.MoleculeGraph

Origin x.

oriy - Variable in class chemaxon.struc.MoleculeGraph

Origin y.

oriz - Variable in class chemaxon.struc.MoleculeGraph

Origin z.

Os - Static variable in class chemaxon.core.ChemConst

OSRA - Static variable in class chemaxon.formats.MFileFormat

otell() - Method in class chemaxon.formats.MolConverter

Get the current file position.

outputIn3d() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Returns true if 3D structures will be generated.

outputPath - Variable in class chemaxon.checkers.StructureCheckOptions

The path of the valid/fixed output structures

outputPrecision - Variable in class chemaxon.descriptors.MDParameters

number of fraction digits in floating point output format

OVERLAPPING_ATOMS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that overlapping atoms had found in the molecule

OVERLAPPING_BONDS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that overlapping bonds had found in the molecule

OverlappingAtomsChecker - Class in chemaxon.checkers

OverlappingAtomsChecker detects atoms that are too close to each other.

This checker checks 2D structures only.

Two atoms considered as overlapping when their euclidean distance is less than the half of the Chemaxon standard bond length ( MolBond.CCLENGTH ).

OverlappingAtomsChecker() - Constructor for class chemaxon.checkers.OverlappingAtomsChecker

OverlappingBondsChecker - Class in chemaxon.checkers

OverlappingBondsChecker detects bonds that are too close to each other.

This checker checks two dimensional structures only.

Two bonds considered as overlapping when they crossing each other, or their distance is smaller then the 80% of the standard Chemaxon bond length ( MolBond.CCLENGTH ).

OverlappingBondsChecker() - Constructor for class chemaxon.checkers.OverlappingBondsChecker

Default constructor

overridesAtMerge(MolBond) - Method in class chemaxon.struc.MolBond

Checks if this bond should override another one when two structures are merged.

ownOverlap(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.AlignmentMolecule

oxstateOf(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the oxidation states.

P

p - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

p - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

P - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

P - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

P - Static variable in class chemaxon.core.ChemConst

P_CENTER - Static variable in class chemaxon.struc.graphics.MRectangle

Central point ID.

P_E - Static variable in class chemaxon.struc.graphics.MRectangle

Middle point on right edge.

P_N - Static variable in class chemaxon.struc.graphics.MRectangle

Middle point on top edge.

P_NE - Static variable in class chemaxon.struc.graphics.MRectangle

Top-right corner index.

P_NW - Static variable in class chemaxon.struc.graphics.MRectangle

Top-left corner index.

P_S - Static variable in class chemaxon.struc.graphics.MRectangle

Middle point on bottom edge.

P_SE - Static variable in class chemaxon.struc.graphics.MRectangle

Botton-right corner index.

P_SW - Static variable in class chemaxon.struc.graphics.MRectangle

Bottom-left corner index.

P_W - Static variable in class chemaxon.struc.graphics.MRectangle

Middle point on left edge.

Pa - Static variable in class chemaxon.core.ChemConst

pack() - Method in class chemaxon.struc.MolAtom

Reduce memory usage.

pack() - Method in class chemaxon.struc.MoleculeGraph

Reduce memory usage.

PAGE - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the page number, if applicable (e.g.

PageSettings - Class in chemaxon.struc

Page Settings of multipage molecular documents.

PageSettings() - Constructor for class chemaxon.struc.PageSettings

Constructor.

paint(Graphics2D, Dimension) - Method in class chemaxon.marvin.MolPrinter

Paints the molecule on the specified graphics context in the given size.

paint(Graphics2D, Rectangle) - Method in class chemaxon.marvin.MolPrinter

Paints the molecule into the center of the specified rectangle.

paint(Graphics, Rectangle) - Method in class chemaxon.marvin.MolPrinter

Paints the molecule into the center of the specified rectangle.

paintComponent(Graphics) - Method in class chemaxon.marvin.beans.MolRenderer

PAIRED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties

PairwiseAlignment - Class in chemaxon.marvin.alignment

Align pairs of molecules (query and the target) using the shape Alignment

PairwiseAlignment() - Constructor for class chemaxon.marvin.alignment.PairwiseAlignment

PairwiseAlignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.PairwiseAlignment

PairwiseComparison - Interface in chemaxon.marvin.alignment

This interface designed for comparing two molecules in 3D by various overlay methodologies.

PairwiseSimilarity3D - Class in chemaxon.marvin.alignment

Align pairs of molecules (query and the target) using the atom/atom matcher Similarity3D

PairwiseSimilarity3D() - Constructor for class chemaxon.marvin.alignment.PairwiseSimilarity3D

PairwiseSimilarity3D(boolean) - Constructor for class chemaxon.marvin.alignment.PairwiseSimilarity3D

PARAM_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Parameter separator token of the action string

ParameterConstants - Class in chemaxon.marvin.common

Parameters of Marvin Applets and Beans.

ParameterConstants() - Constructor for class chemaxon.marvin.common.ParameterConstants

ParameterPanel - Class in chemaxon.marvin.plugin.gui

A configurable implementation of the plugin specific parameter setting panel.

ParameterPanel(ParameterTab, ParameterTab[]) - Constructor for class chemaxon.marvin.plugin.gui.ParameterPanel

Constructor.

ParameterPanel(ParameterTab, ParameterTab[], ParameterItem[]) - Constructor for class chemaxon.marvin.plugin.gui.ParameterPanel

Constructor.

ParameterPanelHandler - Interface in com.chemaxon.calculations.gui

Plugin parameter panel handler interface.

parameters - Variable in class chemaxon.descriptors.CDParameters

node in the DOM tree built from the XML configuration

PARAMETERS - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "param".

PARAMETERS_HEADER - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "paramH".

ParameterTab - Class in chemaxon.marvin.plugin.gui

Represents a parameter tab.

ParameterTab(String, String) - Constructor for class chemaxon.marvin.plugin.gui.ParameterTab

parametrizedMetricNodes - Variable in class chemaxon.descriptors.MDParameters

parametrizedMetrics - Variable in class chemaxon.descriptors.MDParameters

symbolic names (mnemonics) of parametrized metrics

parametrizedMetricsNode - Variable in class chemaxon.descriptors.MDParameters

params - Variable in class chemaxon.descriptors.MolecularDescriptor

Parameter settings related to the descriptor.

params - Variable in class chemaxon.marvin.beans.MarvinPane

Parameter string.

params - Variable in class com.chemaxon.calculations.cli.CalculatorPluginOutput

The plugin parameter table.

parent - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The parent component.

parentGraph - Variable in class chemaxon.struc.MoleculeGraph

The structure that contains this molecule graph as a substructure.

parentLine - Variable in class chemaxon.struc.graphics.MMidPoint

parentRect - Variable in class chemaxon.struc.graphics.MRectanglePoint

parentSgroup - Variable in class chemaxon.struc.Sgroup

PARITY_ALLENE - Static variable in interface chemaxon.struc.StereoConstants

Atom with allene like parity.

PARITY_EITHER - Static variable in interface chemaxon.struc.StereoConstants

Odd or even parity.

PARITY_EVEN - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of even parity (counterclockwise arrangement).

PARITY_MASK - Static variable in interface chemaxon.struc.StereoConstants

Parity mask in flags.

PARITY_NONE - Static variable in interface chemaxon.struc.StereoConstants

Atom with no parity.

PARITY_ODD - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of odd parity (clockwise arrangement).

PARITY_TETRAHEDRAL - Static variable in interface chemaxon.struc.StereoConstants

Atom with tetrahedral parity.

PARITY_UNSPEC - Static variable in interface chemaxon.struc.StereoConstants

Unspecified parity flag.

paritySign(int, int, int, int) - Static method in class chemaxon.struc.MolAtom

Calculates the sign of the parity for the specified indexes.

parse(String) - Static method in class chemaxon.checkers.util.AtomLabels

Parses the list of atom labels from a string.

parse(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

parse(String) - Static method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Parses the type of the absolute stereo action

parse(String) - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type

Parses the type of the aromatize action

parse(String) - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Parses the type of the convert double bonds action

parse(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

Parses the measurement of the remove fragment action

parse(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Parses the method of the remove fragment action

parse(String) - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

Parses the hydrogen isotope representation type

parse(String) - Static method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Parses the type of the clean action

parseCharIfOptionSign(String, int) - Method in class chemaxon.marvin.io.MolExportModule

Parse the current character if it is an option sign.

parseConfig(String) - Method in class chemaxon.sss.screen.StrucFPConfig

Parses a text configuration, and sets internal values accordingly.

parseExpression(String) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Use ChemJEP.compile(String) instead.

parseGroupNames(String) - Method in class chemaxon.standardizer.actions.AbstractSgroupAction

parseMolecule(String) - Static method in class chemaxon.marvin.io.MPropHandler

parseMRV(String) - Static method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

No longer supported, use MolImporter.importMol(byte[]) instead.

parseMRV(String) - Static method in class chemaxon.struc.MDocument

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.7, replaced by MolImporter.parseMRV(String)

parseOption(String, int) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Parses the bond length (b###) option.

parseOption(String, int) - Method in class chemaxon.marvin.io.MolExportModule

Parses the following option in the option string.

parseType(String) - Static method in class chemaxon.marvin.util.OptionDescriptor

Parses an option type from a string.

PARTIAL - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Partial clean

PARTIAL_CLEAN_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction

Key for partial clean necessary property change

partialClean(int, int[], String) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Cleaner.partialClean(MoleculeGraph, int, int[], String).

partialClean(Molecule[], 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.partialClean(Molecule, Molecule[], String).

partialClean(MoleculeGraph, 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.partialClean(MoleculeGraph, MoleculeGraph, int[], String).

partialClean(MoleculeGraph, int, int[], String) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates by using fixed atoms.

partialClean(MoleculeGraph, MoleculeGraph, int[], String) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates by using the given template molecule.

partialClean(MoleculeGraph, MoleculeGraph, int[], String, AtomChangeEventListener) - Static method in class chemaxon.calculations.clean.Cleaner

partialClean(Molecule, Molecule[], String) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates by using the given template molecule array.

partialClean(Molecule, Molecule[], String, AtomChangeEventListener) - Static method in class chemaxon.calculations.clean.Cleaner

A specific overloading for partial clean.

PartialCleanFixer - Class in chemaxon.fixers

Partial clean

PartialCleanFixer() - Constructor for class chemaxon.fixers.PartialCleanFixer

partialCleanWithStereo(MoleculeGraph, int, int[], String) - Static method in class chemaxon.calculations.clean.Cleaner

Calculates atom coordinates by using fixed atoms.

PATOM - Static variable in class chemaxon.jep.context.ReactionContext

Pb - Static variable in class chemaxon.core.ChemConst

PBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

Pd - Static variable in class chemaxon.core.ChemConst

PDB - Static variable in class chemaxon.formats.MFileFormat

Protein Data Bank format.

PDBRecognizer - Class in chemaxon.formats.recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

PDBRecognizer() - Constructor for class chemaxon.formats.recognizer.PDBRecognizer

Deprecated.

PDF - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

PDF - Static variable in class chemaxon.formats.MFileFormat

Portable Document Format.

PEPTIDE_DISPLAY_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier for parameter: "peptideDisplayType" See Parameters and Events documentation.

PEPTIDE_IN - Static variable in class chemaxon.formats.MFileFormat

Peptide Sequence.

PEPTIDE1_OUT - Static variable in class chemaxon.formats.MFileFormat

Peptide Sequence (1-letter).

PEPTIDE3_OUT - Static variable in class chemaxon.formats.MFileFormat

Peptide Sequence (3-letter).

PeptideRecognizer - Class in chemaxon.formats.recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

PeptideRecognizer() - Constructor for class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated.

PeriodicSystem - Class in chemaxon.struc

Periodic System of the Elements.

PeriodicSystem() - Constructor for class chemaxon.struc.PeriodicSystem

Persistent - Annotation Interface in chemaxon.checkers

This annotation signs if a property of a StructureChecker should be persisted

PFGenerator - Class in chemaxon.descriptors

The PFGenerator class generates 2-dimensional pharmacophore fingerprints for molecular graphs.

PFGenerator(PMapper) - Constructor for class chemaxon.descriptors.PFGenerator

Creates a new instance of PFGenerator which can be used to generate fingerprints for an arbitrary number of molecules.

PFParameters - Class in chemaxon.descriptors

Manages 2D pharmacophore fingerprint parameters.

PFParameters() - Constructor for class chemaxon.descriptors.PFParameters

Creates an empty object.

PFParameters(File) - Constructor for class chemaxon.descriptors.PFParameters

Creates a new object based on a given configuration file.

PFParameters(String) - Constructor for class chemaxon.descriptors.PFParameters

Creates a new object based on a given configuration string.

PHARMACOPHORE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme

Pharmacophore3D - Class in chemaxon.marvin.alignment

3D Pharmacophore representation for 3D alignments.

Pharmacophore3D() - Constructor for class chemaxon.marvin.alignment.Pharmacophore3D

Pharmacophore3D(Molecule, int[]) - Constructor for class chemaxon.marvin.alignment.Pharmacophore3D

PharmacophoreFingerprint - Class in chemaxon.descriptors

The PharmacophoreFingerprint class implements 2D pharmacophoric fingerprints.

PharmacophoreFingerprint() - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint

Creates a new, empty instance of PharmacophoreFingerprint without allocating internal storage.

PharmacophoreFingerprint(PFParameters) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint

Creates a new instance of PharmacophoreFingerprint according to the parameters given.

PharmacophoreFingerprint(PharmacophoreFingerprint) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint

Copy constructor.

PharmacophoreFingerprint(String) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint

Creates a new instance of PharmacophoreFingerprint according to the parameters given.

PHYSPROP - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod

Calculation method based on the PhysProp database.

PKA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction

PKa calculation for bbb score.

PKA - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Most basic center (pKa).

PKACALCULATOR - Enum constant in enum class chemaxon.calculator.CalculatorTag

pKaPlugin - Class in chemaxon.marvin.calculations

Plugin class for macro/micro pKa calculation.

pKaPlugin() - Constructor for class chemaxon.marvin.calculations.pKaPlugin

Constructor.

PKAT - Enum constant in enum class chemaxon.calculator.CalculatorTag

PKaTrainingResult - Class in chemaxon.calculations.pka

PKa training result object.

PKaTrainingResult.PKaType - Enum Class in chemaxon.calculations.pka

PLAIN - Static variable in class chemaxon.struc.graphics.MFont

Plain font style.

plattIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.

plugin - Variable in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

The plugin object.

plugin - Variable in class com.chemaxon.calculations.cli.CalculatorPluginOutput

The CalculatorPlugin object.

PLUGIN_CLASS_KEY - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Plugin class key in manifest.

PLUGIN_DIR - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

The plugin directory (relative to CLASSPATH).

PluginException - Exception in chemaxon.marvin.plugin

Exception thrown in case of plugin processing or calculation errors.

PluginException() - Constructor for exception chemaxon.marvin.plugin.PluginException

Default constructor.

PluginException(String) - Constructor for exception chemaxon.marvin.plugin.PluginException

Constructor with message.

PluginException(String, Throwable) - Constructor for exception chemaxon.marvin.plugin.PluginException

Constructor with wrapped exception.

PluginException(Throwable) - Constructor for exception chemaxon.marvin.plugin.PluginException

Constructor with wrapped exception.

PluginExecutionException - Exception in chemaxon.marvin.plugin.concurrent

Exception wrapping a cause Throwable and the plugin object which has thrown the Throwable.

PluginExecutionException(CalculatorPlugin, String, Throwable) - Constructor for exception chemaxon.marvin.plugin.concurrent.PluginExecutionException

Constructor.

PluginExecutionException(CalculatorPlugin, Throwable) - Constructor for exception chemaxon.marvin.plugin.concurrent.PluginExecutionException

Constructor.

PluginFactory - Class in com.chemaxon.calculations.gui

Plugin factroy: responsible for plugin parameter panel and plugin creation and central management.

PluginFactory() - Constructor for class com.chemaxon.calculations.gui.PluginFactory

Constructor.

PluginFactory.PluginRecord - Class in com.chemaxon.calculations.gui

Stores plugin data.

PluginInputCheckerException - Exception in chemaxon.marvin.plugin

Exception thrown when a CalculatorInputChecker rejects an input molecule of a CalculatorPlugin.

PluginInputCheckerException(CalculatorError) - Constructor for exception chemaxon.marvin.plugin.PluginInputCheckerException

PluginMDocSource - Class in chemaxon.marvin.plugin

Multimolecular result source object based on result MDocument Iterator.

PluginMDocSource(Iterator, int) - Constructor for class chemaxon.marvin.plugin.PluginMDocSource

Constructor.

PluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent

Work unit performing plugin calculation.

PluginWorkUnit() - Constructor for class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Constructor.

PluginWorkUnit(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Constructor.

Pm - Static variable in class chemaxon.core.ChemConst

PNG - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat

PNG - Static variable in class chemaxon.formats.MFileFormat

Portable Network Graphics.

Po - Static variable in class chemaxon.core.ChemConst

points - Variable in class chemaxon.struc.graphics.MPolyline

POLARIZABILITY - Enum constant in enum class chemaxon.calculator.CalculatorTag

POLARIZABILITY_GEOM3D - Enum constant in enum class chemaxon.calculator.CalculatorTag

PolarizabilityPlugin - Class in chemaxon.marvin.calculations

Plugin class for atom polarizability calculation.

PolarizabilityPlugin() - Constructor for class chemaxon.marvin.calculations.PolarizabilityPlugin

Constructor.

polylinePointIndex - Variable in class chemaxon.struc.graphics.MMidPoint

POLYMERENDGROUP_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup) and the H is not in the same sgroup should be kept.

pop() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Clears the last stored item from the display.

POPUP - Static variable in class chemaxon.marvin.swing.MAction

Popup menu item, MAction.AUTORM, MAction.NO_MNEMONIC and MAction.IN_POPUP are set.

popupImageFormat - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

The image format which should be used for popups in the annotated document.

popupImageFormat(DocumentAnnotatorOptions.ImageFormat) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

PORT - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Property key for port name as String

portionWidth(Graphics, MFont, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the width of this portion.

portionXAdvance(Graphics, MFont, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the x coordinate change from the beginning to the end of this portion.

portionXAdvance(Graphics, MFont, FontMetrics, boolean) - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the width of this portion.

POS - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D

Position(int, int) - Constructor for class chemaxon.marvin.io.MRecordReader.Position

Creates a locator.

POSITION_ON_0TH_HEAVY_ATOM - Static variable in interface chemaxon.sss.SearchConstants

Hit constant denoting hit position of a non-heavy atom (e.g.

PositionedInputStream - Class in chemaxon.marvin.io

Positioned input stream that has the ability to set / get the stream position as well as put back some parts already read.

PositionedInputStream(InputStream) - Constructor for class chemaxon.marvin.io.PositionedInputStream

Constructor.

PositionedInputStream(InputStream, int) - Constructor for class chemaxon.marvin.io.PositionedInputStream

Constructor.

PositionedInputStream(InputStream, int, String) - Constructor for class chemaxon.marvin.io.PositionedInputStream

Constructor.

PositionedInputStream(InputStream, int, String, int) - Constructor for class chemaxon.marvin.io.PositionedInputStream

Constructor.

PositionedInputStream(InputStream, String) - Constructor for class chemaxon.marvin.io.PositionedInputStream

Constructor.

positionInRect - Variable in class chemaxon.struc.graphics.MRectanglePoint

posOxOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the smallest positive oxidation number.

POST - Enum constant in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method

method POST

PostfixMathCommandI - Interface in chemaxon.nfunk.jep.function

Deprecated, for removal: This API element is subject to removal in a future version.

This interface will be removed, use CustomFunction instead.

postModification(Molecule) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode

POVRAY - Static variable in class chemaxon.formats.MFileFormat

POVRay file.

ppm - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit

ppm unit

pptNames - Variable in class chemaxon.descriptors.PFParameters

Pharmacophore point type names.

Pr - Static variable in class chemaxon.core.ChemConst

PR_ATSYMS - Static variable in class chemaxon.struc.Sgroup

Print atom symbols.

PRE_CONFIGURED_TRANSFORMATIONS - Static variable in class chemaxon.standardizer.StandardizerActionFactory

Pre-configured transformation configuration path

preconvert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule

Optionally performs aromatization or addition of explicit Hydrogens atoms.

preconvert(MoleculeGraph, boolean, int, boolean) - Method in class chemaxon.marvin.io.MolExportModule

Deprecated, for removal: This API element is subject to removal in a future version.

Marvin 6.2 use MolExportModule.preconvert(chemaxon.struc.Molecule, boolean, int, boolean) instead

preconvert(Molecule, boolean) - Method in class chemaxon.marvin.io.MolExportModule

Optionally performs aromatization or addition of explicit Hydrogens atoms.

preconvert(Molecule, boolean, int, boolean) - Method in class chemaxon.marvin.io.MolExportModule

Optionally performs aromatization or addition of explicit Hydrogens atoms.

predict(Molecule) - Method in class com.chemaxon.calculations.admet.HergActivityPredictor

Runs the prediction of the given molecule.

predict(Molecule) - Method in class com.chemaxon.calculations.admet.HergClassPredictor

Runs the prediction of the given molecule.

PRELOAD - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "preload".

PRELOAD - Static variable in class com.chemaxon.calculations.gui.PluginFactory

Deprecated, for removal: This API element is subject to removal in a future version.

Not used.

preMatchMap - Variable in class chemaxon.sss.search.Search

Map for storing pre-match data.

preprocess(Molecule, boolean) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

preprocess(InputStream) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter

preprocessFormatAndOptions(String[]) - Static method in class chemaxon.formats.MFileFormatUtil

Parses options like "MULTISET", "MOLMOVIE" or "NOMOLMOVIE".

primaryAtomIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Deprecated, for removal: This API element is subject to removal in a future version.

print() - Method in class chemaxon.marvin.beans.MViewPane

Prints the molecule table.

priority() - Element in annotation interface chemaxon.fixers.FixerInfo

Returns the priority of the fixer.

PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor

priority of fixer

process() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Process the complete input at once, generating the annotated document.

process(String) - Static method in class chemaxon.naming.document.DocumentToStructure

Creates a MolImporter instance to import structures from a given text using the default format options.

process(String, String) - Static method in class chemaxon.naming.document.DocumentToStructure

Creates a MolImporter instance to import structures from a given text.

processDocument(boolean) - Method in class chemaxon.descriptors.CDParameters

Processes parts of the XML configuration that are specific to CustomDescriptor.

processDocument(boolean) - Method in class chemaxon.descriptors.CFParameters

Processes pars of the XML configuration specific to ChemicalFingerprint.

processDocument(boolean) - Method in class chemaxon.descriptors.ECFPParameters

Processes pars of the XML configuration specific to ECFP.

processDocument(boolean) - Method in class chemaxon.descriptors.MDParameters

Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.

processDocument(boolean) - Method in class chemaxon.descriptors.PFParameters

processDocument(boolean) - Method in class chemaxon.descriptors.RFParameters

Processes pars of the XML configuration specific to ReactionFingerprint.

processDocument(boolean) - Method in class chemaxon.descriptors.SDParameters

Processes parts of the XML configuration specific to ScalarDescriptor.

processDocument(boolean) - Method in class chemaxon.descriptors.ShapeParameters

Processes pars of the XML configuration specific to Shape.

processError(Throwable) - Method in interface chemaxon.util.ErrorProcessor

Error processing method.

processMolecule(Molecule) - Method in class chemaxon.descriptors.ECFPFeatureLookup

Performs the necessary preprocessing for the given molecule.

PRODUCT - Static variable in class chemaxon.jep.context.ReactionContext

PRODUCTS - Static variable in class chemaxon.struc.RxnMolecule

"Product" structure type.

progress - Variable in class chemaxon.naming.document.annotate.DocumentAnnotator.ProgressInfo

The estimated ratio of work that has already been done, between 0 and 1.

progress(DocumentAnnotator.ProgressInfo) - Method in interface chemaxon.naming.document.annotate.DocumentAnnotator.Listener

ProgressObserver - Interface in chemaxon.util.progress

Observer for reporting the progress of long running tasks.

Prop() - Constructor for class chemaxon.struc.MDocument.Prop

properties - Variable in class chemaxon.marvin.io.MRecord

properties - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Display properties of the Molecule.

properties() - Method in class chemaxon.calculations.bbb.BBB

Returns the calculated phys-chem properties and scores.

properties() - Method in class chemaxon.calculations.cnsmpo.CnsMpo

Returns the calculated phys-chem properties and scores.

properties() - Method in class chemaxon.struc.MDocument

Gets the property container.

properties() - Method in class chemaxon.struc.MoleculeGraph

Gets the property container.

properties() - Method in class chemaxon.struc.RgMolecule

Gets the property container.

properties() - Method in interface chemaxon.struc.Smolecule

Gets the property container.

PROPERTY_KEY_ABSOLUTE - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Key of type for property change of mode

PROPERTY_KEY_ABSSTEREO - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Key of type for property change of mode

PROPERTY_KEY_ALLOW_VALENCE_ERROR - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction

Property key for serialization/deserialization an event changes for valence check (boolean value type)

PROPERTY_KEY_AROM_TYPE - Static variable in class chemaxon.checkers.AromaticityErrorChecker

This public constant String represents the name of the property which represents the arom type String property

PROPERTY_KEY_AROMATCITY - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Aromaticity atom query property.

PROPERTY_KEY_AROMATICITY_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Aromaticity checking property

PROPERTY_KEY_BRIDGEHEAD - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching Bridgehead property

PROPERTY_KEY_BRIDGEHEAD - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Bridgehead property

PROPERTY_KEY_CHARGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching charged explicit hydrogens in the molecule

PROPERTY_KEY_CHARGED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Charged property

PROPERTY_KEY_CHIRALITY - Static variable in class chemaxon.standardizer.actions.ClearStereoAction

Key of type for property change of mode

PROPERTY_KEY_CONNECTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Connection count atom query property.

PROPERTY_KEY_CONNECTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Connection count checking property

PROPERTY_KEY_CONTRACTED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker

This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups

PROPERTY_KEY_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker

Search for valence properties that are equal to the default valence.

PROPERTY_KEY_DETECT_CUMULATED_DOUBLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker

Property key detect cumulated double bonds

PROPERTY_KEY_DETECT_TRANS_DOUBLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker

Property key detect trans double bonds

PROPERTY_KEY_DETECT_TRIPLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker

Property key detect triple bonds

PROPERTY_KEY_DOUBLE_BOND - Static variable in class chemaxon.standardizer.actions.ClearStereoAction

Key of type for property change of mode

PROPERTY_KEY_ENFORCE_ABS - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Key of type for property change of mode

PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker

This public constant String represents the name of the property which is responsible for the list of excluded groups

PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.AttachedDataChecker

This public constant String represents the name of the property which is responsible for the list of excluded data.

PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.PseudoAtomChecker

This public constant String represents the name of the property which is responsible for the list of excluded pseudo atom labels

PROPERTY_KEY_EXPANDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker

This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups

PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Explicit connection count atom query property.

PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Explicit connection count checking property

PROPERTY_KEY_H_CONNECTED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching H connected property

PROPERTY_KEY_H_CONNECTED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

H connected property

PROPERTY_KEY_HYDROGEN_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Hydrogen count atom query property.

PROPERTY_KEY_HYDROGEN_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Hydrogen count checking property

PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Implicit hydrogen count atom query property.

PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Implicit hydrogen count checking property

PROPERTY_KEY_IS_EXCLUSION_REGEXP - Static variable in class chemaxon.checkers.AttachedDataChecker

The name of the property, which is responsible for the decision if the excluded data should be treated as a regular expression instead of a (comma separated) list of strings.

PROPERTY_KEY_ISOTOPIC - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching isotopic explicit hydrogens in the molecule

PROPERTY_KEY_ISOTOPIC - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Isotopic property

PROPERTY_KEY_LONELY - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching lonely explicit hydrogens in the molecule

PROPERTY_KEY_LONELY - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Lonely property

PROPERTY_KEY_MAPPED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching mapped explicit hydrogens in the molecule

PROPERTY_KEY_MAPPED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Mapped property

PROPERTY_KEY_METAL_CONNECTED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Metal connected property

PROPERTY_KEY_NON_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker

Search for valence properties that are not equal to the default valence.

PROPERTY_KEY_POLYMER_END_GROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching Polymer end group property

PROPERTY_KEY_POLYMER_END_GROUP - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Polymer end group property

PROPERTY_KEY_PREFERRED_DESCRIPTION - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor

Property key for preferred service description

PROPERTY_KEY_PREFERRED_NAME - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor

Property key for preferred service name

PROPERTY_KEY_QUERY_ATOM - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction

Property key for serialization/deserialization an event changes for query atom (MolAtom value type)

PROPERTY_KEY_RADICAL - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching radical explicit hydrogens in the molecule

PROPERTY_KEY_RADICAL - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Radical property

PROPERTY_KEY_REPLACE_ATOM - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction

Property key for serialization/deserialization an event changes for replace atom (MolAtom value type)

PROPERTY_KEY_RING_BOND_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Ring bond count atom query property.

PROPERTY_KEY_RING_BOND_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Ring bond count checking property

PROPERTY_KEY_RING_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Ring count atom query property.

PROPERTY_KEY_RING_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Ring count checking property

PROPERTY_KEY_SEARCH_ALL - Static variable in class chemaxon.checkers.RatomChecker

This constant String represents the name of the property which is responsible for searching all ratoms in the molecule

PROPERTY_KEY_SEARCH_BRIDGEHEAD - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searchingBridgehead property

PROPERTY_KEY_SEARCH_CHARGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching charged explicit hydrogens in the molecule

PROPERTY_KEY_SEARCH_CONTRACTED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker

This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups

PROPERTY_KEY_SEARCH_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker

Search default valence property

PROPERTY_KEY_SEARCH_DISCONNECTED - Static variable in class chemaxon.checkers.RatomChecker

This constant String represents the name of the property which is responsible for searching disconnected ratoms in the molecule

PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker

This public constant String represents the name of the property which is responsible for the list of excluded groups

PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.AttachedDataChecker

PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.PseudoAtomChecker

PROPERTY_KEY_SEARCH_EXPANDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker

This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups

PROPERTY_KEY_SEARCH_GENERIC - Static variable in class chemaxon.checkers.RatomChecker

This constant String represents the name of the property which is responsible for searching generic ratoms in the molecule

PROPERTY_KEY_SEARCH_H_CONNECTED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching H connected property

PROPERTY_KEY_SEARCH_ISOTOPIC - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching isotopic explicit hydrogens in the molecule

PROPERTY_KEY_SEARCH_LINKER - Static variable in class chemaxon.checkers.RatomChecker

This private constant String represents the name of the property which is responsible for searching linker ratoms in the molecule

PROPERTY_KEY_SEARCH_LONELY - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching lonely explicit hydrogens in the molecule

PROPERTY_KEY_SEARCH_MAPPED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching mapped explicit hydrogens in the molecule

PROPERTY_KEY_SEARCH_NESTED - Static variable in class chemaxon.checkers.RatomChecker

This private constant String represents the name of the property which is responsible for searching nested ratoms in the molecule

PROPERTY_KEY_SEARCH_NON_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker

Search non default valence property

PROPERTY_KEY_SEARCH_POLYMER_END_GROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searchingPolymer end group property

PROPERTY_KEY_SEARCH_RADICAL - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching radical explicit hydrogens in the molecule

PROPERTY_KEY_SEARCH_SGROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searchingS-group property

PROPERTY_KEY_SEARCH_SGROUP_END - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searchingS-group end property

PROPERTY_KEY_SEARCH_VALENCE_ERROR - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searchingValence error property

PROPERTY_KEY_SEARCH_WEDGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the property which is responsible for searching wedged explicit hydrogens in the molecule

PROPERTY_KEY_SEARCH_WITH_REGEXP_EXCLUSION - Static variable in class chemaxon.checkers.AttachedDataChecker

PROPERTY_KEY_SGROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching S-group property

PROPERTY_KEY_SGROUP - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

S-group property

PROPERTY_KEY_SGROUP_END - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching S-group end property

PROPERTY_KEY_SGROUP_END - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

S-group end property

PROPERTY_KEY_SINGLE_UP_OR_DOWN_BOND - Static variable in class chemaxon.standardizer.actions.ClearStereoAction

Key of type for property change of mode

PROPERTY_KEY_SMALLEST_RING_SIZE - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Smallest ring size atom query property.

PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Smallest ring size checking property

PROPERTY_KEY_SMARTS_QUERY - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

SMARTS query property

PROPERTY_KEY_SMARTS_QUERY_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

SMARTS query checking property

PROPERTY_KEY_STEREO_GROUP - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Key of type for property change of mode

PROPERTY_KEY_SUBSTITUTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Substitution count atom query property.

PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Substitution count checking property

PROPERTY_KEY_TRADITIONAL_N_ALLOWED - Static variable in class chemaxon.checkers.ValenceErrorChecker

This public constant String represents the name of the configuration file property which is responsible for traditional N representation is allowed

PROPERTY_KEY_TYPE - Static variable in class chemaxon.checkers.AromaticityErrorChecker

This public constant String represents the name of the property which is responsible for using the given aromatization type during the check mechanism.

PROPERTY_KEY_TYPE - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Key of type for property change of mode

PROPERTY_KEY_TYPES - Static variable in class chemaxon.checkers.AtomTypeChecker

Types property

PROPERTY_KEY_UNSATURATION - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Unsaturation atom query property.

PROPERTY_KEY_UNSATURATION_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker

Unsaturation checking property

PROPERTY_KEY_USERSETTINGS - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor

Property key for optional client property UserSettings

PROPERTY_KEY_VALENCE_ERROR - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching Valence error property

PROPERTY_KEY_VALENCE_ERROR - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Valence error property

PROPERTY_KEY_VALID - Static variable in interface chemaxon.checkers.StructureChecker

This property key used to be the key of the property change event of valid property

PROPERTY_KEY_VALID - Static variable in interface chemaxon.marvin.services.ServiceDescriptorEditor

Property key for editor validation state as Boolean

PROPERTY_KEY_WEDGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker

This public constant String represents the name of the configuration file property which is responsible for searching wedged explicit hydrogens in the molecule

PROPERTY_KEY_WEDGED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Wedged property

PROPERTY_TYPE_ALL - Static variable in class chemaxon.marvin.common.UserSettings

Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get all properties that are stored.

PROPERTY_TYPE_DEFAULT - Static variable in class chemaxon.marvin.common.UserSettings

Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the default properties.

PROPERTY_TYPE_PERSISTENT - Static variable in class chemaxon.marvin.common.UserSettings

Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the properties set by UserSettings.setProperty(String, String) method or by the setter methods.

PROPERTY_TYPE_TRANSIENT - Static variable in class chemaxon.marvin.common.UserSettings

Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the properties that are being stored temporary, and will not be saved to the properties file.

propertyChange(PropertyChangeEvent) - Method in class chemaxon.checkers.AbstractStructureChecker

propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Handles "ancestor" events or sets parameters if a bean property is changed.

propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.beans.MSketchPane

Handles property change events.

propertyChange(PropertyChangeEvent) - Method in class chemaxon.standardizer.AbstractStandardizerAction

propertyChangeSupport - Variable in class chemaxon.checkers.AbstractStructureChecker

property change support object bound to this

propertyChangeSupport - Variable in class chemaxon.marvin.services.ServiceDescriptor

Property change support

propertyContainer - Variable in class chemaxon.struc.MoleculeGraph

propertyCount() - Method in class chemaxon.struc.MolAtom

Returns the number of property (property key - property value) mappings of this atom.

propertyCount() - Method in class chemaxon.struc.MolBond

Returns the number of property (property key - property value) mappings of this bond.

propertyKeySet() - Method in class chemaxon.struc.MolAtom

Returns a set view of the property keys of this atom.

propertyKeySet() - Method in class chemaxon.struc.MolBond

Returns a set view of the property keys of this bond.

propertySet() - Method in class chemaxon.struc.MolAtom

Returns a collection view of the properties (property key - property value mappings) of this atom.

propertySet() - Method in class chemaxon.struc.MolBond

Returns a set view of the properties (property key - property value mappings) of this bond.

propToString(MProp) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Converts a property to a string.

protectDoubleBondStereo() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Returns the adjusted double bond stereo protection flag.

protectTetrahedralStereo() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Returns the adjusted tetrahedral stereo protection flag.

PSEUDO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom with pseudo property could be converted to abbreviated group had found in the molecule

PSEUDO - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of a pseudoatom.

PSEUDO_NO_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom with pseudo property had found in the molecule

PseudoAtomChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting pseudo atoms.

PseudoAtomChecker() - Constructor for class chemaxon.checkers.PseudoAtomChecker

Default constructor

PseudoAtomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.PseudoAtomChecker

Pt - Static variable in class chemaxon.core.ChemConst

Pu - Static variable in class chemaxon.core.ChemConst

PublicApi - Annotation Interface in com.chemaxon.common.annotations

Marks types that are part of the Chemaxon public API.

put(int, float) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Stores the given value in the specified hitogram bin.

put(int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Stores the given value in the specified hitogram bin.

put(String, MProp) - Method in class chemaxon.struc.prop.MHashProp

Puts a value.

putBackLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Puts back the previous line to the input stream.

putBackLine() - Method in class chemaxon.marvin.io.PositionedInputStream

Puts back the last line into the stream.

putBackLine(int) - Method in class chemaxon.marvin.io.PositionedInputStream

Puts back the last line into the stream.

putProperty(String, Object) - Method in class chemaxon.struc.MolAtom

Associates the specified value with the specified key at this atom.

putProperty(String, Object) - Method in class chemaxon.struc.MolBond

Associates the specified value with the specified key at this bond.

Q

qpropCheck() - Method in class chemaxon.struc.MolAtom

Query property checking.

qpropCheck(List<MolAtom>) - Method in class chemaxon.struc.MoleculeGraph

Check for query property errors.

QUADRIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Quadrivalent radical center.

query - Variable in class chemaxon.sss.search.MolComparator

QUERY_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom with query properties had found in the molecule

QUERY_ATOMS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "queryAtoms".

QUERY_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that bond with query properties had found in the molecule

QueryAtomChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting generic atoms or ones having query properties.

QueryAtomChecker() - Constructor for class chemaxon.checkers.QueryAtomChecker

Default constructor

QueryBond - Class in chemaxon.struc

Chemical bond.

QueryBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.QueryBond

Construct an any bond between two atoms.

QueryBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.QueryBond

Construct an any bond between two atoms.

QueryBond(MolAtom, MolAtom, String) - Constructor for class chemaxon.struc.QueryBond

Construct a query bond between two atoms.

QueryBond(QueryBond) - Constructor for class chemaxon.struc.QueryBond

Copy constructor.

QueryBondChecker - Class in chemaxon.checkers

A descendant of BondChecker detecting query bonds.

QueryBondChecker() - Constructor for class chemaxon.checkers.QueryBondChecker

Default constructor

queryMol - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Query molecule (it is neither cloned nor modified).

querySearchData - Variable in class chemaxon.sss.search.MolComparator

R

r - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

R - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

R_GROUPS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "rgroupsVisible".

Ra - Static variable in class chemaxon.core.ChemConst

RA_IN_EXPAND - Static variable in class chemaxon.struc.Sgroup

Atom removal in expand.

RA_REMOVE_EXCEPT_RU - Static variable in class chemaxon.struc.Sgroup

Replace without duplicating.

RACEMATE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing asymmetric atom without specific stereo configuration.

RacemateChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting asymmetric tetrahedral atoms without specific stereochemistry.

RacemateChecker() - Constructor for class chemaxon.checkers.RacemateChecker

Creates a new RacemateChecker instance.

racemicStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the racemic tetrahedral stereogenic centers.

racemicStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the racemic tetrahedral stereogenic centers (with attached data).

RacemicTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral

Filter for racemic tetrahedral centers.

RacemicTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter

RAD_COUNT_MASK - Static variable in class chemaxon.struc.MolAtom

Radical's free electron count bits in flags for valid radical values.

RAD_MASK - Static variable in class chemaxon.struc.MolAtom

Radical value bits in flags.

RAD_OFF - Static variable in class chemaxon.struc.MolAtom

Radical value offset in flags.

RAD1 - Static variable in class chemaxon.struc.MolAtom

Monovalent radical center.

RAD2 - Static variable in class chemaxon.struc.MolAtom

Divalent radical center.

RAD2_SINGLET - Static variable in class chemaxon.struc.MolAtom

Divalent radical center with singlet electronic configuration.

RAD2_TRIPLET - Static variable in class chemaxon.struc.MolAtom

Divalent radical center with triplet electronic configuration.

RAD3 - Static variable in class chemaxon.struc.MolAtom

Trivalent radical center.

RAD3_DOUBLET - Static variable in class chemaxon.struc.MolAtom

Trivalent radical center with doublet electronic configuration.

RAD3_QUARTET - Static variable in class chemaxon.struc.MolAtom

Trivalent radical center with quartet electronic configuration.

RAD4 - Static variable in class chemaxon.struc.MolAtom

Invalid value for radical center for students.

RADICAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom with radical had found in the molecule

RADICAL_CHAR - Static variable in class chemaxon.struc.MolAtom

RADICAL_H - Static variable in class chemaxon.struc.MolAtom

Include radical Hydrogen atom(s).

RADICAL_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).

RADICAL_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).

RADICAL_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for ignore radical searching (radical information is ignored during searching).

RadicalChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting radical atoms.

RadicalChecker() - Constructor for class chemaxon.checkers.RadicalChecker

Default constructor

radicalCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint

radicalMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets whether the radical information of atoms should be considered in search.

radicalState - Static variable in class chemaxon.struc.graphics.MEFlow

randicIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.

randomizeRotatableDihedrals(Molecule, Random) - Static method in class chemaxon.marvin.alignment.Alignment

Rotates rotatable bonds by a random dihedral angle value.

randomSeed - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Random seed (0 means using the current time).

RARE_ELEMENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that rare element had found in the molecule

RareElementChecker - Class in chemaxon.checkers

A descendant of AtomTypeChecker detecting structures containing elements which are usually rare in organic/drug molecules.

RareElementChecker() - Constructor for class chemaxon.checkers.RareElementChecker

Default constructor

RATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing that the molecule contains R-atom.

RATOM - Static variable in class chemaxon.jep.context.ReactionContext

RatomChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting R-atoms.

RatomChecker() - Constructor for class chemaxon.checkers.RatomChecker

Creates a new anyChecker instance detecting all R-atoms.

RatomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RatomChecker

Creates a new anyChecker instance reading checking options from the params argument.

Rb - Static variable in class chemaxon.core.ChemConst

RC_CHANGE - Static variable in class chemaxon.struc.MolBond

The bond (order) has changed in the reaction.

RC_MAKE_AND_CHANGE - Static variable in class chemaxon.struc.MolBond

The bond is created and changed.

RC_MAKE_OR_BREAK - Static variable in class chemaxon.struc.MolBond

The bond is made or broken in the reaction.

RC_NOT_CENTER - Static variable in class chemaxon.struc.MolBond

The bond is not a reacting center.

RC_NOT_MODIFIED - Static variable in class chemaxon.struc.MolBond

The bond is not modified in the reaction.

RC_REACTING_CENTER - Static variable in class chemaxon.struc.MolBond

The bond is a reacting center.

RC_UNMAPPED - Static variable in class chemaxon.struc.MolBond

Unmapped bond in reacting center.

RDF - Static variable in class chemaxon.formats.MFileFormat

MDL RDfiles.

Re - Static variable in class chemaxon.core.ChemConst

REACTANT - Static variable in class chemaxon.jep.context.ReactionContext

REACTANTS - Static variable in class chemaxon.struc.RxnMolecule

"Reactant" structure type.

REACTING_CENTER_BOND_MARK - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule contains reacting center bond marks.

REACTING_CENTER_MASK - Static variable in class chemaxon.struc.MolBond

Mask for reacting center bits.

ReactingCenterBondMarkChecker - Class in chemaxon.checkers

Checker detects bonds with reacting center bond marks.

ReactingCenterBondMarkChecker() - Constructor for class chemaxon.checkers.ReactingCenterBondMarkChecker

Default constructor

REACTION_ERROR_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Deprecated, for removal: This API element is subject to removal in a future version.

As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.

REACTION_SUPPORT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "reactionSupport".

reactionArrow - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The reaction arrow endpoints, null if not a reaction.

ReactionChecker - Class in chemaxon.checkers

Descendants of ReactionChecker detect reaction scheme problems.

ReactionChecker(StructureCheckerErrorType, StructureChecker) - Constructor for class chemaxon.checkers.ReactionChecker

Default constructor.

ReactionCheckerResult - Class in chemaxon.checkers.result

Deprecated, for removal: This API element is subject to removal in a future version.

ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.ReactionCheckerResult

Deprecated.

use ReactionCheckerResult(StructureChecker, List, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead

ReactionCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, List<Long>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.ReactionCheckerResult

Deprecated.

Constructor which initialize all the properties.

ReactionContext - Class in chemaxon.jep.context

Expression evaluation context to evaluate reaction conditions.

ReactionContext() - Constructor for class chemaxon.jep.context.ReactionContext

Constructor.

ReactionContext(boolean) - Constructor for class chemaxon.jep.context.ReactionContext

Deprecated, for removal: This API element is subject to removal in a future version.

Copy feature is no longer required. Constructor.

ReactionContext(RxnMolecule) - Constructor for class chemaxon.jep.context.ReactionContext

Constructs a reaction context with specified reaction.

ReactionFingerprint - Class in chemaxon.descriptors

ReactionFingerprint class.

ReactionFingerprint() - Constructor for class chemaxon.descriptors.ReactionFingerprint

Creates a new, empty instance of ReactionFingerprint without allocating internal storage.

ReactionFingerprint(ReactionFingerprint) - Constructor for class chemaxon.descriptors.ReactionFingerprint

Copy constructor.

ReactionFingerprint(RFParameters) - Constructor for class chemaxon.descriptors.ReactionFingerprint

Creates a new instance of ReactionFingerprint according to the parameters given.

ReactionFingerprint(String) - Constructor for class chemaxon.descriptors.ReactionFingerprint

Creates a new instance of ReactionFingerprint according to the parameters given.

ReactionMapErrorChecker - Class in chemaxon.checkers

A descendant of ReactionChecker detecting reactions with invalid mapping.

Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.

ReactionMapErrorChecker() - Constructor for class chemaxon.checkers.ReactionMapErrorChecker

Default constructor

read() - Method in class chemaxon.formats.MolImporter

Read the next molecule.

read() - Method in class chemaxon.marvin.io.formats.MoleculeImporter

read() - Method in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Read the next molecule from the stream/file.

read() - Method in class chemaxon.marvin.io.PositionedInputStream

Reads a character.

read() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Find the next structure in the source document and return it, or null when the end of the document has been reached.

read(byte[], int, int) - Method in class chemaxon.marvin.io.PositionedInputStream

Reads a byte array.

read(MolImporter) - Method in class chemaxon.util.concurrent.marvin.MolInputProducer

read(Molecule) - Method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 14.7.7. use MolImporter.read() instead

read(ObjectInput) - Static method in class chemaxon.marvin.io.Encoding

Reads an externalized encoding object.

read16doubles(ObjectInput) - Method in class chemaxon.struc.CTransform3D

Reads the 4x4 matrix components as double precision floating point numbers.

read16floats(ObjectInput) - Method in class chemaxon.struc.CTransform3D

Reads the 4x4 matrix components as single precision floating point numbers.

readAttribute(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Jar attributes are no longer used to store information related to calculator plugins. No replacement.

readDoc() - Method in class chemaxon.marvin.io.MRecordImporter

Reads the next document.

readDoc(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane

readDocument(MDocument) - Method in class chemaxon.marvin.io.MolImportModule

Reads the next document.

readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MarvinPane

Restores object state.

readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketch

Restores the sketcher's state.

readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketchPane

Restores object state.

readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MView

Restores the viewer's state.

readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MViewPane

Restores object state.

readExternal(ObjectInput) - Method in class chemaxon.marvin.io.Encoding

Restores object state.

readExternal(ObjectInput) - Method in class chemaxon.struc.CTransform3D

Deserializes a transformation matrix.

readExternal(ObjectInput) - Method in class chemaxon.struc.DPoint3

Deserializes a 3D point.

readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextAttributes

readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextDocument

Restores the document.

readExternal(ObjectInput) - Method in class chemaxon.struc.MPropertyContainer

Restores the property container's state.

readExternal(ObjectInput) - Method in class chemaxon.struc.PageSettings

readFromString(String) - Method in class chemaxon.struc.graphics.MTextDocument

Reads the document from a string.

readFromXmlFile(File, boolean, boolean) - Method in class chemaxon.descriptors.MDParameters

Reads configuration from XML file.

readFromXmlString(String, boolean, boolean) - Method in class chemaxon.descriptors.MDParameters

Reads configuration from XML string.

readLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Reads the next line.

readLine() - Method in class chemaxon.marvin.io.PositionedInputStream

Reads a line.

readMetricParameters() - Method in class chemaxon.descriptors.MDParameters

Processes all ParametrizedMetric nodes in the DOM tree.

readMetricParameters() - Method in class chemaxon.descriptors.PFParameters

readMetricWeights(Element, int) - Method in class chemaxon.descriptors.MDParameters

readMetricWeights(Element, int) - Method in class chemaxon.descriptors.PFParameters

readMol(Molecule) - Method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 14.7.7. use MolImporter.read() instead

readMol(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolImport

Reads a molecule from MDL mol/sdf/rxn file.

readMol(Molecule) - Method in class chemaxon.marvin.io.MolImportModule

Reads the next molecule.

readMol(Molecule) - Method in class chemaxon.marvin.io.MRecordImporter

Reads the next molecule.

readMol(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane

readMolecules(InputStream, boolean) - Method in class chemaxon.sss.screen.StrucFPConfig

Read the structures from a stream.

readMolMovie(MDocument) - Method in class chemaxon.marvin.io.MRecordImporter

Reads molecules as a movie.

readMultiSet(Molecule) - Method in class chemaxon.marvin.io.MRecordImporter

Reads molecules as one multi-set molecule.

readRecordAsText() - Method in class chemaxon.formats.MolImporter

Reads the next molecule in text format without creating a Molecule object.

readRecordAsText() - Method in class chemaxon.marvin.io.MRecordImporter

Reads the next record.

readResources(Class<?>, String) - Static method in class chemaxon.marvin.beans.MarvinPane

Reads resources from the specified file.

readSaltDictionary() - Static method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Reads the default salt dictionary.

readServiceDescriptors(InputStream) - Method in interface chemaxon.marvin.services.ServiceDescriptorReader

Returns a list of configured ServiceDescriptor objects from specified InputStream

readSolventDictionary() - Static method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Reads the default solvent dictionary.

readValues(boolean) - Method in class chemaxon.descriptors.BCUTParameters

Retrieves relavant parameters values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.CDParameters

Picks parameter values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.CFParameters

Picks parameter values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.ECFPParameters

Picks parameter values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.MDParameters

Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.

readValues(boolean) - Method in class chemaxon.descriptors.PFParameters

readValues(boolean) - Method in class chemaxon.descriptors.RFParameters

Picks parameters values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.scalars.HBParameters

Picks relevant parameters values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.scalars.LDParameters

Picks parameters values from the DOM tree.

readValues(boolean) - Method in class chemaxon.descriptors.SDParameters

Reads attribute values form the XML configuration.

readValues(boolean) - Method in class chemaxon.descriptors.ShapeParameters

RearomatizeFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which rearomatize the molecule

RearomatizeFixer() - Constructor for class chemaxon.fixers.RearomatizeFixer

RearrangeReactionAction - Class in chemaxon.standardizer.actions

RearrangeReactionAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RearrangeReactionAction

Initializes the action

rearrangeSgroups(int[]) - Method in class chemaxon.struc.Molecule

Orders S-groups in the vector of S-groups in the given order corresponding to the given new indexes.

RearrangeWedgesFixer - Class in chemaxon.fixers

Rearranges stereo wedge bonds according to IUPAC recommendations.

RearrangeWedgesFixer() - Constructor for class chemaxon.fixers.RearrangeWedgesFixer

rebuildStructures() - Method in class chemaxon.struc.RxnMolecule

For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow.

rebuildStructures(DPoint3[], int) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow.

recalcCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Recalculates and sets the coordinates of the central atom of this sgroup.

recalcReactionArrow() - Method in class chemaxon.struc.RxnMolecule

Recalculates the coordinates of the reaction arrow from the reactants and products, forced recalculation.

recognize(byte[], int, int) - Static method in class chemaxon.marvin.io.Encoding

Tries to recognize the encoding of a byte array.

recognizeByBOM(byte[], int, int) - Static method in class chemaxon.marvin.io.Encoding

Tries to recognize the encoding of a byte array by the byte order mark.

recognizeOneLineFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil

Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.

recognizeOneLineFormat(String, MFileFormat...) - Static method in class chemaxon.formats.MFileFormatUtil

Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.

Recognizer - Class in chemaxon.formats.recognizer

File format recognizer.

Recognizer() - Constructor for class chemaxon.formats.recognizer.Recognizer

RecognizerFactory - Interface in chemaxon.formats.factory

Factory interface for Recognizers.

RecognizerList - Class in chemaxon.formats.recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

Not used, will be removed

RECURSIVE_UNGROUP - Static variable in class chemaxon.struc.Molecule

Ungroup and expand (if possible) the child S-groups.

RED - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Constant storing the red rgb value (the acidic pKa result color).

redo() - Method in class chemaxon.marvin.beans.MSketchPane

Invokes a redo command.

RefractivityPlugin - Class in chemaxon.marvin.calculations

Plugin class for refractivity calculation.

RefractivityPlugin() - Constructor for class chemaxon.marvin.calculations.RefractivityPlugin

Constructor.

regenBonds() - Method in class chemaxon.struc.MoleculeGraph

Regenerates the bond vector: remove its elements, then put the bond objects from the atoms into it.

regenBonds() - Method in class chemaxon.struc.RgMolecule

Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.

regenBonds() - Method in class chemaxon.struc.RxnMolecule

Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.

regenBtab() - Method in class chemaxon.struc.MoleculeGraph

Regenerates the bond table.

regenBtab() - Method in class chemaxon.struc.SelectionMolecule

Regenerates the bond table.

regenCtab() - Method in class chemaxon.struc.MoleculeGraph

Regenerates the connection table.

regenCtab() - Method in class chemaxon.struc.SelectionMolecule

Regenerates the connection table.

regenGearch() - Method in class chemaxon.struc.MoleculeGraph

Recreate graph search results object.

registerFormat(MFileFormat) - Static method in class chemaxon.formats.MFileFormatUtil

Registers a user defined file format.

registerNativeNames() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Registers the Native names supported by the implementation.

registerNativeNames() - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable

Registers the Native names supported by the implementation.

REGNO_MAX_LENGTH_IN_HEADER - Static variable in class chemaxon.marvin.io.formats.mdl.MolExport

REGULAR_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule

Regular double reaction arrow type.

REGULAR_SINGLE - Static variable in class chemaxon.struc.RxnMolecule

Regular single reaction arrow type.

RELATIVE_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecules having multiple stereogenic center groups

RelativeStereoChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting molecules having multiple stereogenic center groups

RelativeStereoChecker() - Constructor for class chemaxon.checkers.RelativeStereoChecker

Initializes relative stereo checker

releaseBaseMElectrons() - Method in class chemaxon.struc.graphics.MEFlow

releaseNewEMFGenerator() - Static method in class chemaxon.util.ImageExportUtil

Releases and disposes native resources needed by the .NET based EMF generator.

reload() - Method in class chemaxon.fixers.StructureFixerFactory

Deprecated.

Forces reload of configuration on next fixer list request.

reloadDefaultInstance() - Static method in class chemaxon.structurechecker.factory.CheckerFixerFactory

Reloads the content of the default factory instance

reloadDefaultMap() - Static method in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Forces reload of factory data.

reloadDefaults() - Static method in class chemaxon.fixers.StructureFixerFactory

Deprecated.

Forces reload of factory defaults.

reloadParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Reloads previously stored parameters to parameter panel.

reloadParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Reloads previously stored parameters to parameter panel.

RemovalDate - Enum Class in com.chemaxon.common.annotations

Date values accepted by the SubjectToRemoval annotation.

remove() - Method in class chemaxon.util.iterator.IteratorFactory.AtomIterator

Removes the next atom in the iteration.

remove() - Method in class chemaxon.util.iterator.IteratorFactory.BondIterator

Removes the next bond in the iteration.

remove() - Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

The remove operation is not supported by this Iterator implementation.

remove() - Method in class chemaxon.util.iterator.IteratorFactory.RgComponentIterator

The remove operation is not supported by this Iterator implementation.

remove() - Method in class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator

The remove operation is not supported by this Iterator implementation.

remove() - Method in class chemaxon.util.iterator.IteratorFactory.SgroupIterator

Removes the next s-group in the iteration.

remove(int) - Method in class chemaxon.struc.prop.MListProp

Removes an element.

remove(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Deletes a substring in the document.

remove(NameConverter) - Static method in class chemaxon.naming.NameConverters

Remove the converter from the converter list.

remove(MProp) - Method in class chemaxon.struc.MPropertyContainer

Removes a property.

remove(String) - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Removes the recognizer with the specified codename.

RemoveAbsoluteStereoAction - Class in chemaxon.standardizer.actions

Set absolute stereo standardizer action

RemoveAbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAbsoluteStereoAction

Initializes a remove absolute stereo action

removeAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Removes an action of the configuration

removeActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane

Removes an action listener.

removeActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions

Removes an action listener.

removeActions(Collection<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Removes actions of the configuration

RemoveAliasFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the alias information from the atoms of the molecule

RemoveAliasFixer() - Constructor for class chemaxon.fixers.RemoveAliasFixer

removeAll() - Method in class chemaxon.struc.Molecule

Removes all the atoms and bonds.

removeAll() - Method in class chemaxon.struc.MoleculeGraph

Removes all the atoms and bonds.

removeAll() - Method in class chemaxon.struc.RgMolecule

Remove all the atoms and bonds from the root structure, and from all the R-groups.

removeAll() - Method in class chemaxon.struc.RxnMolecule

Remove all the atoms and bonds from the root structure, and from all the R-groups.

removeAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes

Adds atoms to the "removed atom" list

removeAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes

Adds atoms to the "removed atom" list

removeAllAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Removes all attachment points of the Superatom s-group.

removeAllBonds() - Method in class chemaxon.struc.MolAtom

Removes all bonds.

removeAllBonds() - Method in class chemaxon.struc.Molecule

Removes all bonds.

removeAllBonds() - Method in class chemaxon.struc.MoleculeGraph

Removes all bonds.

removeAllBonds() - Method in class chemaxon.struc.RgMolecule

Remove all bonds from the root structure, and from all the R-groups.

removeAllBonds() - Method in class chemaxon.struc.RxnMolecule

Removes all bonds from the reactants, products and agents.

removeAllBonds() - Method in class chemaxon.struc.sgroup.SgroupAtom

Remove all edges.

removeAllBonds(boolean) - Method in class chemaxon.struc.MolAtom

Removes all bonds.

removeAllBonds(boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom

Removes all edges.

removeAllConstraints() - Method in class chemaxon.marvin.alignment.Alignment

removeAllExcept(long, long) - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Removes all recognizers except those with the specified flags.

removeAllExcept(String) - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Removes all recognizers except the specified.

removeAllFromDocument(MDocument) - Static method in class chemaxon.struc.NoStructure

Removes all NoStructure labels from the target document.

removeAllGroups() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Removes all group definitions from the group list of the action.

removeAllMolecules() - Method in class chemaxon.marvin.alignment.Alignment

before every new alignment the molecules have to be removed.

removeAllMolecules() - Method in class chemaxon.marvin.alignment.PairwiseAlignment

removeAllMolecules() - Method in interface chemaxon.marvin.alignment.PairwiseComparison

removeAllMolecules() - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

removeAllPairs() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Removes all user defined atom pairs.

removeAllProperty() - Method in class chemaxon.marvin.common.UserSettings

Removes all property that are stored in this UserSettings object.

removeAllSalts() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Removes all salts from the salt list of the action.

removeAllSgroups() - Method in class chemaxon.struc.Molecule

Removes all S-groups.

removeAllSolvents() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Removes all solvents from the solvents list of the action.

removeArgument(int) - Method in class chemaxon.marvin.services.ServiceDescriptor

Removes the specified argument from the argument list

removeAtom(int) - Method in class chemaxon.struc.MoleculeGraph

Removes an atom and its bonds by index.

removeAtom(int) - Method in class chemaxon.struc.SelectionMolecule

Removes an atom and its bonds from the graph.

removeAtom(int, int) - Method in class chemaxon.struc.Molecule

Removes an atom and its bonds by index.

removeAtom(int, int) - Method in class chemaxon.struc.MoleculeGraph

Removes an atom and its bonds with extra clean-up options.

removeAtom(int, int) - Method in class chemaxon.struc.RgMolecule

Removes an atom and its bonds from the root structure.

removeAtom(int, int) - Method in class chemaxon.struc.RxnMolecule

Removes an atom from the reactants, products or agents.

removeAtom(MolAtom) - Method in class chemaxon.standardizer.Changes

Adds an atom to the "removed atom" list.

removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct

removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlow

removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MElectron

removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MElectronContainer

removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MMoleculeMovie

removeAtom(MolAtom) - Method in class chemaxon.struc.MDocument

Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.

removeAtom(MolAtom) - Method in class chemaxon.struc.MObject

Removes the atom from the corresponding molecule object.

removeAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Removes an atom and its bonds by reference.

removeAtom(MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Removes an atom and its bonds.

removeAtom(MolAtom) - Method in class chemaxon.struc.Sgroup

Removes an atom and its bonds from the S-group.

removeAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes

Adds an atom to the "removed atom" list.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.MDocument

Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.Molecule

Removes an atom and its bonds by reference.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph

Removes an atom and its bonds with extra clean-up options.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.RgMolecule

Removes an atom and its bonds from the root structure and from all the R-groups.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.RxnMolecule

Removes an atom from the reactants, products or agents.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Removes an atom from the S-group.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.Sgroup

Removes an atom and its bonds from the S-group.

removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Removes an atom from the S-group.

removeAtom(Sgroup, MolAtom, int) - Static method in class chemaxon.struc.Sgroup

Wrapper method that calls Sgroup.removeAtom(MolAtom, int) of sg.

removeAtomAliases(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

RemoveAtomFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the atoms of the molecule signed in the result

RemoveAtomFixer() - Constructor for class chemaxon.fixers.RemoveAtomFixer

removeAtomFromChildren(Sgroup, MolAtom) - Method in class chemaxon.struc.Molecule

Removes the parameter atom from the parameter S-group and it's descendants.

removeAtomFromGraphs(MolAtom) - Method in class chemaxon.struc.MDocument

Removes the specified node from all molecule graphs.

RemoveAtomMapFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the atom maps from the molecule

RemoveAtomMapFixer() - Constructor for class chemaxon.fixers.RemoveAtomMapFixer

RemoveAtomQueryPropertyFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes query properties from the given atoms.

RemoveAtomQueryPropertyFixer() - Constructor for class chemaxon.fixers.RemoveAtomQueryPropertyFixer

RemoveAtomValueFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the atom value from the molecule

RemoveAtomValueFixer() - Constructor for class chemaxon.fixers.RemoveAtomValueFixer

RemoveAtomValuesAction - Class in chemaxon.standardizer.actions

Remove Atom Values standardizer action

RemoveAtomValuesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAtomValuesAction

Initializes the action

RemoveAttachedDataAction - Class in chemaxon.standardizer.actions

Remove Attached Data standardizer action

RemoveAttachedDataAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAttachedDataAction

Initializes the action

RemoveAttachedDataFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the attached data from the molecule.

RemoveAttachedDataFixer() - Constructor for class chemaxon.fixers.RemoveAttachedDataFixer

removeAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Removes the attachment point with the given order.

removeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Removes all attachment points of the given attachment atom.

removeBond(int) - Method in class chemaxon.struc.MolAtom

Removes a bond.

removeBond(int) - Method in class chemaxon.struc.MoleculeGraph

Removes a bond by index.

removeBond(int) - Method in class chemaxon.struc.SelectionMolecule

Removes a bond from the graph.

removeBond(int, boolean) - Method in class chemaxon.struc.MolAtom

Removes a bond.

removeBond(int, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom

Removes a bond.

removeBond(int, int) - Method in class chemaxon.struc.Molecule

Removes a bond by index.

removeBond(int, int) - Method in class chemaxon.struc.MoleculeGraph

Removes a bond by index.

removeBond(int, int) - Method in class chemaxon.struc.RgMolecule

Remove a bond from the root structure.

removeBond(int, int) - Method in class chemaxon.struc.RxnMolecule

Removes an edge from a reactant, agent or product.

removeBond(MolBond) - Method in class chemaxon.struc.MolAtom

Removes a bond by reference.

removeBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph

Removes a bond by reference.

removeBond(MolBond) - Method in class chemaxon.struc.SelectionMolecule

Removes a bond by reference.

removeBond(MolBond) - Method in class chemaxon.struc.Sgroup

Removes a bond from the S-group.

removeBond(MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Removes a the given bond from the S-group.

removeBond(MolBond, boolean) - Method in class chemaxon.struc.MolAtom

Removes a bond by reference.

removeBond(MolBond, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom

Removes a bond by reference.

removeBond(MolBond, int) - Method in class chemaxon.struc.Molecule

Removes a bond by reference.

removeBond(MolBond, int) - Method in class chemaxon.struc.MoleculeGraph

Removes a bond by reference.

removeBond(MolBond, int) - Method in class chemaxon.struc.RgMolecule

Remove a bond from the root structure, and from all the R-groups.

removeBond(MolBond, int) - Method in class chemaxon.struc.RxnMolecule

Removes a bond from the reactants, products or agents.

RemoveBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the bonds of the molecule signed by the result

RemoveBondFixer() - Constructor for class chemaxon.fixers.RemoveBondFixer

removeBonds() - Method in class chemaxon.struc.Sgroup

Removes the edge references.

RemoveBondTopologyFixer - Class in chemaxon.fixers

Fixer removes reactiong center bond marks from bonds.

RemoveBondTopologyFixer() - Constructor for class chemaxon.fixers.RemoveBondTopologyFixer

RemoveBracketsFixer - Class in chemaxon.fixers

Removes brackets from molecule by ungrouping S-groups surrounded by brackets.

RemoveBracketsFixer() - Constructor for class chemaxon.fixers.RemoveBracketsFixer

removeChild(MObject) - Method in class chemaxon.struc.graphics.MPolyline

removeChild(MObject) - Method in class chemaxon.struc.graphics.MRArrow

removeChild(MObject) - Method in class chemaxon.struc.graphics.MRectangle

removeChild(MObject) - Method in class chemaxon.struc.MObject

Removes a child object.

removeChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup

Removes an S-group from the children list.

RemoveChiralFlagFixer - Class in chemaxon.fixers

A StructureFixer implementation which removes absolute stereo property from the molecule.

RemoveChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveChiralFlagFixer

removeColorsFromMolecules() - Method in class chemaxon.struc.MDocument

Removes coloring from all molecular objects in the document.

removeComparator(MolComparator) - Method in class chemaxon.sss.search.MolSearch

Delete a comparator from the search object.

removeComponent(int, int) - Method in class chemaxon.struc.RxnMolecule

Removes a reactant, product or agent.

removeCTflagFromSmallRings(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Remove CIS|TRANS flag from bonds in rings smaller than size 8.

removeDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule

Removes the dependent R-group definition of the referenced R-group definition.

removeElectronsOf(MolAtom) - Method in class chemaxon.struc.MDocument

Removes the Electron containers belongs to targetAtom,

removeElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct

removeEmptyComponents() - Method in class chemaxon.struc.RxnMolecule

Checks all the componentes and removes those that are empty (node count is zero).

RemoveExplicitHydrogenFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which implicitize the hydrogens in the molecule

RemoveExplicitHydrogenFixer() - Constructor for class chemaxon.fixers.RemoveExplicitHydrogenFixer

RemoveExplicitHydrogensAction - Class in chemaxon.standardizer.actions

Remove explicit H standardizer action

RemoveExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Initializes the remove explicit H action

removeExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.7, replaced by Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph).

RemoveFragmentAction - Class in chemaxon.standardizer.actions

Removal standardizer action

RemoveFragmentAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveFragmentAction

Initializes the action with parameters

RemoveFragmentAction.Measurement - Enum Class in chemaxon.standardizer.actions

Type of measurement

RemoveFragmentAction.Method - Enum Class in chemaxon.standardizer.actions

Type of removal methods

removeFromDocument(NoStructure, MDocument) - Static method in class chemaxon.struc.NoStructure

Removes the given NoStructre from the target document.

removeFunction(String) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The function table will become unmodifiable. Configure the Evaluator instead before creating the ChemJEP.

removeGroup(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Removes a group definition from the group list of the action

removeGroupedAtom(MoleculeGraph, MolAtom, MolBond[], int) - Static method in class chemaxon.struc.Sgroup

Removes an atom from the molecule and remove its specified bonds.

removeHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertExplicitHToImplicit(MoleculeGraph) instead

removeHAtoms(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int) instead

removeHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) instead

removeHAtoms(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) instead

removeInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil

Removes the Standardizer tasks specified in the configuration parameter from the inactive tasks list.

RemoveInvalidChiralFlagFixer - Class in chemaxon.fixers

A StructureFixer implementation which removes absolute stereo property from the molecule.

RemoveInvalidChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveInvalidChiralFlagFixer

removeIsolatedAtoms() - Method in class chemaxon.struc.MoleculeGraph

Removes the null atom entries in the atoms array and sets the index fields appropriately.

removeIsolatedBonds() - Method in class chemaxon.struc.MoleculeGraph

Removes the null bond entries in the bonds array and sets the index fields appropriately.

removeItemListener(ItemListener) - Method in class com.chemaxon.calculations.gui.MChart

REMOVELARGEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Remove largest fragment

removeListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage

Removes a listener.

removeLonePairs(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

removeLonePairs(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 5.11, use Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph) instead

removeMolecules() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MEFlow

removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MElectronContainer

removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint

Point removed from a document.

removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MPolyline

removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint

Point removed from a document.

removeNotify(MDocument) - Method in class chemaxon.struc.MObject

Called when the object is removed from a document.

removeObject(int) - Method in class chemaxon.struc.MDocument

Removes an object from the document.

removeObject(int) - Method in class chemaxon.struc.MSelectionDocument

Removes an object from the document.

removeObject(MObject) - Method in class chemaxon.struc.MDocument

Removes an object from the document or from the chemical structure of the document.

removeObject(MObject) - Method in class chemaxon.struc.Molecule

removeObject(MObject) - Method in class chemaxon.struc.MSelectionDocument

Removes an object from the document.

removeObject(MObject) - Method in class chemaxon.struc.RgMolecule

removeObject(MObject) - Method in class chemaxon.struc.RxnMolecule

Removes a graphical object from this.

removeObject(MObject) - Method in class chemaxon.struc.Sgroup

Removes the specified MObject from this Sgroup.

removeOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings

Removes an owner.

removeProperty(String) - Method in class chemaxon.struc.MolAtom

Removes the mapping for this property key from this atom if present.

removeProperty(String) - Method in class chemaxon.struc.MolBond

Removes the mapping for this property key from this bond if present.

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker

removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker

Remove a PropertyChangeListener from the listener list.

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Remove a PropertyChangeListener from the listener list.

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor

Remove a PropertyChangeListener from the listener list.

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings

Remove a property change listener

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction

Remove a PropertyChangeListener from the listener list.

removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Remove a PropertyChangeListener from the listener list.

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker

removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker

Remove a PropertyChangeListener for a specific property.

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Remove a PropertyChangeListener for a specific property.

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor

Remove a PropertyChangeListener for a specific property.

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction

Remove a PropertyChangeListener for a specific property.

removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Remove a PropertyChangeListener for a specific property.

RemoveRadicalFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes the radicals from the atoms of the molecule

RemoveRadicalFixer() - Constructor for class chemaxon.fixers.RemoveRadicalFixer

RemoveReactingCenterBondMarkFixer - Class in chemaxon.fixers

Fixer removes reactiong center bond marks from bonds.

RemoveReactingCenterBondMarkFixer() - Constructor for class chemaxon.fixers.RemoveReactingCenterBondMarkFixer

removeReactionArrow() - Method in class chemaxon.struc.RxnMolecule

Removes the reaction arrow of this reacion.

removeRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Removes an atom from the list of paradigmatic repeating unit atoms.

removeRestH(int) - Method in class chemaxon.struc.RgMolecule

Removes the restH condition from an R-group definition.

removeRgroup(int) - Method in class chemaxon.struc.RgMolecule

Removes an R-group.

removeRgroupBridge(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule

Removes an R-group bridge.

removeRgroupBridgeMember(RgroupBridgeId, int) - Method in class chemaxon.struc.RgMolecule

Removes a definition member of an R-group bridge.

RemoveRGroupDefinitionsAction - Class in chemaxon.standardizer.actions

Remove R-group definition standardizer action

RemoveRGroupDefinitionsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveRGroupDefinitionsAction

Initializes the action

removeRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule

Removes an R-group definition member.

removeRgroupMembers(int, int[]) - Method in class chemaxon.struc.RgMolecule

Removes R-group members.

removeSalt(int) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Removes a salt from the salt list of the action

removeSalts(int...) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Removes a salt from the salt list of the action

removeSelectedFrom(MDocument) - Static method in class chemaxon.struc.NoStructure

Removes the selected NoStructres from the document.

removeSgroupFromList(Sgroup) - Method in class chemaxon.struc.Molecule

Removes an S-group from the sgroupVector.

removeSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule

Removes S-groups from this object and its parent.

removeSgroupsOf(Molecule, int) - Method in class chemaxon.struc.Molecule

Removes S-groups that are contained in a given molecule but not contained in another molecule.

removeSketchRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings

Remove a file from marvinsketch's recent file list

REMOVESMALLEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Remove smallest fragment

removeSolvent(int) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Removes a solvent from the solvent list of the action

removeSolvents(int...) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Removes a solvent from the solvent list of the action

RemoveSolventsAction - Class in chemaxon.standardizer.advancedactions

Remove solvents standardizer action.

RemoveSolventsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Initializes remove solvents action

removeStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Changes terminal star atoms (*) to carbon atoms (C).

RemoveStereoCareBoxAction - Class in chemaxon.standardizer.actions

Remove Stereo Care Box standardizer action

RemoveStereoCareBoxAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveStereoCareBoxAction

Initializes the action

RemoveStereoCareBoxFixer - Class in chemaxon.fixers

Fixer for molecules containing Stereo Care Boxes.

RemoveStereoCareBoxFixer() - Constructor for class chemaxon.fixers.RemoveStereoCareBoxFixer

RemoveStereoInversionRetentionMarkFixer - Class in chemaxon.fixers

Removes stereo inversion retention marks.

RemoveStereoInversionRetentionMarkFixer() - Constructor for class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer

RemoveUnreferencedRgroupDefinitionsFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer that removes unused R-group definitions.

RemoveUnreferencedRgroupDefinitionsFixer() - Constructor for class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer

removeUnSelectedFrom(MDocument) - Static method in class chemaxon.struc.NoStructure

Removes the non-selected NoStructures from the document.

RemoveValencePropertyFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which removes valence properties from the given atoms.

RemoveValencePropertyFixer() - Constructor for class chemaxon.fixers.RemoveValencePropertyFixer

removeVariable(String) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

The symbol table has been replaced with the constant table, and it will become unmodifiable. Use Evaluator.compile(String, Class, ConstantTable) instead.

removeViewRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings

Remove a file from marvinview's recent file list

removeWhitespace(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Removes whitespace characters from the given string.

REMOVEZCOORDINATE - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Convert 3D to 2D

RemoveZCoordinateFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which sets the z-coordinates of atoms to zero.

RemoveZCoordinateFixer() - Constructor for class chemaxon.fixers.RemoveZCoordinateFixer

RENDERING - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "rendering".

reparentSgroups(Molecule) - Method in class chemaxon.struc.Molecule

Change parents of all S-groups in this molecule.

RepeatingUnitSgroup - Class in chemaxon.struc.sgroup

Source-based and structure-based representation of repeating unit groups (polymers and repeating units with repetition ranges).

RepeatingUnitSgroup(Molecule, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup

Constructs an SRU S-group.

RepeatingUnitSgroup(Molecule, String, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup

Constructs an SRU S-group with connectivity.

RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup

Copy constructor.

RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup

Copy constructor.

replace(int, int, String) - Method in class chemaxon.struc.graphics.MTextDocument

Replaces a substring in the document.

replace(MolAtom, MolAtom, Molecule) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Replaces an atom to the replace atom in the target molecule

replace(MProp, MProp) - Method in class chemaxon.struc.MPropertyContainer

Replaces or removes a property.

replace(MProp, MProp) - Method in class chemaxon.struc.prop.MCollectionProp

Replaces or removes a property.

replace(MProp, MProp) - Method in class chemaxon.struc.prop.MHashProp

Replaces or removes a property.

replace(MProp, MProp) - Method in class chemaxon.struc.prop.MListProp

Replaces or removes a property.

REPLACE_COORDINATE_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory

Replace coordinate bonds to multicenter atoms with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).

replaceAtom(int, MolAtom) - Method in class chemaxon.struc.Molecule

Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.

replaceAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.

replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Replaces a contained atom with another one.

replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Replaces a contained atom with another one.

replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MElectronContainer

replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MPolyline

Replaces a contained atom with another one.

replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.MObject

Replaces a contained atom with another one.

replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.Sgroup

Replace an existing atom by a new one in this S-group and its parent (recursively).

replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MulticenterSgroup

replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Replace an existing atom by a new one.

replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.Sgroup

Replace an existing atom by a new one in this S-group and its parent (recursively).

replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Replace an existing atom by a new one.

ReplaceAtomsAction - Class in chemaxon.standardizer.actions

Replace atoms standardizer action

ReplaceAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ReplaceAtomsAction

Initializes a replace atom standardizer action

replaceAtomsWithNewRgroup(SelectionMolecule, int) - Method in class chemaxon.struc.RgMolecule

Replaces selected atoms with a new R-group.

replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.

replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.

replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RxnMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.

replaceMulticenterAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 2014.08.25.0, use MulticenterSgroup.setCentralAtom(chemaxon.struc.MolAtom) instead

replaceSgroup(Sgroup, Sgroup) - Method in class chemaxon.struc.Molecule

Replaces an S-group with a new sgroup in the molecule.

reportFormat - Variable in class chemaxon.checkers.StructureCheckOptions

The path of the report file

reportPath - Variable in class chemaxon.checkers.StructureCheckOptions

The path of the report file

reportPattern - Variable in class chemaxon.checkers.StructureCheckOptions

The path of the report file

reportProperty - Variable in class chemaxon.checkers.StructureCheckOptions

The name of the report property, in the output structure file(s)

REPUNIT - Static variable in class chemaxon.sss.search.MarkushFeature

Deprecated.

Expansion type: repeating unit.

requireBinaryVector() - Method in class chemaxon.descriptors.ECFP

Checks the binary vector storage and generates it from the identifier list if necessary.

reset() - Method in class chemaxon.marvin.io.PositionedInputStream

Repositions this stream to the position at the time the mark method was last called on this input stream.

reset() - Method in class chemaxon.struc.PageSettings

Resets the settings of multipage molecular documents.

resetBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow

resetCtab() - Method in class chemaxon.struc.MoleculeGraph

An operation performed that changed the connection table and the graph invariants.

resetFilePointer() - Method in class chemaxon.marvin.io.PositionedInputStream

Resets file pointer to zero.

resetGrinvInParents() - Method in class chemaxon.struc.MoleculeGraph

Graph invariants must be recalculated for this graph and all parent graphs.

resetMap() - Method in class chemaxon.marvin.alignment.MinMaxDistance

residueSymbolOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the name of a residue.

residueSymbolOf(int) - Static method in class chemaxon.struc.Molecule

Gets the name of a residue.

residueTypeOf(String) - Static method in class chemaxon.struc.MolAtom

Gets the residue identifier for a residue name.

residueTypeOf(String) - Static method in class chemaxon.struc.Molecule

Gets the residue identifier for a residue name.

RESONANCE - Static variable in class chemaxon.struc.RxnMolecule

Resonance arrow, the same as the two-headed single reaction arrow.

RESONANCE_ALL - Enum constant in enum class chemaxon.calculator.CalculatorTag

RESONANCE_CANONICAL - Enum constant in enum class chemaxon.calculator.CalculatorTag

RESONANCE_MAJORCONTRIBUTORS - Enum constant in enum class chemaxon.calculator.CalculatorTag

ResonancePlugin - Class in chemaxon.marvin.calculations

Plugin class for finding resonant structures.

ResonancePlugin() - Constructor for class chemaxon.marvin.calculations.ResonancePlugin

Constructor.

RESSEQ_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum residue sequence number is currently 8191.

restoreCache(int) - Method in class chemaxon.struc.MoleculeGraph

Restores caches like connection table, bond table, etc.

restoreCoords(MoleculeGraph, double[]) - Static method in class chemaxon.marvin.util.CleanUtil

Restores atomic coordinates.

restoreDefaultParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Restores default parameters to parameter panel.

restoreDefaultParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Restores default parameters to parameter panel.

restoreExplicitHydrogens(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

When the input molecule is set, the explicit H-s may be stored CalculatorPlugin.setMolecule(Molecule, boolean, boolean, boolean) The parameter should be topologically equal to the input molecule for a successfull restore.

RESTYPE_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum residue type is currently 63.

resultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Deprecated.

use StandardizerRunner.closeableResultIterator(Iterator, StandardizerConfiguration, int, String) instead

resultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String, boolean) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Deprecated.

use StandardizerRunner.closeableResultIterator(Iterator, StandardizerConfiguration, int, String, boolean) instead

resultMolList - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The result molecules to be displayed.

resultValues - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The result values to be displayed in MarvinSpace.

ResultView - Class in chemaxon.marvin.plugin.gui

Complex result panel.

ResultView(Dialog, String, MolPanel) - Constructor for class chemaxon.marvin.plugin.gui.ResultView

Constructor.

ResultView(Frame, String, MolPanel) - Constructor for class chemaxon.marvin.plugin.gui.ResultView

Constructor.

ResultView(String) - Constructor for class chemaxon.marvin.plugin.gui.ResultView

Constructor.

ResultView(String, MolPanel) - Constructor for class chemaxon.marvin.plugin.gui.ResultView

Constructor.

RETROSYNTHETIC - Static variable in class chemaxon.struc.RxnMolecule

Retrosynthetic arrow, the same as the regular double reaction arrow.

returnOptionString(boolean) - Method in class chemaxon.sss.search.SearchOptions

ReusablePluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent

Work unit performing plugin calculation.

ReusablePluginWorkUnit() - Constructor for class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit

Constructor.

reuseAtom(int, int) - Method in class chemaxon.struc.Molecule

Reuse an atom or create a new one.

reuseAtom(int, int) - Method in class chemaxon.struc.RgMolecule

Reuse an atom or create a new one.

reuseFont(String, int, double) - Method in class chemaxon.struc.graphics.MTextDocument

revalidateCoordDependentProps() - Method in class chemaxon.struc.MoleculeGraph

Revalidate coordinate dependent properties.

revalidateCoordDependentProps() - Method in class chemaxon.struc.RgMolecule

Revalidate coordinate dependent properties.

revalidateCoordDependentProps() - Method in class chemaxon.struc.RxnMolecule

Revalidate coordinate dependent properties.

reverse() - Method in class chemaxon.struc.graphics.MPolyline

Reverses the order of points.

REVERSIBLE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.2, use Expandable.LEAVE_COORDS_UNCHANGED instead

Rf - Static variable in class chemaxon.core.ChemConst

RFGenerator - Class in chemaxon.descriptors

Generator class for the ReactionFingerprint descriptor.

RFGenerator() - Constructor for class chemaxon.descriptors.RFGenerator

RFParameters - Class in chemaxon.descriptors

Manages reaction fingerprint parameters.

RFParameters() - Constructor for class chemaxon.descriptors.RFParameters

Creates an empty object.

RFParameters(File) - Constructor for class chemaxon.descriptors.RFParameters

Creates a new object based on a given configuration file.

RFParameters(String) - Constructor for class chemaxon.descriptors.RFParameters

Creates a new object based on a given configuration string.

Rg - Static variable in class chemaxon.core.ChemConst

RG_ID_MASK - Static variable in class chemaxon.struc.RgMolecule

R-group id mask in R-logic.

RG_ID2_FLAG - Static variable in class chemaxon.struc.RgMolecule

Other R-group ID's presence flag in R-logic.

RG_ID2_MASK - Static variable in class chemaxon.struc.RgMolecule

Mask of the other R-group's id in R-logic.

RG_ID2_OFF - Static variable in class chemaxon.struc.RgMolecule

Offset of the other R-group's id in R-logic.

RG_RESTH - Static variable in class chemaxon.struc.RgMolecule

The RestH flag in R-logic.

RgComponentIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.RgComponentIterator

Constructs an iterator to process the rgroup definition components, if the specified molecule in the factory is an RgMolecule, the iterator is empty otherwise.

RgDecompResults - Class in chemaxon.sss.search

Convenience class for generating, storing and returning results of a search in different forms: as r-group decomposition or Markush molecule.

RgDecompResults(Molecule, int, Molecule[][], RgMolecule, int[]) - Constructor for class chemaxon.sss.search.RgDecompResults

This constructor is used only for storing results.

RgDecompResults(Molecule, int, Molecule[][], RgMolecule, int[], int[]) - Constructor for class chemaxon.sss.search.RgDecompResults

This constructor is used only for storing results.

RgDecompResults(Molecule, Molecule[], SearchOptions, int) - Constructor for class chemaxon.sss.search.RgDecompResults

Constructor used for generating results.

RgDecompResults(Molecule, Molecule[], SearchOptions, int, int[]) - Constructor for class chemaxon.sss.search.RgDecompResults

Constructor used for generating results.

RgMolecule - Class in chemaxon.struc

A molecule or reaction containing R-groups.

RgMolecule() - Constructor for class chemaxon.struc.RgMolecule

Creates a 2 dimensional RgMolecule.

RgMolecule(Molecule) - Constructor for class chemaxon.struc.RgMolecule

Creates an RgMolecule with the given root structure.

RGROUP - Static variable in class chemaxon.sss.search.MarkushFeature

Deprecated.

Expansion type: R-grgoup.

RGROUP - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the Rgroup query "atom".

RGROUP_ATTACHMENT - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of an ordered R-group attachment point.

RGROUP_ATTACHMENT_ERROR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing invalid attachments in R-group definitions.

RGROUP_BRIDGE_RATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing invalid R-atoms corresponding to R-group bridge definitions.

RGROUP_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum R-group number (32767).

RGROUP_MAX - Static variable in interface chemaxon.struc.Smolecule

Maximum R-group index (32767).

RgroupAttachmentErrorChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting invalid attachments in R-group definitions.

RgroupAttachmentErrorChecker() - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker

Creates a new RgroupAttachmentErrorChecker instance.

RgroupAttachmentErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker

Parameterized constructor.

RgroupAttachmentFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer that can fix attachment errors in R-group definition members.

RgroupAttachmentFixer() - Constructor for class chemaxon.fixers.RgroupAttachmentFixer

RgroupBridgeId - Class in chemaxon.struc

Identifies an R-group bridge position by storing a pair of R-group IDs.

RgroupBridgeId(int, int) - Constructor for class chemaxon.struc.RgroupBridgeId

Constructor.

RgroupBridgeRatomChecker - Class in chemaxon.checkers

Checker for R-atoms that form R-group bridges: One R-group can be involved in at most one bridge. Two R-atoms that represent a bridge must be in the scaffold or in the same R-group definition member. The R-group number that represents an R-group bridge cannot represent an ordinary R-group.

RgroupBridgeRatomChecker() - Constructor for class chemaxon.checkers.RgroupBridgeRatomChecker

RgroupCheckerResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult providing information of R-group issues.

RgroupCheckerResult(StructureChecker, StructureCheckerErrorType, List<MolAtom>, List<MolBond>, List<Integer>, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.RgroupCheckerResult

Constructor which initialize all the properties.

RGroupDecomposition - Class in chemaxon.sss.search

R-group decomposition.

RGroupDecomposition() - Constructor for class chemaxon.sss.search.RGroupDecomposition

Constructor.

RGROUPED - Static variable in class chemaxon.struc.RxnMolecule

Add R-groups to component structure.

rgroupIdOf(MolAtom) - Method in class chemaxon.struc.RgMolecule

Finds the ID of the R-group (the number in R#) that contains the specified atom.

rgroupIndexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule

Finds the index of the R-group (the number in R#) that contains the specified atom.

Rh - Static variable in class chemaxon.core.ChemConst

Ring - Class in chemaxon.calculations

The ring class provides information of the ring types in a molecule.

Ring() - Constructor for class chemaxon.calculations.Ring

ringAtomCount() - Method in class chemaxon.calculations.Ring

Calculates the number of ring atoms in the molecule.

ringAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringAtomCount()

ringBondCount() - Method in class chemaxon.calculations.Ring

Calculates the number of ring bonds in the molecule.

ringBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringBondCount()

ringCount() - Method in class chemaxon.calculations.Ring

Calculates the number of rings (SSSR smallest set of smallest rings) in the molecule.

ringCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringCount()

ringCount(int) - Method in class chemaxon.calculations.Ring

Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.

ringCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringCount(int)

ringCountOfAtom(int) - Method in class chemaxon.calculations.Ring

Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.

ringCountOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringCountOfAtom(int)

ringHandlingMode(RingHandlingMode) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

Sets how rings should be handled during the search.

RingHandlingMode - Enum Class in com.chemaxon.search.mcs

Enum type for the ring handling modes of MaxCommonSubstructure (MCS) algorithms.

rings() - Method in class chemaxon.calculations.Ring

Identifies the rings in the molecule.

rings() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.rings()

rings(int) - Method in class chemaxon.calculations.Ring

Identifies rings in the molecule having a given size.

rings(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.rings(int)

RingStrainErrorChecker - Class in chemaxon.checkers

RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.

RingStrainErrorChecker() - Constructor for class chemaxon.checkers.RingStrainErrorChecker

Default constructor

RingStrainErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RingStrainErrorChecker

Parameterized constructor.
If params contains "transDoubleBond"/"cumulatedDoubleBond"/"tripelBond" key with value "true" then trans double bonds/cummulated double bonds/triple bonds will be checked.

ringSystemCount() - Method in class chemaxon.calculations.Ring

Calculates the number of ring systems.

ringSystemCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringSystemCount()

ringSystemCount(int) - Method in class chemaxon.calculations.Ring

Identifies ring systems having a given size (number of rings) in the molecule.

ringSystemCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringSystemCount(int)

ringSystems() - Method in class chemaxon.calculations.Ring

Identifies the ring systems in the molecule.

ringSystems() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringSystems()

ringSystems(int) - Method in class chemaxon.calculations.Ring

Indentifies the ring systems in the molecule having a given size (number of rings).

ringSystems(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.ringSystems(int)

RLOGIC_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "RLogicVisible" or "RLogic".

RMCLEANUP_ALL - Static variable in class chemaxon.struc.MoleculeGraph

Perform all clean-up methods when removing an atom or a bond.

RMCLEANUP_EDGES - Static variable in class chemaxon.struc.MoleculeGraph

When removing an atom or a bond, also remove the bond(s) from the atom object(s).

RMCLEANUP_FIXCOMPONENT - Static variable in class chemaxon.struc.MoleculeGraph

Remove called from RxnMolecule.fixComponent.

RMCLEANUP_FROMSGROUPS - Static variable in class chemaxon.struc.Molecule

Remove atoms from S-groups.

RMCLEANUP_MOBJECT - Static variable in class chemaxon.struc.MoleculeGraph

Remove graphics objects containing the removed atom.

RMCLEANUP_NONE - Static variable in class chemaxon.struc.MoleculeGraph

Do not perform any clean-up methods when removing an atom or a bond.

RMCLEANUP_PARENTDOC - Static variable in class chemaxon.struc.MoleculeGraph

Remove atom from parent document.

RMCLEANUP_SGROUPATOMS - Static variable in class chemaxon.struc.Molecule

Remove S-groups of removed superatoms.

RMCLEANUP_STEREO - Static variable in class chemaxon.struc.MoleculeGraph

When removing a H atom, keep stereo information unchanged.

rmsd() - Method in class chemaxon.marvin.alignment.AlignRigidEasy

calculates the rmsd value

rmsd() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult

Root mean square deviation from the reference molecule.

RMSG_DEFAULT - Static variable in class chemaxon.struc.Molecule

Remove S-group's children and remove S-group from its parent.

RMSG_KEEP_CHILDREN - Static variable in class chemaxon.struc.Molecule

Do not remove S-group's children.

RMSG_KEEP_MULTICENTER - Static variable in class chemaxon.struc.Molecule

Do not remove central atom of multicenter S-groups.

RMSG_KEEP_PARENT - Static variable in class chemaxon.struc.Molecule

Do not remove S-group from its parent.

Rn - Static variable in class chemaxon.core.ChemConst

RNA - Static variable in class chemaxon.formats.MFileFormat

RNA sequence.

rotatableBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of rotatable bonds in the molecule.

RotatableBondDetector - Class in chemaxon.marvin.alignment

RotatableBondDetector(Molecule, boolean) - Constructor for class chemaxon.marvin.alignment.RotatableBondDetector

rotate(DPoint3, double, DPoint3) - Static method in class chemaxon.struc.graphics.MPolyline

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.1, replaced by CTransform3D.setRotation(double, double, double, double) and CTransform3D.setRotationCenter(DPoint3).

rotateBy(double, int, int, int, int) - Method in class chemaxon.marvin.alignment.DihedralRotator

Rotates the selected dihedral by the defined angle

rotatedAndReferenceFused() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult

Fuse the rotated and the reference molecule.

rotatedMolecule() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult

The rotated molecule.

rotateTo(double, int, int, int, int) - Method in class chemaxon.marvin.alignment.DihedralRotator

Sets the dihedral defined by the atoms a1-a4 to the angle

roundTo(int) - Method in class chemaxon.struc.DPoint3

Rounds the represented value to the given decimal precision.

ROWS - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "rows".

Ru - Static variable in class chemaxon.core.ChemConst

run() - Method in class chemaxon.marvin.calculations.AlignmentPlugin

run() - Method in class chemaxon.marvin.calculations.ChargePlugin

Runs the charge calculation.

run() - Method in class chemaxon.marvin.calculations.ConformerPlugin

Runs the conformer calculation.

run() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Runs the tool.

run() - Method in class chemaxon.marvin.calculations.GeometryPlugin

Runs the tool.

run() - Method in class chemaxon.marvin.calculations.HBDAPlugin

Runs the charge calculation.

run() - Method in interface chemaxon.marvin.calculations.HlbPlugin

Run the calculation.

run() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Runs the Huckel analysis calculation.

run() - Method in class chemaxon.marvin.calculations.IonChargePlugin

Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH.

run() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Runs the isoelectric point and charge distribution calculations.

run() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

run() - Method in class chemaxon.marvin.calculations.logDPlugin

Runs the logD calculation.

run() - Method in class chemaxon.marvin.calculations.logPPlugin

Runs the logP calculation.

run() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Stores the input molecule with ungrouped sgroups.

run() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Creates enumerated structures.

run() - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Runs the tool.

run() - Method in class chemaxon.marvin.calculations.MSAPlugin

Runs the surface area calculation.

run() - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Runs the orbital electornegativity calculation.

run() - Method in class chemaxon.marvin.calculations.pKaPlugin

Runs the macro pKa calculation.

run() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Runs the charge calculation.

run() - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Runs the refractivity calculation.

run() - Method in class chemaxon.marvin.calculations.ResonancePlugin

Calculates the resonant structures.

run() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Runs the plugin.

run() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Run calculation

run() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Calculates the tautomers.

run() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Runs the tool.

run() - Method in class chemaxon.marvin.calculations.TPSAPlugin

Runs the surface area calculation.

run() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Runs the tool.

run() - Method in class chemaxon.sss.search.RgDecompResults

Generates the results if no valid results are available (see RgDecompResults.hasResults())

run(Stack<Object>) - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

Run the function on the stack.

runScript(String) - Method in class chemaxon.jep.Evaluator

Runs a script, variables will be added to the base variable table and can be referenced by chemical expressions.

RXN - Static variable in class chemaxon.formats.MFileFormat

MDL Rxnfiles.

RXN_V3_OUT - Static variable in class chemaxon.formats.MFileFormat

MDL Extended Rxnfiles.

RxnComponentIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator

Constructs an iterator to process the components (reactant, product and agent components), if the specified molecule in the factory is an RxnMolecule, the iterator is empty otherwise.

RxnMolecule - Class in chemaxon.struc

Reaction.

RxnMolecule() - Constructor for class chemaxon.struc.RxnMolecule

Create a reaction.

RXNSTEREO_INVERSION - Static variable in class chemaxon.struc.MolAtom

The stereo configuration of the atom is inverted during the reaction.

RXNSTEREO_NONE - Static variable in class chemaxon.struc.MolAtom

The stereo configuration of the atom is not considered during the reaction.

RXNSTEREO_RETENTION - Static variable in class chemaxon.struc.MolAtom

The stereo configuration of the atom is retained during the reaction.

S

s - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

S - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

S - Static variable in class chemaxon.core.ChemConst

SAFE - Enum constant in enum class com.chemaxon.calculations.admet.HergClass

SALT_ID_PROPERTY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction

Property key for salt ID

SALT_LIST_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction

Property key for salt list modification

SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme

save(String) - Method in class chemaxon.marvin.common.UserSettings

Save the persistent properties to the config file set by the constructor.

save(String, String) - Method in class chemaxon.marvin.common.UserSettings

Save the persistent properties to the file given as the first parameter.

SAVE_PROPERTIES - Static variable in class chemaxon.marvin.common.ParameterConstants

saveCache(int) - Method in class chemaxon.struc.MoleculeGraph

Saves caches like connection table, bond table, etc.

saveCoords(MoleculeGraph, double[]) - Static method in class chemaxon.marvin.util.CleanUtil

Saves atomic coordinates.

SAVED - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult

saveParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Saves parameters from parameter panel.

saveParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Saves parameters from parameter panel.

saveParameterSettings() - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

saveParameterSettings() - Method in class com.chemaxon.calculations.gui.PluginFactory

Saves plugin parameter settings to file $HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or $HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).

Sb - Static variable in class chemaxon.core.ChemConst

SBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

Sc - Static variable in class chemaxon.core.ChemConst

scalar(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3

Calculates the scalar product of the two vectors

SCALAR - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation

ScalarDescriptor - Class in chemaxon.descriptors

Base class for all scalar descriptors.

ScalarDescriptor() - Constructor for class chemaxon.descriptors.ScalarDescriptor

Creates a new, empty instance of ScalarDescriptor.

ScalarDescriptor(ScalarDescriptor) - Constructor for class chemaxon.descriptors.ScalarDescriptor

Copy constructor.

ScalarDescriptor(SDParameters) - Constructor for class chemaxon.descriptors.ScalarDescriptor

Creates a new instance of ScalarDescriptor according to the parameters given.

ScalarDescriptor(String) - Constructor for class chemaxon.descriptors.ScalarDescriptor

Creates a new instance of ScalarDescriptor according to the parameters given.

scale(double) - Method in class chemaxon.struc.DPoint3

Scales the vector with the given factor.

SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "scale".

scaledAsymmetricTanimoto(float[], float[], float[], float, float) - Static method in class chemaxon.descriptors.Metrics

Calculates the scaled asymmetric Tanimoto dissimilarity for floating point values.

scaledAsymmetricTanimoto(int[], int[], float[], float, float) - Static method in class chemaxon.descriptors.Metrics

Calculates the scaled asymmetric Tanimoto dissimilarity for floating point values.

scaledTanimoto(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the scaled Tanimoto dissimilarity for floating point values.

scaledTanimoto(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the scaled Tanimoto dissimilarity for floating point values.

scaleFactors - Variable in class chemaxon.descriptors.MDParameters

scale factor of scalable parametrized metrics

scaleShift(double) - Method in class chemaxon.calculations.nmr.Shift

Scales the stored chemical shift and shift standard deviation values.

scanFinished(BondInfo) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener

Called when dihedral scan finished.

scheduler - Variable in class chemaxon.marvin.view.swing.TableSupport

Record access task scheduler.

SCN_EITHER_UNKNOWN - Static variable in class chemaxon.struc.Sgroup

Either unknown S-group connectivity.

SCN_HEAD_TO_HEAD - Static variable in class chemaxon.struc.Sgroup

Head-to-head S-group connectivity.

SCN_HEAD_TO_TAIL - Static variable in class chemaxon.struc.Sgroup

Head-to-tail S-group connectivity.

score() - Method in class chemaxon.calculations.bbb.BBB.Property

score() - Method in class chemaxon.calculations.bbb.BBB

Calculates the BBB score from properties.

score() - Method in class chemaxon.calculations.cnsmpo.CnsMpo.Property

score() - Method in class chemaxon.calculations.cnsmpo.CnsMpo

Calculates the CNS MPO score from properties.

screeningConfigurationNode - Variable in class chemaxon.descriptors.MDParameters

SCRIPT - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "script".

SDF - Static variable in class chemaxon.formats.MdlCompressor

SDF - Static variable in class chemaxon.formats.MFileFormat

MDL SDfiles.

SDParameters - Class in chemaxon.descriptors

Manages ScalarDescriptor parameters.

SDParameters() - Constructor for class chemaxon.descriptors.SDParameters

Creates an empty object.

SDParameters(File) - Constructor for class chemaxon.descriptors.SDParameters

Creates a new object from the given configuration file.

SDParameters(String) - Constructor for class chemaxon.descriptors.SDParameters

Creates a new object from the given configuration string.

Se - Static variable in class chemaxon.core.ChemConst

Search - Class in chemaxon.sss.search

Abstract base class of all structural search classes.

Search() - Constructor for class chemaxon.sss.search.Search

SEARCH_MODE_NAMES - Static variable in interface chemaxon.sss.SearchConstants

Deprecated, for removal: This API element is subject to removal in a future version.

As of JChem 5.12, replaced by SearchConstants.SEARCH_TYPE_NAMES.

SEARCH_OPTIONS_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction

Key of search options for parsing and property change

SEARCH_TYPE_NAMES - Static variable in interface chemaxon.sss.SearchConstants

The names of the search types.

SearchConstants - Interface in chemaxon.sss

Constants for structure searching

SearchException - Exception in chemaxon.sss.search

Exception denoting errors during the search process.

SearchException() - Constructor for exception chemaxon.sss.search.SearchException

Constructs a new exception with null as its detail message.

SearchException(String) - Constructor for exception chemaxon.sss.search.SearchException

Constructs a new exception with the specified detail message.

SearchException(String, Throwable) - Constructor for exception chemaxon.sss.search.SearchException

Constructs a new exception with the specified detail message and cause.

SearchException(Throwable) - Constructor for exception chemaxon.sss.search.SearchException

Constructs a new exception with the specified cause and a detail message of (cause==null ? null : cause.toString()) (which typically contains the class and detail message of cause).

SearchHit - Class in chemaxon.sss.search

Search hit object.

SearchHit(int[]) - Constructor for class chemaxon.sss.search.SearchHit

Constructor: creates a hit object from a single (1 dimensional) hit mapping array.

SearchHit(int[][]) - Constructor for class chemaxon.sss.search.SearchHit

Constructor: creates a hit object from a group (2 dimensional) hit mapping array.

searchMode - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Search mode.

SearchMode - Enum Class in com.chemaxon.search.mcs

Enum type for search modes of MaxCommonSubstructure (MCS) algorithms.

searchOptions - Variable in class chemaxon.sss.search.MolComparator

searchOptions - Variable in class chemaxon.sss.search.Search

Object to store all search parameters.

SearchOptions - Class in chemaxon.sss.search

Class to encapsulate common search parameters.

SearchOptions(int) - Constructor for class chemaxon.sss.search.SearchOptions

Creates a SearchOptions object while setting different search options according to a predefined search type.

searchOpts - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Search options.

secondaryAtomIndexes() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Deprecated, for removal: This API element is subject to removal in a future version.

secondaryBonds - Variable in class chemaxon.util.iterator.IteratorFactory.BondIterator

Secondary bonds that replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).

secondaryBonds - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Secondary bonds that replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).

Section(int, String) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section

Constructs a text section.

Section(int, String, MTextAttributes) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section

Constructs a text section.

Section(MTextDocument.Section) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section

Copy constructor.

SECTION - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the section of the document where the structure was found.

seek(long, int) - Method in class chemaxon.marvin.io.PositionedInputStream

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

seek(long, int, int) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

seek(long, int, int) - Method in class chemaxon.marvin.io.MRecordImporter

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

seek(long, int, int) - Method in interface chemaxon.marvin.io.MRecordReader

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

seekForward(int, MProgressMonitor, int, Runnable) - Method in class chemaxon.marvin.io.MDocSource

Seeks in forward direction.

seekRecord(int, MProgressMonitor) - Method in class chemaxon.formats.MolImporter

Seek the specified record.

seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.io.ArrayMDocSource

Seeks the specified record.

seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.io.MDocSource

Seeks the specified record.

seekRecord(int, MProgressMonitor) - Method in class chemaxon.marvin.plugin.PluginMDocSource

seekRecordAtFraction(double, int, int, int, MProgressMonitor) - Method in class chemaxon.marvin.io.MDocSource

Seeks an approximate file position.

seekVisitedRecord(int) - Method in class chemaxon.formats.MolImporter

Seeks an already visited position in case of rewindable input.

seekVisitedRecord(int) - Method in class chemaxon.marvin.io.ArrayMDocSource

Seeks an already visited position in case of rewindable input.

seekVisitedRecord(int) - Method in class chemaxon.marvin.io.MDocSource

Seeks an already visited position in case of rewindable input.

seekVisitedRecord(int) - Method in class chemaxon.marvin.plugin.PluginMDocSource

SELECTABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "selectable".

selectAllConnectedObjects(boolean) - Method in class chemaxon.struc.MDocument

Selects or unselects all objects in this document and objects that belong to the chemical structure of this document.

selectAllObjects(boolean) - Method in class chemaxon.struc.MDocument

Selects or unselects all objects.

selectAllObjects(boolean) - Method in class chemaxon.struc.Molecule

selectAllObjects(boolean) - Method in class chemaxon.struc.RgMolecule

selectAllObjects(boolean) - Method in class chemaxon.struc.RxnMolecule

selectAllObjects(boolean) - Method in class chemaxon.struc.Sgroup

Sets the selection state of the MObject-s that belong to this Sgroup.

SELECTED_INDEX - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "selectedIndex".

SELECTION - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "selection".

SelectionMolecule - Class in chemaxon.struc

A selection object which can contain atoms and bonds without real parent relationship (the real parent of atoms and bonds is another MoleculeGraph ancestor).

SelectionMolecule() - Constructor for class chemaxon.struc.SelectionMolecule

self() - Method in class chemaxon.formats.GeneralExportOptions.Builder

Separated - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type

Indicates, that the structure checker puts valid or fixed structures to the output file, the others to the discarded file.

separator - Variable in class com.chemaxon.calculations.cli.CalculatorPluginOutput

The separator string separating the results for different result types.

SEPARATOR - Static variable in enum class chemaxon.descriptors.MetricsType

SEPARATOR - Static variable in class chemaxon.descriptors.SimilarityCalculatorFactory

This character is used to separate fields of the parameter string.

SEPARATOR - Static variable in class chemaxon.sss.search.RGroupDecomposition

Separator in atom color code property string representation.

SEPARATOR - Static variable in class com.chemaxon.calculations.gui.PluginFactory

Menuitem separator in Tools menu: if present then separator will be added to the Tools menu after the plugin menuitem.

seqCis - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

seqTrans - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

SERVICE - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Property key for service name as String

ServiceArgument<T> - Class in chemaxon.marvin.services

Describes an argument passed to services

ServiceArgument(Class<T>, T) - Constructor for class chemaxon.marvin.services.ServiceArgument

Constructs a service argument with specified type and value

ServiceArgument(Class<T>, T, boolean) - Constructor for class chemaxon.marvin.services.ServiceArgument

Constructs a service argument with specified type and value

ServiceDescriptor - Class in chemaxon.marvin.services

Descriptor class for marvin services

ServiceDescriptor() - Constructor for class chemaxon.marvin.services.ServiceDescriptor

Subclasses must have public argless constructor.

ServiceDescriptorEditor<T extends ServiceDescriptor> - Interface in chemaxon.marvin.services

Provides editor suport for ServiceDescriptor

ServiceDescriptorEditorProvider - Interface in chemaxon.marvin.services

Provides ServiceDescriptorEditor instances based on ServiceDescriptor classes.

ServiceDescriptorReader - Interface in chemaxon.marvin.services

Reader for ServiceDescriptors

ServiceDescriptorWriter - Interface in chemaxon.marvin.services

Writer for ServiceDescriptors

ServiceDialogProvider - Interface in chemaxon.marvin.services

Provides Dialog instances to provide argument editor and result view for ServiceDescriptor

ServiceException - Exception in chemaxon.marvin.services

Exception for failure indication for services.

ServiceException(String) - Constructor for exception chemaxon.marvin.services.ServiceException

Creates a ServiceException with specified message

ServiceException(String, Throwable) - Constructor for exception chemaxon.marvin.services.ServiceException

Creates a ServiceException with specified message and cause

ServiceException(Throwable) - Constructor for exception chemaxon.marvin.services.ServiceException

Creates a ServiceException with specified cause

serviceHandler - Variable in class chemaxon.marvin.services.ServiceDescriptor

ServiceHandler<DT extends ServiceDescriptor> - Class in chemaxon.marvin.services

Manages service calls.
ServiceHandler keeps track of the previous call and if it is not yet finished cancels it.

ServiceHandler() - Constructor for class chemaxon.marvin.services.ServiceHandler

set(float) - Method in class chemaxon.descriptors.ScalarDescriptor

Set the value of the descriptor.

set(int, float) - Method in class chemaxon.descriptors.CustomDescriptor

Sets the value of one cell of the descriptor.

set(int, float[]) - Method in class chemaxon.descriptors.CustomDescriptor

Sets values of the descriptor.

set(int, int) - Method in class chemaxon.descriptors.CustomDescriptor

Sets the value of one cell of the descriptor.

set(int, int[]) - Method in class chemaxon.descriptors.CustomDescriptor

Sets values of the descriptor.

set(int, GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Sets the group definition at specified index, and returns the previous value.

set(int, MProp) - Method in class chemaxon.struc.prop.MListProp

Sets an element.

set(CTransform3D) - Method in class chemaxon.struc.CTransform3D

Copy.

set(DPoint3) - Method in class chemaxon.struc.DPoint3

Set coordinates.

set(MolAtom) - Method in class chemaxon.struc.MolAtom

Set all atom properties except the coordinates.

set(MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom

Set properties of this S-group superatom.

set(String, MProp) - Method in class chemaxon.struc.MPropertyContainer

Sets a property object.

set(String, MProp, int) - Method in class chemaxon.struc.MPropertyContainer

Sets a property object.

SET_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "setColoringEnabled".

setAbbreviation(int, String) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Sets the abbreviation of the group at the provided index

setAbbreviation(String) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Sets the abbreviation of the group.

setAbsoluteLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Set 'Absolute' label visibility.

setAbsoluteLabelVisible(String) - Method in class chemaxon.marvin.common.UserSettings

Show or hide Abolute labels

setAbsolutePlacement(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets whether the placement of this attached data is absolute or relative to the objects it is attached.

SetAbsoluteStereoAction - Class in chemaxon.standardizer.actions

Set absolute stereo standardizer action

SetAbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.SetAbsoluteStereoAction

Initializes a set absolute stereo action

setAbsoluteXY(double, double) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.

setAbsoluteXY(DPoint3) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.

setAbsStereo(boolean) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Sets the absoluteLegacy value of the action

setAbsStereo(boolean) - Method in class chemaxon.struc.MoleculeGraph

Sets the absolute stereoconfiguration flag.

setAbsStereo(boolean) - Method in class chemaxon.struc.RgMolecule

Sets the absolute stereoconfiguration flag for the root structure and the R-groups.

setAbsStereo(boolean) - Method in class chemaxon.struc.RxnMolecule

Sets the absolute stereoconfiguration flag for all the structures.

setAccuracyMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

setAcidicpKaUpperLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the maximum acidic pKa (default: 20).

setAction(StandardizerAction) - Method in class chemaxon.standardizer.Changes

Sets the base StandardizerAction of the changes

setActionB(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets the action string (URL or JavaScript expression) of a button in a GridBagView table.

setActionC(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets one of the two action strings (JavaScript expressions) of a checkbox in a GridBagView table.

setActionCommand(String) - Method in class chemaxon.marvin.swing.MAction

Sets the action command string.

setActionMap(ActionMap) - Method in class chemaxon.struc.graphics.MTextBox

Sets the ActionMap to map.

setActionsEnabled(boolean) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Enables / disables action buttons.

setActionState(ActionEvent) - Method in class chemaxon.marvin.swing.MAction

Sets the action state.

setActionStringTokens(String[]) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the action string token of the checker

setActionStringTokens(String[]) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the action string token of the fixer

setActionStringTokens(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the action string tokens of the action

setActive(boolean) - Method in class chemaxon.standardizer.AbstractStandardizerAction

setActive(boolean) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

setActive(boolean) - Method in interface chemaxon.standardizer.StandardizerAction

Sets whether the action is active, and can be used

setActiveGroups(String[]) - Method in class chemaxon.standardizer.Standardizer

Deprecated.

use ConfigurationUtility.filterGroups(StandardizerConfiguration, String[]) on the configuration returned by the method Standardizer.getConfiguration()

setAdvancedSave(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets wether the user prefers advanced svae or not.

setAlias(String) - Method in class chemaxon.marvin.services.ServiceArgument

Sets the argument alias.

setAlias(String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Sets the service alias.

setAliasstr(String) - Method in class chemaxon.struc.MolAtom

Sets the alias string or pseudo atom type string for pseudo atoms.

setAlign(boolean) - Method in class chemaxon.sss.search.RGroupDecomposition

Sets alignment.

setAlignScaffold(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets the scaffold aligning mode.

setAllowExperimentalFeatures(boolean) - Method in class chemaxon.marvin.common.UserSettings

setAllowTraditionalNitrogen(boolean) - Method in class chemaxon.checkers.ValenceErrorChecker

Sets if the checker should allow traditional N representation

setAllowUndeclared(boolean) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Undeclared variables will always be allowed in the future, changing this will no longer be supported.

setAllowValenceError(boolean) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Sets replace should be applied even in case of invalid valence in the result

setAminoAcid(boolean) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Sets whether the group represents an amino-acid

setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets wether the user uses peptide bridge coloring or not.

setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets peptide bridge coloring enabled.

setAnalysisBoxTerms(String) - Method in class chemaxon.marvin.common.UserSettings

setAnalysisBoxWarning() - Method in class chemaxon.marvin.common.UserSettings

setAnimated(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Starts or stops animation in each cells of the table or in the simple viewer.

setAnimated(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets animation of a cell of the table.

setAnimDelay(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the repeat delay for animations.

setAnimFPS(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the frames per second for animations.

setAnimSync(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets the animation synchronization.

setAnnotatedOutput(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Set the destination file where an annotated version of the source document should be written.

setAnnotatedOutput(OutputStream) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Set the destination output stream where an annotated version of the source document should be written.

setAnnotatedOutputDirectory(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Set the directory where the annotated document and associated resources will be placed.

setAnnotatedOutputDirectory(File, boolean) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Set the directory where the annotated document and associated resources will be placed.

setAnyBondStyles(String) - Method in class chemaxon.marvin.MolPrinter

Sets the any bond style.

setArcAngle(double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the central angle of the arc.

setArcHeight(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

setArcWidth(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

setArgument(int, ServiceArgument<?>) - Method in class chemaxon.marvin.services.ServiceDescriptor

Replaces the argument at specified index with specified argument

setAromaticityChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects aromaticity atom query properties or not.

setAromatizationMethod(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Sets the aromatization method.

setAromatize(boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Deprecated, for removal: This API element is subject to removal in a future version.

setAromatize(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated, for removal: This API element is subject to removal in a future version.

The original input structure is not aromatized. No need to use.

setAromatizeMethod(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the aromatize method.

setArrow(boolean) - Method in class chemaxon.struc.graphics.MPolyline

Sets or unsets arrow mode.

setArrowFlags(int, int) - Method in class chemaxon.struc.graphics.MPolyline

Sets the flags.

setArrowLength(int, double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the arrow head length.

setArrowWidth(int, double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the arrow head width.

setAssigned(int, boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule

setAsymmetryFactor(float) - Method in class chemaxon.descriptors.MDParameters

Sets the value of the asymmetry factor of the current parametrized metric.

setAtno(int) - Method in class chemaxon.struc.MolAtom

Sets the atomic number.

setAtom(int) - Method in class chemaxon.jep.context.AtomContext

Sets the input atom.

setAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(int) for atom removal and MoleculeGraph.add(MolAtom) for adding new atoms.

setAtom(int, MolAtom) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RgMolecule.add(MolAtom) to modify the structure.

setAtom(int, MolAtom) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

As of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RxnMolecule.add(MolAtom) to modify the structure.

setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the specified atom in the S-group graph.

setAtom(int, MolAtom) - Method in class chemaxon.struc.Sgroup

Sets the specified atom in the S-group graph.

setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Sets the specified atom in the S-group graph.

setAtom0(int, MolAtom) - Method in class chemaxon.struc.Molecule

Sets the atom at the specified index.

setAtom0(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Sets the atom at the specified index.

setAtom0(int, MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Sets the atom at the specified index.

setAtom1(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance

setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom

Sets the first atom of a bond.

setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom

Sets the first node of an edge.

setAtom2(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance

setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom

Sets the second atom of a bond.

setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom

Sets the second node of an edge.

setAtomFont(Font) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom symbol font name.

setAtomIndex(int) - Method in class chemaxon.calculations.nmr.Shift

Sets the atom index.

setAtomIndex(int, int) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the index of the ith atom of this multiplet.

setAtomIndexMap(int[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

setAtomIndices(int[]) - Method in class chemaxon.calculations.nmr.Multiplet

sets the indices of the atoms of this multiplet.

setAtomMap(int) - Method in class chemaxon.struc.MolAtom

Sets the atom-atom mapping number.

setAtomMappingMethod(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom mapping method.

setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides the atom mapping.

setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the atom mapping visibility.

setAtomNumberingType(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the atom numbering.

setAtomNumberingType(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom numbering type.

setAtomNumberingType(int) - Method in class chemaxon.marvin.MolPrinter

sets atom numbering type.

setAtomNumbersVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

in 6.2.0. Use setAtomNumberingType() instead

setAtomNumbersVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

in 6.2.0. Use setAtomNumberingType() instead.

setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets atom properties visibility.

setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Set the atom properties visibility

setAtomRefs(CloneStateMapper) - Method in class chemaxon.struc.StereoActivePart

For internal use only.

setAtoms(MolAtom[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Sets the atoms.

setAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

setAtoms(List<MolAtom>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method sets the atoms property

setAtomSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the color of an atom set.

setAtomSetColorMode(int, int) - Method in class chemaxon.struc.MDocument

Sets the atom set coloring mode.

setAtomSetFont(int, MFont) - Method in class chemaxon.struc.MDocument

Sets the font of an atom set.

setAtomSetRGB(int, int) - Method in class chemaxon.struc.MDocument

Sets the color of an atom set.

setAtomSetSeq(int, int, int) - Method in class chemaxon.marvin.beans.MViewPane

Sets the set sequence number of the atom.

setAtomSetSeq(int, String, int, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets the atom set sequence number of an atom.

setAtomSetSeq(int, String, String, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets atom set sequence numbers.

setAtomSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph

Sets the set sequence number of all atoms.

setAtomSetSeqs(int, String, int[]) - Method in class chemaxon.marvin.view.MDocStorage

Sets atom set sequence numbers.

setAtomsize(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the atom size.

setAtomsize(double) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.2.2, replaced by MolPrinter.setAtomSize(double).

setAtomSize(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom size in C-C bond length units.

setAtomSize(double) - Method in class chemaxon.marvin.MolPrinter

Sets the size of displayed atoms in units of regular bond length.

setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides the atom symbols in 3D.

setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets atom symbol visibility in 3D mode.

setAttach(int) - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).

setAttach(int, Sgroup) - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).

setAttachedDataMatch(int) - Method in class chemaxon.sss.search.SearchOptions

Sets whether attached data (in data sgroups) should be used when comparing structures.

setAttachedDataPrefixes(String) - Method in class chemaxon.sss.search.SearchOptions

Sets the prefixes of the names of those data sgroups that will be used during structure comparison.

setAttachmentPointOrder(MolAtom, int, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Sets a new order for the given attachment point.

setAttachmentPointsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the attachment points visibility.

setAttachmentType(int) - Method in class chemaxon.sss.search.RgDecompResults

setAttachmentType(int) - Method in class chemaxon.sss.search.RGroupDecomposition

Sets the attachment point representation type in ligand molecules.

setAttachParentSgroup(Sgroup) - Method in class chemaxon.struc.MolAtom

Sets the attach parent s-group information to the extra atom properties

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MAnalysisBox

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MBracket

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MEFlow

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MElectron

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MElectronContainer

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MPolyline

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRectangle

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRoundedRectangle

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MTextBox

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.MObject

Sets the value of an attribute.

setAttributes(int, int, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument

Sets attributes of selected text.

setAutoAlign(boolean) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the alignment behavior of the text-box.

setAutoCheckStructure(boolean) - Method in class chemaxon.marvin.common.UserSettings

Turn on automatic Structure checking

setAutoHeight(boolean) - Method in class chemaxon.struc.graphics.MNameTextBox

Turns on/off automatic height calculation.

setAutoHeight(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Turns on/off automatic height calculation.

setAutomaticFogEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the fog to automatic calculation mode.

setAutomaticReactionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the calculation of reaction plus signs to automatic.

setAutoResize(boolean) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the resizing behavior of the text-box.

setAutoScale(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the autoscale property.

setAutoSize(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Turns on/off automatic size calculation.

setAutoTabScale(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Allows or disallows automatic changing of tab scale.

setBackground(Color) - Method in class chemaxon.struc.MObject

Sets the background color of the object.

setBackgroundColor(Color) - Method in class chemaxon.marvin.MolPrinter

Sets the background color.

setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer

Sets the background color for the current cell based on selection.

setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer

Sets the background color for the current cell based on selection.

setBackgroundColor(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor

Sets the background color for the current cell based on selection.

setBallRadius(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the ball radius in units of covalent radius.

setBallRadius(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the ball radius for ball and stick mode.

setBallRadius(double) - Method in class chemaxon.marvin.MolPrinter

Sets the ball radius for "ball and stick" mode.

setBarrierLimit(double) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Set the energy barrier limit.

setBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow

setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlow

setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlow

setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

setBaseFontFamily(String) - Method in class chemaxon.struc.graphics.MTextBox

Sets the base font family.

setBaseFontStyle(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the base font style.

setBasicpKaLowerLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the minimum basic pKa (default: -10).

setBestLigandPosition(MolAtom, MolAtom) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates and sets an optimal position for a ligand atom.

setBestLigandPosition(MolAtom, MolAtom, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates and sets an optimal position for a ligand atom.

setBicycloStereo(BicycloStereoDescriptor[]) - Method in class chemaxon.struc.MolAtom

Registers the bicyclo stereo information for this atom.

setBitCount(int) - Method in class chemaxon.descriptors.CFParameters

Sets the bit count (number of fingerprint bits to be set to 1) parameter.

setBitCount(int) - Method in class chemaxon.descriptors.RFParameters

Sets the bit count (number of fingerprint bits to be set to 1) parameter.

setBoldBondWidth(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bold bond width.

setBoldBondWidth(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bold bond width in pt.

setBoldBondWidth(double) - Method in class chemaxon.marvin.MolPrinter

Sets the bold bond with.

setBond(int, MolBond) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.

setBond(int, MolBond) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.

setBond(int, MolBond) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.

setBond(int, MolBond) - Method in class chemaxon.struc.SelectionMolecule

Deprecated.

as of Marvin 6.2. Use SelectionMolecule.removeBond(MolBond) for bond removal and SelectionMolecule.add(MolBond) for adding a new bond to the molecule.

setBondCorrespondence(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the crossing bonds (head and tail) of a ladder-type polymer.

setBondCount(int) - Method in class chemaxon.descriptors.CFParameters

Sets the path length (number of adjacent bonds) parameter.

setBondCount(int) - Method in class chemaxon.descriptors.RFParameters

Sets the path length (number of adjacent bonds) parameter.

setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the visibility of the currently used bond at the mouse cursor.

setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the visibility of the currently used bond at the mouse cursor.

setBondHashSpacing(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond hash spacing.

setBondHashSpacing(double) - Method in class chemaxon.marvin.MolPrinter

Sets the bond hash spacing that is the distance the hashes in a hashed bond.

setBondIndex(int, int, int) - Method in class chemaxon.core.util.BondTable

Sets the index of the bond connecting two atoms.

setBondLength(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bond length.

setBondLength(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond length in pt.

setBondLength(double) - Method in class chemaxon.marvin.MolPrinter

Sets the bond length in pt.

setBondLengthVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bond length display option.

setBondLengthVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the bond length visibility

setBonds(List<MolBond>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

setBonds(List<MolBond>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method sets the bonds property

setBondSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the color of a bond set.

setBondSetColorMode(int, int) - Method in class chemaxon.struc.MDocument

Sets the bond set coloring mode.

setBondSetRGB(int, int) - Method in class chemaxon.struc.MDocument

Sets the color of a bond set.

setBondSetSeq(int, String, int, int, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets bond set sequence numbers.

setBondSetSeq(int, String, String, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets bond set sequence numbers.

setBondSetSeqAll(int, String, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets all bond set sequence numbers.

setBondSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph

Sets the set sequence number of all bonds.

setBondSetSeqs(int, String, List<int[]>) - Method in class chemaxon.marvin.view.MDocStorage

Sets bond set sequence numbers.

setBondSetThickness(int, double) - Method in class chemaxon.struc.MDocument

Sets the thickness of a bond set.

setBondSpacing(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bond spacing.

setBondSpacing(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the double bond spacing.

setBondSpacing(double) - Method in class chemaxon.marvin.MolPrinter

Sets the double bond spacing that is the distance of the two lines representing a double bond.

setBondWidth(double) - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 4.1, replaced by MarvinPane.setBondSpacing(double)

setBondWidth(double) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 4.1, replaced by MolPrinter.setBondSpacing(double)

setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer

Sets the border for the current cell based on selection.

setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewRenderer

Sets the border for the current cell based on selection.

setBorder(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewEditor

Sets the border for the current cell based on selection.

setBorderWidth(int) - Method in class chemaxon.marvin.beans.MViewPane

Sets the width of the border between cells.

setBottomMargin(double) - Method in class chemaxon.struc.PageSettings

setBottomTextArea(String) - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets text area in bottom-left corner.

setBracketOrientation(int) - Method in class chemaxon.struc.graphics.MBracket

Sets the orientation of the bracket.

setBridgehead(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing bridgehead H

setBridgingRAllowed(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets whether different undefined R-atoms can match the same group of atoms.

setByteOrder(ByteBuffer) - Method in class chemaxon.marvin.io.PositionedInputStream

setC(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets the state of a checkbox in a GridBagView table.

setCacheCapacity(int) - Method in class chemaxon.marvin.view.MDocStorage

Sets the maximum number of cached documents.

setCalcAlways(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

replaced by setModel(int)

setCalculateEnergy(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the calculation of dreiding energy.

setCalculateForLEConformer(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the condition for lowest energy conformer calculation before geometry calculations are processed.

setCalculateMMFF94Energy(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the calculation of MMFF94 energy.

setCalculateMoleculeProjections(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the calculation of molecule projections.

setCalculateVolume(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin

setCanceled(boolean) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Sets whether the process is cancelled

setCarbonVisibility(String) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility style of the C labels on Carbon atoms.

setCellIndex(int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the viewer cell index.

setCellSize(int) - Method in class chemaxon.descriptors.MDParameters

Sets the size (number of bits) of the bins (cells).

setCellSize(Dimension) - Method in class chemaxon.marvin.view.swing.TableSupport

Sets the molecule cell size for GridBagView.

setCellwiseWeights(boolean) - Method in class chemaxon.descriptors.MDParameters

Sets boolean telling whether cell weights are to be generated for current parametrized metric.

setCenterMolecule(boolean) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Center the molecule before MD calculation (It is not set by default.)

setCentralAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Sets the central atom of this sgroup.

setChangeSupport(PropertyChangeSupport) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Sets the changeSupport

setCharge(int) - Method in class chemaxon.struc.MolAtom

Sets the charge.

setChargeAngle(double) - Method in class chemaxon.struc.MolAtom

To be called when user changes charge position.

setCharged(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing charged H

setChargeFont(Font) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

in Marvin 15.5.18

setChargeLocation(int) - Method in class chemaxon.struc.Sgroup

Sets the charge location attribute of the S-group.

setChargeMatching(int) - Method in class chemaxon.sss.search.SearchOptions

Set charge matching behavior.

setChargeWithCircle(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility of Charge with Circle

setChart(MChart) - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets chart.

setCheckerConfigFileName(String) - Method in class chemaxon.marvin.common.UserSettings

Deprecated, for removal: This API element is subject to removal in a future version.

Use UserSettings.setCheckerConfigURL(String) instead. Deprecated in 5.12 Sets the name of the configuration file for StructureChecker in marvin sketch

setCheckerConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the URL of the configuration for Checkers in marvin sketch.

setCheckSpHyb(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets whether the sp-hybridization state of the atoms should be considered.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.logDPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.pKaPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated.

For internal use only.

setChemicalTermsParameters(Properties, String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated.

For internal use only.

setChemTermsFilter(String) - Method in class chemaxon.sss.search.SearchOptions

Sets the Chemical Terms filtering expression.

setChemTermsFilterConfig(File) - Method in class chemaxon.sss.search.SearchOptions

Sets the configuration file for Chemical Terms filter.

setChemTermsFilterConfig(String) - Method in class chemaxon.sss.search.SearchOptions

Sets the configuration string for Chemical Terms filter.

setChemTermsFilterOption(ChemTermsFilterOption) - Method in class chemaxon.sss.search.SearchOptions

FOR INTERNAL USE ONLY.

setChirality(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction

Sets the chirality value of absolute stereo action

setChirality(int, int) - Method in class chemaxon.struc.MoleculeGraph

Set chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

setChirality(Map<Integer, Integer>) - Method in class chemaxon.struc.MoleculeGraph

Sets the chiralities of atoms.

setChiralitySupport(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets chirality support to show or hide the R/S labels.

setChiralitySupport(int) - Method in class chemaxon.marvin.MolPrinter

Sets the chirality display mode.

setChiralitySupport(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the chirality support parameter.

setClassification(NMRCoefficient.ErrorClassification) - Method in class chemaxon.calculations.nmr.Shift

Sets the error classification of the stored chemical shift.

setClassName(String) - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

Sets the full class name of the service

setClassName(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the name of the standardizer class

setClassName(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

Sets the name of the checker class

setClean(int, String) - Method in class chemaxon.formats.MolExporter

Sets molecule cleaning in exporter.

setClean(int, String, MolFilter) - Method in class chemaxon.formats.MolExporter

Sets molecule cleaning in exporter.

setClean2dOpts(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the 2D cleaning options.

setClean3dOpts(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the 3D cleaning options.

setCleanDim(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the space dimensions for cleaning.

setCleanHOption(boolean) - Method in class chemaxon.marvin.common.UserSettings

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.4, replaced by UserSettings.setCleanHOptionEnabled(boolean)

setCleanHOptionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets to add an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.

setCleanResultStructures(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets 2D cleaning of the result structures: if true then resonants returned by ResonancePlugin.getStructure(int) and ResonancePlugin.getStructures() methods are cleaned in 2D.

setCleanResultStructures(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

obsolete method

setCleanTemplates(Standardizer, Molecule[]) - Static method in class chemaxon.standardizer.StandardizerUtil

Sets the default clean templates.

setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the Cl- concentration (default: 0.1).

setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the Cl- concentration (default: 0.1).

setCloseEnabled(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Set the accessibility of the Close menu item in the File menu.

setColor(AlignmentProperties.ColoringScheme) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

sets which atomtypes to use.

setColor(Color) - Method in class chemaxon.struc.MObject

Sets the color of the object.

SETCOLOR_COLORLESS - Static variable in class chemaxon.struc.MDocument

The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.

SETCOLOR_DEFAULT - Static variable in class chemaxon.struc.MDocument

Default set colors are used for coloring the atom/bond set.

SETCOLOR_SPECIFIED - Static variable in class chemaxon.struc.MDocument

The user specified set colors are used for coloring the atom/bond set.

setColoring(int) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets hit coloring options.

setColoringScheme(AlignmentProperties.ColoringScheme) - Method in class chemaxon.marvin.alignment.Alignment

setColorScheme(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the color scheme.

setColorScheme(String) - Method in class chemaxon.marvin.MolPrinter

Sets the color scheme.

setColumnCount(int) - Method in class chemaxon.marvin.beans.MViewParams

Sets the nuber of columns.

setColumnCount(int) - Method in class chemaxon.struc.PageSettings

setColumnWidth(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the default column width.

setColumnWidth(int, int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the default width of a specified column.

setComment(String) - Method in class chemaxon.struc.Molecule

Sets the comment.

setComment(String) - Method in class chemaxon.struc.RgMolecule

Sets the comment of the root molecule.

setCompleteHG(boolean) - Method in class chemaxon.sss.search.SearchOptions

Deprecated, for removal: This API element is subject to removal in a future version.

This option is no longer supported. This method does not change anything.

setConfiguration(StandardizerConfiguration) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setConfiguration(StandardizerConfiguration) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets the configuration of the runner

setConfigurationReader(ConfigurationReader) - Method in interface chemaxon.checkers.runner.CheckerRunner

Sets a new configuration for the Runner.

setConfigurationReader(StandardizerConfigurationReader) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setConfigurationReader(StandardizerConfigurationReader) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets a new configuration for the runner.

setConfirmExit(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Sets to drop confirmation dialog about exit or not.

setConformerCount(int) - Method in class chemaxon.marvin.alignment.Alignment

The the dihedral angles of every flexible molecule should be randomized before alignment.

setConformerCount(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects connection count atom query properties or not.

setConnectivity(int) - Method in class chemaxon.struc.Sgroup

Sets S-group connectivity.

setConsiderHPLCEffect(boolean) - Method in class chemaxon.marvin.calculations.logDPlugin

setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets to consider tautomerization.

setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets to consider tautomerization in calculation.

setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets to consider tautomerization.

setConsiderTautomerization(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets to consider tautomerization.

setContainerFree() - Method in class chemaxon.struc.graphics.MElectronContainer

setContainerFull() - Method in class chemaxon.struc.graphics.MElectronContainer

setContext(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the context of this data sgroup.

setContext(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the context of this data sgroup.

setConvergenceLimit(double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setCoordDependent(long) - Method in class chemaxon.struc.MProp

Sets the property as coordinate dependent.

setCoordinateBondStyle(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the "coordinative" bond line style when both atoms are single.

setCoordinateBondStyle(String) - Method in class chemaxon.marvin.MolPrinter

Set the coordinate bond line style when both atoms are single.

setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the "coordinative" bond line style when one of the atoms is multicenter.

setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.MolPrinter

Set the coordinate bond line style.

setCopolymerMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Adjusts copolymer matching mode.

setCopyAsFormat(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the selected format in the Copy As dialog.

setCorners(double, double, double, double) - Method in class chemaxon.struc.MolAtom

Used internally by MolPainter.

setCorners(MPoint, MPoint) - Method in class chemaxon.struc.graphics.MRectangle

Sets the corners.

setCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

setCorrectionData(PKaTrainingResult) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets correction data for calculation

setCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets the correction library.

setCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the correction library.

setCorrectionLibraryPath(String) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets the correction library file directly.

setCorrectionLibraryPath(String) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the correction library file directly.

setCount(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setCount(int) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

setCount(int) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setCoupled(boolean) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Coupled/decoupled spectrum.

setCouplingConstants(double[][]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets coupling constants.

setCouplingNeeded(boolean) - Method in class chemaxon.calculations.nmr.Multiplet

Sets whether spin-spin couplings are taken into account.

setCouplingNeeded(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets whether spin-spin couplings are taken into account.

setCreateStatistics(boolean) - Method in class chemaxon.descriptors.MDGenerator

Toggles the create statistics flag.

setCreateStatistics(boolean) - Method in class chemaxon.descriptors.MDParameters

Toggles the create statistics flag of the MDGenerator object.

setCrossingBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Change the crossing bond of an attachment point.

setCTCrossedBond(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Convert wiggly type double bonds to crossed.

setCTWigglyBond(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Convert crossed double bonds to wiggly type.

setCTWigglyBond(MoleculeGraph, int) - Static method in class chemaxon.marvin.util.CleanUtil

Convert crossed double bond to wiggly type.

setCurNumberOfParameters(int) - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

Sets the number of current number of parameters used in the next call of run().

setCurrentDefaultFontMetrics(FontMetrics) - Method in class chemaxon.struc.graphics.MTextBox

Sets the current height of the text..

setCurrentFont(MFont, int) - Method in class chemaxon.struc.graphics.MTextBox

Sets font for selected text or the next character to be typed.

setCurrentForeground(Color) - Method in class chemaxon.struc.graphics.MTextBox

Sets color for selected text or the next character to be typed.

setCurrentFrameIndex(int) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Sets the current frame index.

setCurrentHeight(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the current height of the text..

setCurrentParametrizedMetric(int) - Method in class chemaxon.descriptors.MDParameters

Selects the specified parametrized metric to be the current.

setCurrentParametrizedMetric(int) - Method in class chemaxon.descriptors.PFParameters

Selects a metric to be used.

setCurrentTextAttributes(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextBox

Sets the attributes for the selected text or the next character to be typed.

setCurrentWidth(double) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the current height of the text..

setCurrentWidth(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the current height of the text..

setCursorPos(int, boolean) - Method in class chemaxon.struc.graphics.MTextBox

Sets the cursor position.

setCursorRow(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the cursor row number.

setCustomHtmlToXmlConverter(XmlToHtmlConverter) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Provide a custom converter from XML to HTML, to be used instead of the default one.

setCustomName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the customName

setD2SOptions(String) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Sets the options string to use for document annotation.

setData(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the data value to be set.

setDataCollectionConsent(Consent) - Method in class chemaxon.marvin.common.UserSettings

setDataDetached(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets whether the data should be displayed close to the objects or separately (detached).

setDataLine(int, String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets a line of data.

setDebug(int) - Method in class chemaxon.marvin.beans.MarvinPane

Switches on the debug messages.

setDefaultFont(MFont) - Method in class chemaxon.struc.graphics.MTextDocument

Sets the default font.

setDefaultFont(JEditorPane) - Static method in class chemaxon.marvin.util.SwingUtil

Sets the SWING default font in the JEditorPane.

setDefaultNodeWeightBehavior(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.marvin.alignment.Alignment

setDefaultSaveFormat(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default molecule format in the "Save As" dialog.

setDehidrogenize(boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Deprecated, for removal: This API element is subject to removal in a future version.

setDehidrogenize(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated, for removal: This API element is subject to removal in a future version.

The explicit Hydrogens are not removed from the original input structure. No need to use.

setDehydrogenize(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set dehydrogenize parameter

setDependentRgroupDefinition(int, int) - Method in class chemaxon.struc.RgMolecule

Sets the dependent R-group definition (rgroupIndexThen) for the referenced R-group definition (rgroupIndexIf).

setDescription(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setDescription(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setDescription(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setDescription(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the description of the concerning checker

setDescription(String) - Method in class chemaxon.fixers.AbstractStructureFixer

Deprecated, for removal: This API element is subject to removal in a future version.

setDescription(String) - Method in interface chemaxon.fixers.StructureFixer

Deprecated, for removal: This API element is subject to removal in a future version.

setDescription(String) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the description of the concerning fixer

setDescription(String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Sets the description (tooltip) of service descriptor

setDescription(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the description of the action

setDescriptor(T) - Method in interface chemaxon.marvin.services.ServiceDescriptorEditor

Updates the editor to represent the specified descriptor NOTE: ServiceDescriptorEditor.getDescriptor() may NOT return same instance

setDescriptorURI(String) - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor

Sets the URI of the JSON RPC descriptor file

setDesiredBufferSize(int) - Method in class chemaxon.marvin.io.PositionedInputStream

Sets desired buffer size.

setDetachable(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets the detachable property.

setDetectCumulatedDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker

Sets the detectCumulatedDoubleBonds property

setDetectTransDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker

Sets the detectTransDoubleBonds

setDetectTripleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker

Sets the detectTripleBonds property

setDiameter(int) - Method in class chemaxon.descriptors.ECFPParameters

Sets the diameter parameter.

setDiaStereoIsomerMixtureAllowedState(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

setDifLoc(double...) - Method in class chemaxon.struc.graphics.MElectron

setDim(int) - Method in class chemaxon.struc.Molecule

Sets the dimension.

setDim(int) - Method in class chemaxon.struc.MoleculeGraph

Sets the dimension.

setDim(int) - Method in class chemaxon.struc.RgMolecule

Sets the dimension of the root structure and the R-groups.

setDim(int) - Method in class chemaxon.struc.RxnMolecule

Sets the dimension for all the structures.

setDirectory(File) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the working directory, if the Load/Save is in Last Opened Mode.

setDirty(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets or clears the dirty flag.

setDisabledGroupTypes(List<String>) - Method in class chemaxon.marvin.beans.MSketchPane

setDisplayChargeWithCircle(boolean) - Method in class chemaxon.marvin.common.UserSettings

setDisplayedChars(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the number of characters to be displayed (1...999 or 0 for no restriction)

setDisplayedLines(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the number of lines to be displayed (0: show all)

setDisplayLonePairsAsLine(boolean) - Method in class chemaxon.marvin.common.UserSettings

setDisplayQuality(int) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 6.4 only high quality exists

setDispopts(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets display options.

setDispopts(int) - Method in class chemaxon.marvin.MolPrinter

Modifies the display options in the advanced way of handling display options.

setDispopts(int, int) - Method in class chemaxon.marvin.MolPrinter

Modifies the display options as in MolPrinter.setDispopts(int), but affects only limited display options using a mask.

setDispoptsExt(int) - Method in class chemaxon.marvin.MolPrinter

Modifies the extended display options in the advanced way of handling display options.

setDispoptsExt(int, int) - Method in class chemaxon.marvin.MolPrinter

Modifies the extended display options as in MolPrinter.setDispoptsExt(int), but affects only limited display options using a mask.

setDistinctFirstAtomMatching(boolean) - Method in class chemaxon.sss.search.MolSearchOptions

Option ensuring that upon the findNext() call the first atom must be stepped as well.

setDiversity(double) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the diversity limit for the calculation.

setDoc(MDocument) - Method in class chemaxon.marvin.MolPrinter

Sets the current document and calculates its bounds.

setDocSource(MDocSource, int, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets the document source.

setDocument(int, MDocument) - Method in class chemaxon.marvin.beans.MViewPane

Sets the document

setDocument(int, MDocument) - Method in class chemaxon.marvin.view.swing.TableSupport

Sets the k-th record directly.

setDocument(MTextDocument) - Method in class chemaxon.struc.graphics.MTextBox

setDocument(MDocument) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the document.

setDocumentStyleName(String) - Method in class chemaxon.marvin.common.UserSettings

setDocumentStyleName(String, boolean) - Method in class chemaxon.marvin.common.UserSettings

setDomainMax(double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the upper end of this multiplet.

setDomainMax(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the upper end of the spectrum.

setDomainMin(double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the lower end of this multiplet.

setDomainMin(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the lower end of the spectrum.

setDominantTautomerDistributionCalculation(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets dominant tautomer distribution calculation: if true then dominant tautomer distribution is calculated.

setDontRemoveLastComponent(boolean) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

setDoubleBond(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction

Sets the double bond value of absolute stereo action

setDoubleBondStereoMatchingMode(int) - Method in class chemaxon.sss.search.SearchOptions

Sets how double bond cis/trans stereo information should match during the search.

setDoublePrecision(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the double -> string conversion precision (maximal number of fraction digits) with zero-padding (12.56 -> 12.5600 if precision=4).

setDoublePrecision(int, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the double -> string conversion precision (maximal number of fraction digits).

setDoublePrecision(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the precision in the decimal format.

setDownWedge(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the wedge bond display convention.

setDownWedge(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the convention to use for displaying a down wedge.

setDownWedge(String) - Method in class chemaxon.marvin.MolPrinter

Set the down wedge orientation.

setDraggable(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Allows or denies mouse dragged events in cells.

setDraggedObject(MObject) - Method in class chemaxon.struc.MDocument

Sets the dragged object.

setEditable(boolean) - Method in class chemaxon.standardizer.advancedactions.TransformAction

Sets if this action is editable.

setEditable(int) - Method in class chemaxon.marvin.beans.MViewEditor

Sets the mode that determines if the structure is editable.

setEditable(int) - Method in class chemaxon.marvin.beans.MViewPane

Sets the mode that determines if the structure is editable.

setEditorClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the editorClassName

setEditorClassName(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the editorClassName

setEditorClassName(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the name of the editor of the standardizer class

setEditorClassName(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor

Sets the name of the editor of the checker class

setElectronIndex(String, int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

setElectronProp(int) - Method in class chemaxon.struc.MolAtom

Sets the number of lone pairs.

setElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct

setEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enables or disables this component, depending on the value of the parameter b.

setEnabled(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Enables or disables this component, depending on the value of the parameter b.

setEnabled(boolean) - Method in class chemaxon.struc.PageSettings

setEnabledT(int, int, boolean) - Method in class chemaxon.marvin.view.MDocStorage

Set the enabled state of a text field in a record.

setEnableStandardization(boolean) - Method in class chemaxon.descriptors.RFParameters

Sets if standardization is applied.

setEnableTranslateAndRotate(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMolecule

setEncoding(Encoding) - Method in class chemaxon.marvin.io.PositionedInputStream

Sets the encoding.

setEncoding(String) - Method in class chemaxon.marvin.io.PositionedInputStream

Sets the encoding.

setEncoding(String, String) - Method in class chemaxon.marvin.io.MolExportModule

Sets the output encoding using the export options.

setEncodings(String) - Method in class chemaxon.formats.MolConverter.Builder

Sets the input and/or output encoding.

setEncodings(String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

setEndgroupMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Adjusts polymer end group matching.

setEndPosition(long) - Method in class chemaxon.struc.MDocument

Sets the end position of this document in the input file.

setEndPosition(long) - Method in class chemaxon.struc.Molecule

Sets the end position of this molecule in the input file.

setEnforceAbsStereo(boolean) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

setEnumCodeNeeded(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Indicates whether unique Markush enumeration code should be generated.

setEnumerateHomology(boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets if homology groups should be enumerated or not.

setErrorProcessor(ErrorProcessor) - Method in class chemaxon.formats.MolExporter

Sets the error handler interface for concurrent mode.

setEuler(double, double, double) - Method in class chemaxon.struc.CTransform3D

Sets the rotational component using the Euler angles provided.

setExact(boolean) - Method in class chemaxon.standardizer.advancedactions.TransformAction

Sets the exact value of the action

setExactBondMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Specifies whether bond types should match exactly - looking for query bonds target.

setExactQueryAtomMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets whether exact query atom matching should be used or not.

setExactSpecialAtomMatching(String) - Method in class chemaxon.sss.search.SearchOptions

Sets the identifiers of those special atoms that should match exactly during structure comparison.

setExcludeAntiAromaticCompounds(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets whether antiaromatic compounds should be generated.

setExcluded(AtomLabels) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Sets the abbreviations to be excluded

setExcluded(AtomLabels) - Method in class chemaxon.checkers.PseudoAtomChecker

setExcluded(DataExclusionList) - Method in class chemaxon.checkers.AttachedDataChecker

setExcludeHalogens(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets if halogens should be excluded from hydrogen bond acceptors.

setExcludePhosphorus(boolean) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Sets to exclude phosphorus from PSA calculation.
Default: true, phosphorus i excluded.

setExcludeString(String) - Method in class chemaxon.standardizer.actions.AbstractSgroupAction

Sets the exclude string of action

setExcludeString(String) - Method in class chemaxon.standardizer.actions.ContractSgroupsAction

setExcludeString(String) - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction

setExcludeString(String) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

setExcludeSulfur(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets if sulfur atom should be excluded from hydrogen bond acceptors.

setExcludeSulfur(boolean) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Sets to exclude sulfur from PSA calculation.
Default: true, sulfur i excluded.

setExclusionRegexp(boolean) - Method in class chemaxon.checkers.AttachedDataChecker

Sets if the descriptor of the excluded-data (AtomLabels) should be treated as a regular expression (see also: AttachedDataChecker.isExclusionRegexp()

setExhaustiveModeLimit(int) - Method in class chemaxon.sss.search.SearchOptions

Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.

setExperimentalEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enable or disable experimental features.

setExplicitConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects explicit connection count atom query properties or not.

setExplicitH(boolean) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.

setExplicitHVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.

setExpression(String) - Method in class chemaxon.marvin.services.DynamicArgument

Sets the expression

setExternalCheckerConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the URL of the configuration file containing the list of external Checkers in marvin sketch.

setExtraLabel(String) - Method in class chemaxon.struc.MolAtom

Sets the extra atom label (also called atom value): "label" or "label1|label2".

setExtraLabelColor(int, int) - Method in class chemaxon.struc.MolAtom

Sets the extra label colors: lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

setExtraLabelColor(long) - Method in class chemaxon.struc.MolAtom

Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

setExtraLabelColorsForDocument(Molecule) - Method in class chemaxon.struc.MDocument

Sets the coloring mode sets and colors of extra labels

setExtraLabelSetColorMode(int, int) - Method in class chemaxon.struc.MDocument

setExtraLabelSetRGBs(int, int) - Method in class chemaxon.struc.MDocument

setExtraLabelSetRGBs(int, int, int) - Method in class chemaxon.struc.MDocument

setExtraLabelSetSeq(int) - Method in class chemaxon.struc.MolAtom

setEZLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility state of absolute double bond stereo configuration labels.

setEzVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the E/Z display option.

setEzVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.2.2, replaced by MolPrinter.setEZLabelsVisible(boolean)

setEZVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide E/Z labels

setField(int, Molecule, String, MProp) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Sets a property.

setFieldAccessor(MFieldAccessor) - Method in class chemaxon.marvin.view.MDocStorage

Sets the field accessor.

setFieldFont(String, Font) - Method in class chemaxon.marvin.beans.MViewPane

Sets the font for a named field in a table.

setFieldFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the field font size.

setFieldName(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the data field name.

setFields(int, Molecule, String[], MProp[]) - Method in class chemaxon.marvin.io.fieldaccess.MFieldAccessor

Sets properties.

setFields(String[]) - Method in class chemaxon.formats.MolConverter.Builder

Sets the included fields to be shown in a table.

setFields(String[]) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

setFieldsShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions

Show or hide SDfile fields in the table

setFieldType(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the field type.

setFieldType(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the field type from string representation.

setFile(File) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the current molecule file but does not load it.

setFilter(MolFilter) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets the molecule filter.

setFinalClean() - Method in class chemaxon.standardizer.Standardizer

Deprecated, for removal: This API element is subject to removal in a future version.

use ConfigurationUtility.setFinalClean(StandardizerConfiguration) on the configuration returned by the method Standardizer.getConfiguration()

setFinalClean(int) - Method in class chemaxon.standardizer.Standardizer

Deprecated, for removal: This API element is subject to removal in a future version.

use ConfigurationUtility.setFinalClean(StandardizerConfiguration, int) on the configuration returned by the method Standardizer.getConfiguration()

setFinalClean(int, boolean) - Method in class chemaxon.standardizer.Standardizer

Deprecated, for removal: This API element is subject to removal in a future version.

use ConfigurationUtility.setFinalClean(StandardizerConfiguration, int, boolean) on the configuration returned by the method Standardizer.getConfiguration()

setFinalClean(StandardizerConfiguration) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility

Deprecated, for removal: This API element is subject to removal in a future version.

It's not required anymore.

setFinalClean(StandardizerConfiguration, int) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility

Deprecated, for removal: This API element is subject to removal in a future version.

It's not required anymore.

setFinalClean(StandardizerConfiguration, int, boolean) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility

Deprecated, for removal: This API element is subject to removal in a future version.

It's not required anymore.

setFinalStereoFix(boolean) - Method in class chemaxon.standardizer.Standardizer

Sets to perform final stereo fixes.

setFingerprint(int[]) - Method in class chemaxon.jep.context.MolContext

Sets the fingerprint of the input molecule.

setFingerprintGenerator(FingerprintGenerator) - Method in class chemaxon.jep.Evaluator

Sets the fingerprint generator object (needed for query strings).

setFiveLongRings(List<List<MolAtom>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

This method sets the fiveLongRings property.

setFixed(int) - Method in class chemaxon.marvin.view.MDocStorage

Sets a document as fixed.

setFixerClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the fixerClassName

setFixMode(FixMode) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the fixMode

setFlags(int) - Method in class chemaxon.struc.graphics.MPolyline

Sets the flags.

setFlags(int) - Method in class chemaxon.struc.MolAtom

Sets the flags.

setFlags(int) - Method in class chemaxon.struc.MolBond

Sets bond type (4 bit), stereo (2+2+1 bit), topology (2 bit) bond set (5 bit) and reacting center (7 bits) information.

setFlags(int) - Method in class chemaxon.struc.MoleculeGraph

Sets the flags of the molecule.

setFlags(int) - Method in class chemaxon.struc.RgMolecule

Sets the dimension and chiral flags.

setFlags(int, int) - Method in class chemaxon.struc.MolAtom

Sets the flags.

setFlags(int, int) - Method in class chemaxon.struc.MolBond

Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit) information.

setFlags(int, int) - Method in class chemaxon.struc.MoleculeGraph

Sets specified bits in the flags.

setFlags(int, int) - Method in class chemaxon.struc.RgMolecule

Sets specified bits in the flags.

setFlexible(boolean) - Method in class chemaxon.descriptors.ShapeParameters

setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

setFlexibleRingSize(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setFlipped(boolean) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the flip property of this sgroup.

setFocus(MObject) - Method in class chemaxon.struc.MDocument

Focus to the specified object.

setFogFactor(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the fog factor.

setFontScale(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the font scaling factor.

setForcedFlexible(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated, for removal: This API element is subject to removal in a future version.

use AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE_EXTRA to get the same behavior in the AlignmentMoleculeFactory.create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType) methods.

setForceField(String) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the force field type.

setFormat(String) - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder

Sets the dipole export format.

setFormat(String) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Sets the spectrum export format.

setFormat(String) - Method in class chemaxon.formats.MolInputStream

Sets the molecule file format.

setFormat(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the default molecule file format.

setFormat(String) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set output format used by CalculatorPlugin.getResultAsString(int, Object)

setFormulaRecognition(boolean) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Recognizes the molecular formulas in pseudo labels.

setForSpecIsotopeSymbol(String) - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.3. use MolAtom.setSpecIsotopeSymbolPreferred(boolean) and MolAtom.setMassno(int) instead.

setFree(int) - Method in class chemaxon.struc.graphics.MElectronContainer

setFree(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Sets NMR measurement frequency.

setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the NMR measurement frequency.

setFromSgroupCopy(SgroupAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom

Make a copy of this S-group superatom.

setFunctionScale(double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the scaling parameter for the function of this multiplet.

setFuzzinessFactor(float) - Method in class chemaxon.descriptors.PFParameters

Sets the value of the fuzziness factor, used in fuzzy bipolar pharmacophore autocorrelogram (FBPA) based convolution product in non-parametrized (generic) FBPA metric.

setFuzzyCutOff(float) - Method in class chemaxon.descriptors.PFParameters

setFuzzyLowerBound(int) - Method in class chemaxon.descriptors.PFParameters

setFuzzySmoothingFactor(float) - Method in class chemaxon.descriptors.PFParameters

Sets the value of the fuzzy smoothing factor used in the generation of fuzzy fingerprints.

setGenerateCASNumber(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Sets CAS number name generation.

setGenerateDistanceRanges(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Generate intermolecular atomic distance ranges by tweaking conformation.

setGeneratePreferredIUPACName(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Sets preferred IUPAC name generation.

setGenerateTraditionalIUPACName(boolean) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Sets traditional IUPAC name generation.

setGenNameFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the IUPAC name font size.

setGenNameShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions

Set visibility of IUPAC names.

setGeom3D(boolean) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Sets 3D geometry consideration.

setGlobalChecker(TaggedCalculatorInputChecker) - Static method in interface chemaxon.calculator.TaggedCalculator

Sets the global input checker that will be used by all calculators implementing this interface.

setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.beans.MarvinPane

setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.io.MolExportModule

Pass and set the global GUI properties container.

setGrabbingEnabled(boolean) - Method in class chemaxon.formats.MolImporter

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.2. It has no effect on the code.

setGraphInvariantVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the graph invariant visibility

setGridVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

setGrinv(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.5, use setGrinvVisible(boolean) instead

setGrinv(long) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the invariant the text box depends on.

setGrinvCC(long) - Method in class chemaxon.struc.MoleculeGraph

Sets the graph invariant change count.

setGrinvOptions(int) - Method in class chemaxon.struc.MoleculeGraph

Sets graph invariant calculation options passed to the module.

setGrinvVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides the graph invariants.

setGroupIndices(List<Integer>) - Method in class chemaxon.checkers.result.DataSgroupCheckerResult

setGroups(Map<String, Molecule>) - Method in class chemaxon.standardizer.actions.AliasToGroupAction

Sets the abbreviated groups of the action

setGUIContracted(boolean) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.2, use Molecule.expandSgroups(int) or Molecule.contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED

setGUIContracted(boolean, int) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.2, use Molecule.expandSgroups(int) or Molecule.contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED

setGUIMode(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used.

setGUIPropertyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument

Sets the property container storing MarvinPane settings

setGUIProperyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.1, replaced by MDocument.setGUIPropertyContainer(MPropertyContainer).

setGUIStateRecursively(boolean) - Method in class chemaxon.struc.Sgroup

Deprecated.

as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality

setGUIStateRecursively(boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated.

setGUIStateRecursively(boolean, int) - Method in class chemaxon.struc.Sgroup

Deprecated.

as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality

setHalfWidth(double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the half-width of the NMR lines.

setHalfWidth(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets NMR half-width.

setHconnected(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing H connected H

setHCountMatching(int) - Method in class chemaxon.sss.search.SearchOptions

Sets the H count matching mode.

setHeadCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the head crossing bonds.

setHeaderCellSize(int, int) - Method in class chemaxon.marvin.beans.MViewParams

Sets a logical cell extent by interpreting rows and columns as part of a sub-table.

setHeight(double) - Method in class chemaxon.struc.PageSettings

setHelpText(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setHelpText(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setHelpText(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setHelpText(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the help text of the concerning checker

setHelpText(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the help text of the action

setHitIndexType(int) - Method in class chemaxon.sss.search.MolSearchOptions

Set the representation to use for hit indexes in case of Markush search.

setHitOrdering(int) - Method in class chemaxon.sss.search.SearchOptions

Sets the hit ordering type.

setHomologyBroadTranslation(HomologyTranslationOption) - Method in class chemaxon.sss.search.SearchOptions

Adjusts for which query atoms broad translation on target homology groups is allowed.

setHomologyNarrowTranslation(HomologyTranslationOption) - Method in class chemaxon.sss.search.SearchOptions

Adjusts for which query homology atoms narrow translation on target specific atoms is allowed.

setHorizontalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the horizontal alignment.

setHybridizationState(int) - Method in class chemaxon.struc.MolAtom

Sets the hybridization state.

setHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects hydrogen count atom query properties or not.

SetHydrogenIsotopeSymbolAction - Class in chemaxon.standardizer.actions

Set hydrogen isotope symbol standardizer action

SetHydrogenIsotopeSymbolAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

Initializes the action

SetHydrogenIsotopeSymbolAction.Type - Enum Class in chemaxon.standardizer.actions

Hydrogen isotope representation type

setHydrogenize(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set hydrogenize parameter

setHyperfine(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the hyperfine option for calculation.

setIcon(Icon) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setIcon(Icon) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setIcon(Icon) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setIconPath(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the icon path

setIconPath(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the path of icon associated to the action

setId(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the id of the action

setId(String) - Method in class chemaxon.struc.Molecule

setId(String) - Method in class chemaxon.struc.Sgroup

setID(String) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Sets the identifier string of the standardizer action

setID(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the id of the standardizer class

setID(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

Sets the id of the checker class

setIDBackgroundRGBA(int, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets the background color's RGBA value in a record.

setIdentifier(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the checker identifier

setIdentifier(String) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the fixer identifier

setIdentity() - Method in class chemaxon.struc.CTransform3D

Makes identity transformation.

setIDForegroundRGBA(int, int) - Method in class chemaxon.marvin.view.MDocStorage

Sets the foreground color's RGBA value in a record.

setIgnoreAxialStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets ignoring axial stereo information during serching.

setIgnoreConfigurationErrors(boolean) - Method in interface chemaxon.checkers.runner.CheckerRunner

Sets whether configuration errors should be ignored on execution.

setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setIgnoreConfigurationErrors(boolean) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets whether configuration errors should be ignored

setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.standardizer.Standardizer

Sets whether the configuration errors should be ignored by the standardization process.
When configuration errors are ignored, invalid standardizer actions in the configuration are not executed, however all valid actions are to be executed.
When configuration errors are not ignored, IllegalArgumentException thrown when Standardizer.standardize(Molecule) method is called on an invalid configuration.

setIgnoreCumuleneOrRingCisTransStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets ignoring cumulene cis-trans stereo information during serching.

setIgnoreDoubleBondStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets ignoring double bond stereo information during serching.

setIgnoreError(boolean) - Method in class chemaxon.formats.MolConverter

Sets the 'ignoreError' option.

setIgnoreRotatableBonds(boolean) - Method in class chemaxon.descriptors.PFParameters

setIgnoreSynAntiStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets ignoring syn-anti stereo information during serching.

setIgnoreTetrahedralStereo(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets ignoring tetrahedral stereo information during serching.

setImageImportServiceURL(String) - Method in class chemaxon.marvin.common.UserSettings

setImplicitH(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the display method of implicit hydrogens.

setImplicitH(String) - Method in class chemaxon.marvin.MolPrinter

Sets the display method of implicit hydrogens.

setImplicitHBasedOnValence(Valence) - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.0.1, exists only for internal usage
Usage:

Internal usage only.

setImplicitHcount(int) - Method in class chemaxon.struc.MolAtom

Sets the number of implicit hydrogens.

setImplicitHMatching(int) - Method in class chemaxon.sss.search.SearchOptions

Set option for matching implicit and explicit hydrogens.

setImplicitHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects implicit hydrogen count atom query properties or not.

setImplicitHydrogenMode(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets implicit hydrogen mode.

setImplicitMul(boolean) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

This option will be removed without replacement.

setInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil

Sets the tasks with the provided ID inactive.

setIndex(int) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

Sets the index of the actual action of the configuration

setIndexOfOriginalLigand(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin.HydrogenData

setInitialTemperature(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the initial temperature.

setInput(Object) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Sets the input molecule.

setInput(Object) - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit

Sets the plugin object and the input molecule.

setInputFormat(String) - Method in class chemaxon.struc.MDocument

Sets the input file format.

setInputFormat(String) - Method in class chemaxon.struc.Molecule

Sets the input file format.

setInputFormat(String) - Method in class chemaxon.struc.RgMolecule

Sets the input file format.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ChargePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set input molecule to process

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the input molecule.

setInputMoleculeModified(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Not used.

setInputMoleculeModified(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Not used.

setIntegrator(String) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the integrator used for calculations.

setIntensity(int, double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the intensity of the ith NMR line.

setInvisibleSets(long) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the visibility of the specified atom sets.

setIsotopeMatching(int) - Method in class chemaxon.sss.search.SearchOptions

Set the isotope matching mode.

setIsotopic(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing isotopic H

setIsValenceCheckNeeded(boolean) - Method in class chemaxon.struc.MolAtom

Sets the boolean value if MolAtom.isValenceCheckNeeded.

setJar(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the path of the jar containing the standardizer class

setJar(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

Sets the path of the jar containing the checker class

setKeepCounts(boolean) - Method in class chemaxon.descriptors.ECFPParameters

Sets the counts (multiplicity) parameter.

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets if result molecule keeps explicit hydrogens or not

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets if result molecule keeps explicit hydrogens or not

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets if result molecule keeps explicit hydrogens or not

setKeepHydrogens(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

setKeepMapping(boolean) - Method in class chemaxon.standardizer.actions.MapAction

Sets keep mapping for the underlying mapper.

setKeepMapping(boolean) - Method in class chemaxon.standardizer.actions.MapReactionAction

Sets keep mapping for the underlying mapper.

setKeepMapping(boolean) - Method in class com.chemaxon.mapper.AutoMapper.Options

Default value true

setKeepMapping(boolean) - Method in class com.chemaxon.mapper.AutoMapper

setKeepMapping(boolean) - Method in interface com.chemaxon.mapper.Mapper

Sets if the initial mapping of the given object should be kept or not.

setKeepQueryOrder(boolean) - Method in class chemaxon.sss.search.SearchOptions

Set option for rearranging query atoms to increase search performance.

setKeepSingleAtom(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set behavior on acyclic input

setL(int, int, String) - Method in class chemaxon.marvin.view.MDocStorage

Sets a text label in a record.

setL(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets a label in a GridBagView table.

setLabelCenter(int) - Method in class chemaxon.struc.sgroup.SgroupAtom

Sets the index of the character in the label the bonds should point to.

setLabelProperty(int, boolean, boolean) - Method in class chemaxon.marvin.beans.MViewParams

Defines properties for cells containing label components.

setLabels(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

use setAtomSymbolsVisible(v) instead

setLastLicense(LastLicense) - Method in class chemaxon.marvin.common.UserSettings

For internal use only.

setLastSketchFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings

setLastViewFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings

setLeftMargin(double) - Method in class chemaxon.struc.PageSettings

setLeftName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom

Set the string that will be shown at the left side of the molecule.

setLegendImages(Molecule[]) - Method in class com.chemaxon.calculations.gui.MChart

setLegendLabels(String[]) - Method in class com.chemaxon.calculations.gui.MChart

setLegendTexts(String[]) - Method in class com.chemaxon.calculations.gui.MChart

setLength(int) - Method in class chemaxon.descriptors.CDParameters

setLength(int) - Method in class chemaxon.descriptors.CFParameters

setLength(int) - Method in class chemaxon.descriptors.ECFPParameters

setLength(int) - Method in class chemaxon.descriptors.MDParameters

Sets the length (number of cells) of the descriptor.

setLength(int) - Method in class chemaxon.descriptors.RFParameters

Sets the length (number of bits) of the reaction fingerprint.

setLength(int) - Method in class chemaxon.descriptors.SDParameters

setLfin(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set handling option for multi fragment (disconnected) inputs

setLfout(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set handling option for multi fragment (disconnected) results.

setLicenseEnvironment(String) - Method in class chemaxon.calculations.Ring

This method is for internal use only.

setLicenseEnvironment(String) - Method in class chemaxon.calculations.TopologyAnalyser

setLicenseEnvironment(String) - Method in class chemaxon.checkers.AbstractStructureChecker

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.BCUT

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ECFP

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ECFPGenerator

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ShapeDescriptor

setLicenseEnvironment(String) - Method in class chemaxon.jep.Evaluator

For internal usage only.

setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AlignRigidEasy

setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setLicenseEnvironment(String) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

setLicenseEnvironment(String) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.GeometryPlugin

setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

setLicenseEnvironment(String) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

setLicenseEnvironment(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets license environment to be stored.

setLicenseEnvironment(String) - Method in class chemaxon.sss.search.MolSearch

setLicenseEnvironment(String) - Method in class chemaxon.sss.search.RGroupDecomposition

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.AbstractStandardizerAction

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setLicenseEnvironment(String) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets the license environment of the runner

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.Standardizer

Sets the license environment.

setLicenseEnvironment(String) - Method in interface chemaxon.standardizer.StandardizerAction

Sets the license environment of the action

setLicenseEnvironment(String) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

setLicenseEnvironment(String) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the license environment.

setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide ligand errors

setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the bond's ligand error visibility

setLigandOrder(int, MolAtom) - Method in class chemaxon.struc.MolAtom

Sets the order of a specified ligand.

setLigandOrderVisibility(String) - Method in class chemaxon.marvin.MolPrinter

Sets the ligand order visibility.

setLineColor(Color) - Method in class chemaxon.struc.MObject

Sets the color of the object.

setLineNumberInFile(int) - Method in exception chemaxon.formats.MolFormatException

Sets the line number relative to the first line of the file.

setLineNumberInRecord(int) - Method in exception chemaxon.formats.MolFormatException

Sets the line number relative to the first line of the record.

setLinkNodeDefaultOuters() - Method in class chemaxon.struc.MolAtom

Sets link node outer atoms to default values, if they are not set yet.

setLinkNodeDefaultOuters(MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Sets link node outer atoms to default values, if they are not set yet; making sure that the resulting link node configuration is valid.

setLinkNodeOuterAtom(int, int) - Method in class chemaxon.struc.MolAtom

Sets one of the link node's outer neighbor atoms.

setList(int[]) - Method in class chemaxon.struc.MolAtom

Sets the list elements.

setList(int[], int) - Method in class chemaxon.struc.MolAtom

Sets the list elements.

setListener(DocumentAnnotator.Listener) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

setListeners(MDocStorage.Listener[]) - Method in class chemaxon.marvin.view.MDocStorage

setListFont(Font) - Method in class chemaxon.marvin.view.swing.TableOptions

setLoadSaveLocation(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the load/save filechooser working directory selection method names, based on the preferences dialog.

setLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the filechooser's default working directory, if the filechooser working directory selection method is saveCustomLocation.

setLocalAromaticChecking(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

setLocalAromatiChecking(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 14.7.7, Use ValenceCheckOptions.Builder.setLocalAromaticChecking(boolean) instead.

setLocalMenuName(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setLocalMenuName(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setLocalMenuName(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setLocalMenuName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the local menu name of the concerning checker

setLocalParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

In case of 2D molecule change the bonds flag (UP/DOWN), in case of 0D molecule set the atom flags to achieve the specified parity array.

setLocalParity(int[], int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

Set given local parity for the given atomic indexes.

setLocation(DPoint3) - Method in class chemaxon.struc.MolAtom

Sets the coordinates.

setLocation(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Set the origin of the molecule.

setLocation(DPoint3) - Method in class chemaxon.struc.RgMolecule

Set the origin of the molecule.

setLocation(DPoint3) - Method in class chemaxon.struc.RxnMolecule

Set the origin of the molecule.

setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Sets the atom coordinates.

setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Sets the atom coordinates.

setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint

Sets the location

setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint

Sets the coordinates.

setLocation(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint

Sets the point's location.

setLogger(CalculatorLogger) - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder

setLogger(CalculatorLogger) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

setLogger(StructureCheckerLogger) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

Sets the logger.

setlogPMethod(int) - Method in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use {@link #setlogPMethod(LogPMethod))} instead.

setlogPMethod(int) - Method in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use logPPlugin.setlogPMethod(LogPMethod) instead.

setlogPMethod(LogPMethod) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the logP calculation method.

setlogPMethod(LogPMethod) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the logP calculation method.

setLogPTraining(InputStream) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the user defined logP training from a stream of parameters.

setLogPTrainingId(String) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the user defined logP training.

setLonely(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing lonely H

setLonePairAsLine(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility of Lone Pairs

setLonePairAutoCalc(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the state of the automatic lone pair calculation.

setLonePairsAsLines(boolean) - Method in class chemaxon.struc.graphics.MElectronContainer

setLonePairsAutoCalculated(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the state of the automatic calculation of lone pairs.

setLonePairsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides (implicit) lone pairs.

setLonePairsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility state of lone pairs.

setLowestEnergyConformerCalculation(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Switchs the lowest energy conformer calculation on/off.

setM(int, Molecule...) - Method in class chemaxon.marvin.beans.MViewPane

Sets the nth animation or structure.

setM(int, File, String) - Method in class chemaxon.marvin.beans.MViewPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by using MolImporter, then set the cell synchronously using MViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.

setM(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by using MolImporter, then set the cell synchronously using MViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.

setM(int, String, String) - Method in class chemaxon.marvin.beans.MViewPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.2.5, it is recommended to import the molecule in advance, e.g. by using MolImporter, then set the cell synchronously using MViewPane.setM(int, Molecule...). The reason is to simplify the public API and minimize the risk of related concurrency problems in user codes.

setMag(double) - Method in class chemaxon.marvin.beans.MSketchPane

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 2.8.1, replaced by setScale()

setMainMoleculeGraph(MoleculeGraph) - Method in class chemaxon.struc.MDocument

Sets the main molecule graph.

setMapped(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing mapped H

setMappingStyle(Mapper.MappingStyle) - Method in class chemaxon.standardizer.actions.MapAction

Sets Mapping Style for the underlying mapper.

setMappingStyle(Mapper.MappingStyle) - Method in class chemaxon.standardizer.actions.MapReactionAction

Sets Mapping Style for the underlying mapper.

setMappingStyle(Mapper.MappingStyle) - Method in class com.chemaxon.mapper.AutoMapper.Options

Default value Mapper.MappingStyle.COMPLETE

setMappingStyle(Mapper.MappingStyle) - Method in class com.chemaxon.mapper.AutoMapper

Sets the mapping style

setMappingStyle(Mapper.MappingStyle) - Method in interface com.chemaxon.mapper.Mapper

Sets the mapping style

setMarginInPt(double) - Method in class chemaxon.marvin.MolPrinter

Sets the Margin of the painted molecule.

setMarginSize(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the documents margin size.

setMarginSize(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the documents margin size.

setMarkBonds(boolean) - Method in class chemaxon.standardizer.actions.MapAction

Sets mark bonds for the underlying mapper.

setMarkBonds(boolean) - Method in class chemaxon.standardizer.actions.MapReactionAction

Sets mark bonds for the underlying mapper.

setMarkBonds(boolean) - Method in class com.chemaxon.mapper.AutoMapper.Options

Default value false

setMarkBonds(boolean) - Method in class com.chemaxon.mapper.AutoMapper

setMarkBonds(boolean) - Method in interface com.chemaxon.mapper.Mapper

Sets if the changing bonds should be marked or not.

setMarkushAromHandling(MarkushAromaticityHandlingOption) - Method in class chemaxon.sss.search.SearchOptions

Set handling of Markush aromatization information (ambiguous aromatic rings) during Markush search

setMarkushEnabled(boolean) - Method in class chemaxon.sss.search.MolSearchOptions

Sets whether targets containing Markush features should be treated as Markush libraries

setMarvinCompMode(boolean) - Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Marvin compatibility mode.

setMassno(int) - Method in class chemaxon.struc.MolAtom

Sets the mass number.

setMaxCols(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Set maximum value of columns in the table

setMaximum(int) - Method in interface chemaxon.common.util.MProgressMonitor

Gets the maximum value.

setMaximum(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setMaximumTautomerizationPathLength(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the maximum allowed length of the tautomerization path in chemical bonds.

setMaxIons(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

In case of pKaPlugin.MODEL_SMALL model, it sets the maximum number of ionizable atoms to be considered and uses simple calculation method to compute pKa values.

setMaxNumberOfConformers(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the maximum number of conformers to be calculated.

setMaxRepetitions(int) - Method in class chemaxon.struc.MolAtom

Sets the maximum number of repetitions for a link atom.

setMaxRows(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Set maximum value of rows in the table

setMaxSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Set the maximum number of molecules displayed in the table.

setMaxStereoisomerCount(int) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Sets the maxinum number of stereoisomers to be generated.

setMaxStructureCount(int) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets the maximum number of structures to be generated.

setMaxStructureCount(int) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the maximum number of structures to be generated.

setMaxStructureCount(long) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets the maximum number of structures to be generated.

setMaxThreadCount(int) - Method in class com.chemaxon.mapper.AutoMapper.Options

Default value Integer.MAX_VALUE
The number of threads used for mapping will be the minimum of maxThreadCount and the number of available processors.

setMeasure(RemoveFragmentAction.Measurement) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

Sets the measurement of the action

setMElectrons(MElectron[]) - Method in class chemaxon.struc.graphics.MElectronContainer

setMenu() - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets File/Edit menu.

setMenu(String[]) - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets File/Edit/View menu.

setMenuItem(JMenuItem, int) - Method in class chemaxon.marvin.swing.MAction

setMergedst(double) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the merge distance.

setMessage(String) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setMetalAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

This method sets the metalAtoms property

setMetalconnected(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing metal connected H

setMethod(RemoveFragmentAction.Method) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

Sets the method of the action

setMethod(TautomerizeAction.TautomerForm) - Method in class chemaxon.standardizer.actions.TautomerizeAction

setMethodName(String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Sets the method name to call

setMethylsRotatable(boolean) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

This is a speedup heuristics.

setMicropKaCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets micro pKa calculation.

setMinDistTryCount(int) - Method in class chemaxon.marvin.alignment.MinMaxDistance

setMinimum(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setMinimumCommonSize(int) - Method in class chemaxon.marvin.alignment.Alignment

Deprecated, for removal: This API element is subject to removal in a future version.

setMinimumCommonSize(int) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

Deprecated, for removal: This API element is subject to removal in a future version.

setMinimumCommonSize(int) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

setMinimumHeight(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the minimum height of the text..

setMinimumHeightSet(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Turns on/off minimum height calculation.

setMinRepetitions(int) - Method in class chemaxon.struc.MolAtom

Sets the minimum number of repetitions for a link node.

setMixSgroupMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Set options for mixed S-group matching.

setMMFF94(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the forcefield to MMFF94.

setMMFF94Optimization(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets MMFF94 optimization.

setMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.Alignment

setMode(AlignmentAccuracyMode) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setModel(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the calculation model.

setModified(boolean) - Method in class chemaxon.standardizer.Changes

Sets whether any modifications were applied on the molecule.

setMol(Molecule) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the molecule.

setMol(Molecule) - Method in class chemaxon.marvin.MolPrinter

Sets the current molecule and calculate its bounds.

setMol(Molecule, boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Deprecated, for removal: This API element is subject to removal in a future version.

use MSketchPane.setMol(Molecule) instead of this method.

setMol(File, String) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the molecule.

setMol(String) - Method in class chemaxon.marvin.beans.MSketchPane

Starts loading a molecule into the sketcher.

setMol(String) - Method in class chemaxon.marvin.MolPrinter

Sets the current molecule and calculate its bounds.

setMol(String, String) - Method in class chemaxon.marvin.beans.MSketchPane

Starts loading a molecule into the sketcher.

setMolbg(Color) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the molecule background color.

setMolBytes(byte[]) - Method in class chemaxon.marvin.io.MRecord

Sets the molecule bytes.

setMolCenter(int, String, DPoint3) - Method in class chemaxon.marvin.view.MDocStorage

Sets a molecule center.

setMolconvert(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

setMolecule(int, Molecule) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

Sets the molecule of the group at the provided index

setMolecule(int, Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Sets the molecule of the solvent at the provided index

setMolecule(int, Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Sets the molecule of the salt at the provided index

setMolecule(Molecule) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

setMolecule(Molecule) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method sets the molecule

setMolecule(Molecule) - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner

setMolecule(Molecule) - Method in interface chemaxon.checkers.runner.CheckerRunner

Sets the molecule to be checked by the checkers

setMolecule(Molecule) - Method in class chemaxon.checkers.runner.SketchCheckerRunner

Deprecated.

setMolecule(Molecule) - Method in class chemaxon.jep.context.MolContext

Sets the input molecule.

setMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MinMaxDistance

setMolecule(Molecule) - Method in interface chemaxon.marvin.calculations.HlbPlugin

Sets the input molecule.

setMolecule(Molecule) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Sets the Molecule which will be represented by the MTransferable.

setMolecule(Molecule) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable

Sets the Molecule which will be represented by the transferable.

setMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the input molecule after standardization.

setMolecule(Molecule) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setMolecule(Molecule) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets the molecule to be standardized by the standardizer actions

setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.ElementalAnalyser

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.Ring

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.stereo.Stereochemistry

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.TopologyAnalyser

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph, int) - Method in class chemaxon.calculations.Ring

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph, int) - Method in class chemaxon.calculations.TopologyAnalyser

Specifies a molecule to calculate with.

setMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the input molecule after an optional standardization.

setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.calculations.ChargePlugin

setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the input molecule after an optional standardization and/or modification.

setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

setMolecule(Smolecule) - Method in class chemaxon.calculations.ElementalAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.0, replaced by ElementalAnalyser.setMolecule(MoleculeGraph mol).

setMolecule(String) - Method in class chemaxon.calculations.ElementalAnalyser

Specifies a molecule to calculate with.

setMolecule(String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Specifies a molecule to calculate with.

setMoleculeCellSize(int, int) - Method in class chemaxon.marvin.beans.MViewParams

Sets the preferred size of the cells containing molecules.

setMoleculeIterator(MoleculeIterator) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the molecule iterator.

setMoleculeMovie(MMoleculeMovie) - Method in class chemaxon.struc.MDocument

Sets the molecule movie.

setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.marvin.alignment.Alignment

setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setMolecules(Molecule, Molecule) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the two molecular structures to be matched.

setMoleculeToAlign(Molecule, boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Sets the molecule to align to the reference.

setMolID(int) - Method in class chemaxon.marvin.alignment.AlignmentMolecule

setMolIndex(int) - Method in exception chemaxon.marvin.io.MolExportException

Sets the molecule index.

setMolNameFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the molecule name font size.

setMolNameShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets visibility of molecule names.

setMolPainter(int, String, MolPainter) - Method in class chemaxon.marvin.view.MDocStorage

Sets a molecule painter.

setMolString(String) - Method in class chemaxon.marvin.io.MRecord

setMolStrings(List<String>, boolean) - Method in class chemaxon.sss.screen.StrucFPConfig

setMolTemplate(Molecule) - Method in class chemaxon.marvin.MolPrinter

setMonomerTransform(boolean) - Method in class chemaxon.sss.search.SearchOptions

Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.

setMoreErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setMoreErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setMoreErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setMoreErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the more error message of the concerning checker

setMPLabelsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility state of M/P labels.

setMPVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the M/P display option.

setMPVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

setMrvWithSettings(String) - Method in class chemaxon.marvin.beans.MSketchPane

Deprecated, for removal: This API element is subject to removal in a future version.

use MSketchPane.setMol(String)

setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets microspecies calculation.

setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets calculation of microspecies distributions.

setMSLogic(Map<MRArrow, RxnMolecule>) - Method in class chemaxon.struc.RxnMolecule

Deprecated, for removal: This API element is subject to removal in a future version.

Multi-step reactions not supported. Method performs no operations.

setMultiplets(Multiplet[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets Multiplet array of the spectrum.

setMultiplier(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the multiplier.

setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the Na+, K+ concentration (default: 0.1).

setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the Na+, K+ concentration (default: 0.1).

setName(String) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the name of the NMR spectrum

setName(String) - Method in class chemaxon.calculations.pka.PKaTrainingResult

Sets the name

setName(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setName(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setName(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the checker name

setName(String) - Method in class chemaxon.fixers.AbstractStructureFixer

Deprecated, for removal: This API element is subject to removal in a future version.

setName(String) - Method in interface chemaxon.fixers.StructureFixer

Deprecated, for removal: This API element is subject to removal in a future version.

setName(String) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the fixer name

setName(String) - Method in class chemaxon.marvin.services.ServiceArgument

Sets the name of the argument

setName(String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Sets the name of the service

setName(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the name of the action

setName(String) - Method in class chemaxon.struc.Molecule

Sets the molecule name/title.

setName(String) - Method in class chemaxon.struc.RgMolecule

Sets the name of the root molecule.

setNameAndMnemonic(String) - Method in class chemaxon.marvin.swing.MAction

Sets the label and the mnemonic character.

setNameIOServiceURL(String) - Method in class chemaxon.marvin.common.UserSettings

setNameSpace(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Sets the namespace

setNavmode(String) - Method in class chemaxon.marvin.beans.MViewPane

Sets the mouse drag action.

setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

setNoErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setNoErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setNoErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setNoErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the no error message of the concerning checker

setNonQueryImplicitHcount(int) - Method in class chemaxon.struc.MolAtom

Sets the number of non-query implicit hydrogens attached.

setNormalized(boolean) - Method in class chemaxon.descriptors.MDParameters

Toggles the normalized flag of the current parametrized metric.

setNormalTautomerGenerationMode(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Generates only normal tautomers.

setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

setNucleus(NMRSpectrum.Nucleus) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Sets the NMR active nucleus.

setNumberOfAtomsAcceptToRotate(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

If only a given number of atoms (or less) can be found at one of the side of the dihedral skip this.

setNumberOfNMRActiveNuclei(int) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets number of the NMR active nuclei.

setObject(MObject, int) - Method in class chemaxon.struc.MDocument

Sets an object

setObject(MObject, int) - Method in class chemaxon.struc.MSelectionDocument

Sets an object

setObject(String, Object) - Method in class chemaxon.struc.MPropertyContainer

Sets a property object.

setObjectContainingSelection(MObject) - Method in class chemaxon.struc.MDocument

Sets the object that contains the selection.

setOccupied(int) - Method in class chemaxon.struc.graphics.MElectronContainer

setOccupied(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

setOeqcheck(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set oeqcheck parameter

SetOfSmallestRingsOption - Enum Class in chemaxon.sss.search.options

Option type describing the supported smallest set of rings used for property calculations.

setOKActionListener(ActionListener) - Method in class com.chemaxon.calculations.gui.PluginFactory

Sets the "OK" button pressed action listener.

setOneErrorMessage(String) - Method in class chemaxon.checkers.AbstractStructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setOneErrorMessage(String) - Method in class chemaxon.checkers.InvalidChecker

Deprecated, for removal: This API element is subject to removal in a future version.

setOneErrorMessage(String) - Method in interface chemaxon.checkers.StructureChecker

Deprecated, for removal: This API element is subject to removal in a future version.

This method isn't needed anymore and will be removed in 6.0

setOneErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the one error message of the concerning checker

setOnlyExpanded(boolean) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

setOptimization(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the optimization criteria for the calculation.

setOptimization(int) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the optimization criteria for lowest energy conformer calculation.

setOptimizeProjection(boolean) - Method in class chemaxon.marvin.calculations.GeometryPlugin

setOption(String, String) - Method in class chemaxon.sss.search.SearchOptions

Sets search options.

setOptions(DocumentAnnotatorOptions) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Sets the options used for document annotation.

setOptions(String) - Method in class chemaxon.marvin.io.formats.mdl.MolImport

Sets the import options.

setOptions(String) - Method in class chemaxon.marvin.io.MolImportModule

Sets the import options.

setOptions(String) - Method in class chemaxon.marvin.io.MRecordImporter

Sets the options for the import module.

setOptions(String) - Method in class chemaxon.sss.search.SearchOptions

Sets search options.

setOrder(int) - Method in class chemaxon.struc.graphics.MAssigner

Sets the order of an assigner.

setOrderSensitiveSearch(boolean) - Method in class chemaxon.sss.search.SearchOptions

Specifies whether the same set of target atoms found in a different order should be considered as a different hit.

setOrientationType(AlignmentProperties.OrientationType) - Method in class chemaxon.marvin.alignment.Alignment

setOriginal(Molecule) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

Sets the original molecule of the group.

setOriginalIds(int[]) - Method in class chemaxon.sss.search.RgDecompResults

setOrigTargetMayBeMarkush(boolean) - Method in class chemaxon.sss.search.MolSearch

Only for internal use!
Used for indicating that any bonds appeared after generating the generic tautomer of the target.

setOutput(File, String) - Method in class chemaxon.formats.MolConverter.Builder

Sets the output file.

setOutput(File, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

setOutput(OutputStream, String) - Method in class chemaxon.formats.MolConverter.Builder

Sets the output stream.

setOutput(OutputStream, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

setOutput(String, String) - Method in class chemaxon.formats.MolConverter.Builder

Sets the output file.

setOutput(String, String) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

setOutputFlags(int) - Method in class chemaxon.formats.MolConverter.Builder

Sets output flags.

setOutputFlags(int) - Method in class chemaxon.formats.MolConverter.Options

Deprecated, for removal: This API element is subject to removal in a future version.

setOutputIn3d(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

3D structures are generated (invalid 3D structure are filtered)

setOutputParameters(Object[]) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Prepares the output based on the result type string.

setOutputPrecision(int) - Method in class chemaxon.descriptors.MDParameters

Specifies the output precision for floating point values.

setOutputStream(OutputStream) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Sets the output stream.

setPageFormat(PageFormat, String) - Method in class chemaxon.marvin.common.UserSettings

setPageSettings(PageSettings) - Method in class chemaxon.struc.MDocument

Sets the page settings of multipage molecular document.

setParameter(String, String) - Method in class chemaxon.descriptors.DescriptorGenerator

Sets a parameter of the current descriptor configuration.

setParameters() - Method in class chemaxon.sss.search.MolSearch

setParameters() - Method in class chemaxon.sss.search.RGroupDecomposition

setParameters(CDParameters) - Method in class chemaxon.descriptors.CustomDescriptor

Sets parameters, allocates internal storage if needed and clears the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.BCUT

Sets the parameters of an already created BCUT object.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ChemicalFingerprint

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ECFP

Sets the parameters of an already created ECFP object.

setParameters(MDParameters) - Method in class chemaxon.descriptors.MolecularDescriptor

Sets the parameters for an already created MolecularDescriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ReactionFingerprint

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ScalarDescriptor

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(File) - Method in class chemaxon.descriptors.MDParameters

Sets parameters from an XML file representation overwriting all previous settings with the new ones.

setParameters(File) - Method in class chemaxon.descriptors.PFParameters

Sets parameters from an XML file representation overwriting all previous settings with the new ones.

setParameters(String) - Method in class chemaxon.descriptors.BCUT

Sets the parameters of an already created BCUT object.

setParameters(String) - Method in class chemaxon.descriptors.ChemicalFingerprint

Sets the parameters of an already created ChemicalFingerprint object.

setParameters(String) - Method in class chemaxon.descriptors.CustomDescriptor

Sets the parameters of an already created CustomDescriptor object.

setParameters(String) - Method in class chemaxon.descriptors.ECFP

Sets the parameters of an already created ECFP object.

setParameters(String) - Method in class chemaxon.descriptors.MDParameters

Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.

setParameters(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Sets the parameters for an already created MolecularDescriptor.

setParameters(String) - Method in class chemaxon.descriptors.PFParameters

Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.

setParameters(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Sets the parameters of an already created PharmacophoreFingerprint object.

setParameters(String) - Method in class chemaxon.descriptors.ReactionFingerprint

Sets the parameters of an already created ReactionFingerprint object.

setParameters(String) - Method in class chemaxon.descriptors.ScalarDescriptor

Sets the parameters of an already created ScalarDescriptor object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.HAcc

Sets the parameters of an already created HAcc object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.HDon

Sets the parameters of an already created HDon object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.Heavy

Sets the parameters of an already created HeavyAtomCount object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.LogD

Sets the parameters of an already created LogD object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.LogP

Sets the parameters of an already created LogP object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.Mass

Sets the parameters of an already created Mass object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.TPSA

Sets the parameters of an already created TPSA object.

setParameters(String) - Method in class chemaxon.descriptors.ShapeDescriptor

Sets the parameters of an already created ShapeDescriptor object.

setParameters(String) - Method in interface chemaxon.jep.MolCondition

Deprecated.

Sets condition parameters.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.ChargePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

setParameters(Properties) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.MSAPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Sets the input parameters for the plugin Accepted parameters: type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem| largestring|keep] Framework calculation type bmf: Bemis-Murcko framework bmfl: Bemis-Murcko loose framework mcs: Pairwise Maximum Common Substructure sssr: SSSR cssr: CSSR allringsystems: all fused ring systems largestringsystem: largest fused ring system largestring: largest ring keep: no framework reduction; useful for testing pre/post process keepsingleatom: [true|false] If set true then a single atom will be assigned to acyclic fragments.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Sets the parameter table.

setParameters(Properties) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Sets parameters.

setParams(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the parameter string.

setParent(Component) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the parent component.

setParentComponent(Component) - Method in class com.chemaxon.calculations.gui.PluginFactory

Sets the parent component - this is used to set options panes positions.

setParentMolecule(Molecule) - Method in class chemaxon.struc.Sgroup

Sets the parent molecule.

setParity(int[]) - Method in class chemaxon.struc.MoleculeGraph

Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.

setParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.

setParity(int, int) - Method in class chemaxon.struc.MoleculeGraph

Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity.

setPath(String) - Method in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

setPath(String) - Method in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader

Sets the base path of the configuration.

setPath(String) - Method in class chemaxon.standardizer.configuration.reader.StandardizerXMLReader

setPatternMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MolAligner

Sets pattern molecule and calculates its dimension

setPeakDomainMax(double[]) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the array of peak upper ends.

setPeakDomainMax(int, double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the upper end of the ith peak.

setPeakDomainMin(double[]) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the array of peak lower ends.

setPeakDomainMin(int, double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the lower end of the ith peak.

setPeptideDisplay(String) - Method in class chemaxon.marvin.MolPrinter

Sets the Peptide display settings.

setPeptideDisplayType(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the peptide displaying tpye.

setpH(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets a single pH value for the calculation of charge distribution.

setpH(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets a single pH value for the logD calculation.

setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.

setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.

setpH(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the pH value for the calculation of microspecies distributions.

setpH(double) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.0 pH effect is not considered

setpH(double) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the pH to be considered in dominant tautomer generation.

setPhaseShiftedMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Adjusts if the phase shifted polymer should match on the original.

setpHLower(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets pH lower limit for the calculation of microspecies distributions.

setpHLower(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets pH lower limit for the calculation of charge distribution (default: 0.0).

setpHLower(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets pH lower limit (default: 0.0).

setpHLower(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets pH lower limit for the calculation of microspecies distributions.

setpHStep(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets pH step for the calculation of microspecies distributions.

setpHStep(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets pH step for the calculation of charge distribution.

setpHStep(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets pH step to be taken between the pH lower and upper limits (default: 1.0).

setpHStep(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets pH step for the calculation of microspecies distributions.

setpHUpper(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Sets pH upper limit for the calculation of microspecies distributions.

setpHUpper(double) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets pH upper limit for the calculation of charge distribution (default: 14.0).

setpHUpper(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets pH upper limit (default: 14.0).

setpHUpper(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets pH upper limit for the calculation of microspecies distributions.

setPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the molecule piece.

setpKaCorrectionLibrary(InputStream) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the pKa correction library from a stream.

setpKaCorrectionLibrary(String) - Method in class chemaxon.marvin.calculations.logDPlugin

Sets the pKa correction library.

setpKaPrefixType(int) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets pKa prefix type (default: pKaPlugin.STATICpKaPREFIX) STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state

setPlainText(String) - Method in class chemaxon.struc.graphics.MTextDocument

Sets the document as plain text.

setPlugin(CalculatorPlugin) - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Sets the plugin object.

setPlugin(CalculatorPlugin) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Deprecated, for removal: This API element is subject to removal in a future version.

use CalculatorPluginOutput.setPluginChecked(CalculatorPlugin) instead

setPlugin(CalculatorPlugin) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Deprecated, for removal: This API element is subject to removal in a future version.

use CalculatorPluginDisplay.setPluginChecked(CalculatorPlugin) instead

setPluginChecked(P) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Sets the calculator plugin object.

setPluginChecked(P) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the plugin.

setPMAPTagName(String) - Method in class chemaxon.descriptors.PFGenerator

Sets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.

setPMAPTagName(String) - Method in class chemaxon.descriptors.PFParameters

Sets the name of the pharmacophore map tag to be considered in the input SDfile.

setPointed(boolean) - Method in class chemaxon.struc.graphics.MElectron

setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the points.

setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MPolyline

Sets the points.

setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MTextBox

Sets the points.

setPolymerendgroup(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing polymer end group H

setPolymerMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Adjust polymer matching.

setPopupMenusEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Allows popup menus.

setPortName(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Sets the port name

setPos(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the data display DASP position (0...9).

setPosition(int, double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the position of the ith NMR line.

setPreferredSize(Dimension) - Method in class chemaxon.marvin.beans.MViewPane

Sets the preferred size of the component.

setPreferredWidth(double) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the preferred width of the text-box.

setPrehydrogenize(boolean) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Turns the prehydrogenization on/off.

setPreprocessor(ConcurrentStandardizerProcessor.MolTransformer) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the preprocessor.

setPrintEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Set the accessibility of the Print menu item in the File menu.

setPriority(int) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the fixer priority.

setProductAtomsByMap(MolAtom[]) - Method in class chemaxon.jep.context.ReactionContext

Deprecated.

use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> product atom array.

setProducts(Molecule[]) - Method in class chemaxon.jep.context.ReactionContext

Deprecated.

Use ReactionContext.setReaction(RxnMolecule) instead. Sets the products.

setProgress(int) - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

Sets a progress observer to be used in AlignmentPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets a progress observer to be used in ConformerPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Sets a progress observer to be used to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Sets a progress observer to be used in IsoelectricPointPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets a progress observer to be used in MolecularDynamicsPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets a progress observer to be used in pKaPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets a progress observer to be used in ResonancePlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Sets a progress monitor to be used in StereoisomerPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets a progress observer to be used in TautomerizationPlugin.run() to display progress status.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Sets the progress monitor.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.io.MRecordImporter

Sets the progress monitor.

setProgressMonitor(MProgressMonitor) - Method in interface chemaxon.marvin.io.MRecordReader

Sets the progress monitor.

setProgressMonitor(MProgressMonitor) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Sets a progress observer to be used in CalculatorPlugin.run() to display progress status.

setProgressValue(int) - Method in interface chemaxon.common.util.MProgressMonitor

Set progress.

setProperties(Properties) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Sets display properties of the Molecule.

setProperties(Properties) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable

Sets display properties of the Molecule.

setProperty(AlignmentProperties) - Method in class chemaxon.marvin.alignment.Alignment

setProperty(AlignmentProperties) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setProperty(String, String) - Method in class chemaxon.marvin.common.UserSettings

Sets a property for the given key with the given value.

setProperty(String, String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Sets a descriptor property

setProperty(String, String) - Method in class chemaxon.struc.Molecule

Sets an RDfile/SDfile property.

setProperty(String, String, boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets a property for the given key with the given value.

setPropertyObject(String, Object) - Method in class chemaxon.struc.Molecule

Sets an RDfile/SDfile property object.

setProtectAllTetrahedralStereoCenters(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the protection of all tetrahedral stereo centers: if true then all tetrahedral stereo information is preserved by the tautomer generator.

setProtectAromaticity(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets aromaticity protection: if true then aromatic bonds are not modified by the tautomer generator.

setProtectCharge(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets charge protection: if true then the charge of charged atoms are not modified by the tautomer generator.

setProtectDoubleBondStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Sets double bond stereo protection: if true then the stereo configuration of double bonds with preset stereo information will not be changed.

setProtectDoubleBondStereo(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets double bond stereo protection: if true then double bonds stereo information is preserved by the tautomer generator.

setProtectDoubleBondStereo(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Sets double bond stereo protection.

setProtectEsterGroups(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the protection of ester groups: if true then ester groups are excluded from the tautomerization.

setProtectLabeledTetrahedralStereoCenters(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets the protection of labeled tetrahedral stereo centers: if true then labeled tetrahedral stereo centers are protected by the tautomer generator.

setProtectTetrahedralStereo(boolean) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Sets the protection of tetrahedral stereo centers: if true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed.

setProtectTetrahedralStereo(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Sets the protection of tetrahedral stereo centers.

setProximity(AlignmentProperties.ProximityPotentialType) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setPruneIn(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set prunein parameter

setPruneOut(boolean) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set pruneout parameter

setQProp(String, int) - Method in class chemaxon.struc.MolAtom

Sets a query property as an integer.

setQProp(String, Object) - Method in class chemaxon.struc.MolAtom

Sets a query property.

setQuery(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setQuery(AlignmentMolecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

setQuery(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setQuery(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setQuery(Molecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

setQuery(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setQuery(Molecule) - Method in class chemaxon.sss.search.MarkushGenerator

Sets the query.

setQuery(Molecule) - Method in class chemaxon.sss.search.MolComparator

Loads the query molecule into this comparator.

setQuery(Molecule) - Method in class chemaxon.sss.search.MolSearch

setQuery(Molecule) - Method in class chemaxon.sss.search.RgDecompResults

setQuery(Molecule) - Method in class chemaxon.sss.search.RGroupDecomposition

Specifies the query structure to search for.

setQuery(Molecule) - Method in class chemaxon.sss.search.Search

Specifies the query structure to search for.

setQuery(Molecule) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the query structure.

setQuery(Molecule) - Method in interface com.chemaxon.search.SimpleSearcher

Sets the query structure of the searcher.

setQuery(Molecule, int[]) - Method in class chemaxon.sss.search.MolSearch

setQuery(Molecule, int[]) - Method in class chemaxon.sss.search.Search

Specifies the query structure to search for.

setQuery(Molecule, int[]) - Method in interface com.chemaxon.search.SimpleSearcher

Sets the query structure of the searcher with excluded atoms.

setQuery(String) - Method in class chemaxon.sss.formula.FormulaSearch

Sets the chemical formula query string used for searching

setQuery(String) - Method in class chemaxon.sss.search.MolSearch

Specifies the query structure to search for in String format.

setQueryAbsoluteStereo(boolean) - Method in class chemaxon.sss.search.MolSearchOptions

Sets whether the chiral flag should be ignored or not for the query molecule.

setQueryAromaticity(int) - Method in class chemaxon.struc.MolAtom

Sets the aromatic/aliphatic query property.

setQueryAtom(MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Sets the atom to be searched for by the action (the query atom)

setQueryCode(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the program code for the query option.

setQueryFingerprint(T) - Method in class chemaxon.descriptors.SimilarityCalculator

Sets the query fingerprint

setQueryMode(boolean) - Method in class chemaxon.formats.MolImporter

Sets query mode.

setQueryMode(boolean) - Method in class chemaxon.marvin.io.MRecordImporter

Sets the query mode.

setQueryOp(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the data query operator.

setQueryRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setQueryRigidForced(boolean) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

Set this molecule to be rigid in the input conformation even if it contains rotatable bonds

setQueryRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setQuerystr(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Assigns the query properties string to this atom while setting all necessary atom and query properties.

setQuerystr(MolAtom, String, int) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Assigns the query properties string to this atom while setting all necessary atom and query properties.

setQuerystr(String) - Method in class chemaxon.struc.MolAtom

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s) and MolAtom.setQueryString(String).

setQuerystr(String) - Method in class chemaxon.struc.QueryBond

Sets the query string.

setQuerystr(String, int) - Method in class chemaxon.struc.MolAtom

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options) and MolAtom.setQueryString(String).

setQueryString(String) - Method in class chemaxon.struc.MolAtom

Assigns the query string to this atom.

setRadical(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing radical H

setRadical(int) - Method in class chemaxon.struc.MolAtom

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.2. Use MolAtom.setRadicalValue(AtomProperty.Radical) instead.

setRadicalMatching(int) - Method in class chemaxon.sss.search.SearchOptions

Set the radical matching mode.

setRadicalValue(AtomProperty.Radical) - Method in class chemaxon.struc.MolAtom

Sets the radical value.

setRadius(double) - Method in class chemaxon.struc.graphics.MElectron

setRadius(double) - Method in class chemaxon.struc.graphics.MElectronContainer

Sets Radius for all MElectrons

setRandomEnumeration() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets random enumeration.

setRandomSeed(long) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets the random seed to be used in case of random enumeration.

setRandomSeed(long) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the random seed value.

setRange(double, double) - Method in class com.chemaxon.calculations.gui.MChart

setRangeDecimalCount(int) - Method in class com.chemaxon.calculations.gui.MChart

setRationalTautomerGenerationMode(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

setReactantAtomsByMap(MolAtom[]) - Method in class chemaxon.jep.context.ReactionContext

Deprecated.

use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> reactant atom array.

setReactants(Molecule[]) - Method in class chemaxon.jep.context.ReactionContext

Deprecated.

Use ReactionContext.setReaction(RxnMolecule) instead. Sets the reactants.

setReaction(RxnMolecule) - Method in class chemaxon.jep.context.ReactionContext

Sets the reaction.

setReactionArrow(DPoint3...) - Method in class chemaxon.struc.RxnMolecule

Sets the endpoint coordinates of the reaction arrow.

setReactionArrow(DPoint3[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the reaction arrow.

setReactionArrow(MRArrow) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow.

setReactionArrow0(DPoint3...) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow.

setReactionArrowEndPoints(DPoint3[]) - Method in class chemaxon.struc.RxnMolecule

Sets the endpoints of the reaction arrow in this reaction.

setReactionArrowType(int) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow type.

setReactionArrowType(String) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow type from type name.

setReactionSmarts(String) - Method in class chemaxon.checkers.SubstructureChecker

Sets the reactionSmarts

setReactionStereo(int) - Method in class chemaxon.struc.MolAtom

Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.

setReactionSupport(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Allows or disallows reaction drawing.

setReactionUnpairedMapMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Set option for matching unpaired(orphan or widow) atom maps to any atom.

setRecordIDBackground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane

Highlights a record by setting the background of its identifier field.

setRecordIDForeground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane

Highlights a record by setting the foreground of its identifier field.

setReference(double[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy

sets the coordinates of the reference molecule directly If this used the AlignRigidEasy.getReferenceAndRotatedFused() cannot be applied

setReference(Molecule) - Method in class chemaxon.marvin.alignment.AlignRigidEasy

sets the reference molecule which remains intact

setReferenceMolecule(Molecule, boolean) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

Sets the reference molecule to align to.

setRendering(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the rendering style.

setRendering(String) - Method in class chemaxon.marvin.MolPrinter

Sets the rendering style of atoms and bonds.

setRepeatingUnitAtom(MolAtom, boolean) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Adds or removes an atom to/from the list of paradigmatic repeating unit atoms.

setReplaceAtom(MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Sets the atom to replaced with by the action

setRequestMethod(JsonServiceDescriptor.Method) - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor

Sets the HTTP method of the request.

setResidueAtomId(int) - Method in class chemaxon.struc.MolAtom

Sets the residue atom identifier.

setResidueSeq(int) - Method in class chemaxon.struc.MolAtom

Sets the residue sequence number.

setResidueType(int) - Method in class chemaxon.struc.MolAtom

Sets the residue type.

setResourceDirectory(File) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

Set the directory where resources will be stored.

setRestH(int) - Method in class chemaxon.struc.RgMolecule

Sets the restH condition on an R-group definition.

setReturnTypes(Class<?>[]) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Sets the array of return types

setRgroup(int) - Method in class chemaxon.struc.MolAtom

Sets the R-group ID.

setRgroupAttachmentPointOrder(int) - Method in class chemaxon.struc.MolAtom

Sets the attachment point order of an R-group attachment point.

setRgroupsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides R-group definitions.

setRgroupsVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets whether the R-group definitions are visible.

setRHLB(boolean) - Method in interface chemaxon.marvin.calculations.HlbPlugin

User can inquire the so called rHLB value.

setRightMargin(double) - Method in class chemaxon.struc.PageSettings

setRightName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom

Set the string that will be shown at the right side of the molecule.

setRingBondCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects ring bond count atom query properties or not.

setRingChainTautomerizationAllowed(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets if ring tautomers are allowed or not.
Default true

setRingCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects ring count atom query properties or not.

setRingFlexibility(int, int) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

If BOTH the two parameters is true for the ring then the ring is treated flexible.

setRLigandEqualityCheck(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets whether undefined R-atoms with the same R-group ID should match the same structure.

setRlogic(int, int) - Method in class chemaxon.struc.RgMolecule

Sets R-logic flags.

setRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule

Sets R-logic occurrence range.

setRLogicVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Set R-logic visibility.

setRLogicVisible(String) - Method in class chemaxon.marvin.common.UserSettings

Sets R-logic visibility

setRoot(Molecule) - Method in class chemaxon.struc.RgMolecule

Sets the root structure.

setRotatable(double[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy

sets the coordinates of the rotatable molecule directly If this used the AlignRigidEasy.getReferenceAndRotatedFused() and AlignRigidEasy.getRotatedMolecule() cannot be applied

setRotatable(Molecule) - Method in class chemaxon.marvin.alignment.AlignRigidEasy

sets the molecule to translate and rotate during the alignment

setRotation(double, double, double, double) - Method in class chemaxon.struc.CTransform3D

Sets the rotation components.

setRotationCenter(DPoint3) - Method in class chemaxon.struc.CTransform3D

Sets the rotation center.

setRowAndColumn0(int) - Method in class chemaxon.struc.graphics.MTextBox

setRowCount(int) - Method in class chemaxon.marvin.beans.MViewParams

Sets the total nuber of rows.

setRowCount(int) - Method in class chemaxon.struc.PageSettings

setRowHeight(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the row height.

setSaltID(int, String) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Sets the name of the salt at the provided index

setSampleHighlightOn(boolean) - Method in class com.chemaxon.calculations.gui.MChart

setSampleLabels(String[]) - Method in class com.chemaxon.calculations.gui.MChart

setSampleValues(double[][]) - Method in class com.chemaxon.calculations.gui.MChart

setSamplingAccuracy(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Set sampling accuracy.

setSamplingAccuracy(AtropIsomerDetector.Accuracy) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Set sampling accuracy.

setSamplingInterval(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Number of trajectory frames to be stored from the sampling start time to the end of calculation.

setSamplingStart(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the beginning of trajectory sampling.

setSaveBOM(boolean) - Method in class chemaxon.marvin.common.UserSettings

setSaveGUIPropertiesInMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets whether the GUI properties should be saved when saving as a Marvin file

setSaveIniEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enables or disables automatic preference saving.

setSaveLoadZoomFactorToMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings

Tells wether to save the zoom factor information to mrv files or not.

setScale(double) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the scale factor and changes magnification of the canvas.

setScale(double) - Method in class chemaxon.marvin.MolPrinter

Sets the scale factor in units of regular bond length.

setScale(double) - Method in class chemaxon.struc.CTransform3D

Sets the scale factor.

setScaleFactor(float) - Method in class chemaxon.descriptors.MDParameters

Sets scaleFactor used with the current parametrized metrics.

setScalingHypothesis(MolecularDescriptor) - Method in class chemaxon.descriptors.MDParameters

Sets (stores) the specified scaling hypothesis.

setScreeningConfiguration(String) - Method in class chemaxon.descriptors.MolecularDescriptor

Sets the screening configuration.

setSDFColoring(String, Properties) - Method in class chemaxon.marvin.view.swing.TableSupport

Sets SDF coloring.

setSearchAll(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects all R-atoms or not.

setSearchBridgehead(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for bridgehead explicit hydrogens

setSearchCharged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for charged explicit hydrogens

setSearchContracted(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Sets the checker should search for contracted abbreviated groups or not

setSearchDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker

Sets checker to detect valence properties with the default valence of the current atom type.

setSearchDisconnected(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms not connected to any other atoms or not.

setSearchExpanded(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Sets the checker should search for expanded abbreviated groups or not

setSearchGeneric(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms without identifier numbers or not.

setSearchHConnected(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for H connected explicit hydrogens

setSearchIsotopic(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for isotopic explicit hydrogens

setSearchLinker(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms with more than one connection or not.

setSearchLonely(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for lonely explicit hydrogens

setSearchMapped(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for mapped explicit hydrogens

setSearchMode(SearchMode) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the search mode that controls the running time and the accuracy of the algorithm.

setSearchNested(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms within R-groups or not.

setSearchNonDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker

Sets checker to detect valence properties with non-default valence of the current atom type.

setSearchOptions(MolSearchOptions) - Method in class chemaxon.sss.search.MolComparator

setSearchOptions(MolSearchOptions) - Method in class chemaxon.sss.search.MolSearch

Sets search options.

setSearchOptions(MolSearchOptions) - Method in class chemaxon.sss.search.RGroupDecomposition

setSearchOptions(SearchOptions) - Method in class chemaxon.sss.search.MarkushGenerator

Copies all search parameters from options.

setSearchOptions(SearchOptions) - Method in class chemaxon.sss.search.RgDecompResults

setSearchOptions(SearchOptions) - Method in class chemaxon.sss.search.Search

Sets search options.

setSearchOptions(String) - Method in class chemaxon.standardizer.advancedactions.TransformAction

Sets the search options of the action

setSearchPolymerEndGroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for polymer end group explicit hydrogens

setSearchRadical(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for radical explicit hydrogens

setSearchSgroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for S-group explicit hydrogens

setSearchSgroupEnd(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for S-group end explicit hydrogens

setSearchType(int) - Method in class chemaxon.sss.formula.FormulaSearch

Sets the type of the formula search.

setSearchValenceError(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for valence errored explicit hydrogens

setSearchWedged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for wedged explicit hydrogens

setSelectable(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Enables the user to select a cell by clicking on it or using the cursor movement keys.

setSelected(boolean) - Method in class chemaxon.struc.graphics.MChemicalStruct

Selects or unselects the object.

setSelected(boolean) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Selects or unselects the object.

setSelected(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Selects or unselects the text box.

setSelected(boolean) - Method in class chemaxon.struc.MObject

Selects or unselects the object.

setSelected(boolean) - Method in class chemaxon.struc.MolAtom

Selects or unselects this atom.

setSelected(boolean) - Method in class chemaxon.struc.NoStructure

Sets whether this NoStructure is selected.

setSelected(MoleculeGraph, boolean) - Static method in class chemaxon.struc.graphics.MChemicalStruct

Selects or unselects atoms in a molecule graph.

setSelectedAtoms(int, String, int[]) - Method in class chemaxon.marvin.view.MDocStorage

Sets the selected atom indices.

setSelectedAtoms(int, String, String) - Method in class chemaxon.marvin.view.MDocStorage

Sets the selected atom indices.

setSelectedFields(String[]) - Method in class chemaxon.marvin.view.swing.TableOptions

Set selected fields array in Table Options dialog box

setSelectedIndex(int) - Method in class chemaxon.marvin.beans.MViewPane

Selects a molecule.

setSelectedPage(int) - Method in class chemaxon.struc.PageSettings

setSeparator(String) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Sets the separator string.

SETSEQ_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom set sequence number is currently 63.

SETSEQ_MAX - Static variable in class chemaxon.struc.MolBond

Maximum bond set sequence number.

SETSEQ_OFF - Static variable in class chemaxon.struc.MolBond

Bond set sequence number offset in flags.

setSeriesColors(Color[]) - Method in class com.chemaxon.calculations.gui.MChart

setServicesConfigurationPath(String) - Method in class chemaxon.jep.Evaluator

Sets the custom services configuration path.

setServicesConfigURL(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the URL of the configuration for Services in marvin

setSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.3, replaced by setAtomSetColor

setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enable or disable atom/bond set coloring.

setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.MolPrinter

Colors atoms and bonds according to the color of the pre-defined set they belong to.

setSetSeq(int) - Method in class chemaxon.struc.MolAtom

Sets the atom set sequence number.

setSetSeq(int) - Method in class chemaxon.struc.MolBond

Sets the bond set.

setSetSeq(int, int, int) - Method in class chemaxon.marvin.beans.MViewPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.3, replaced by setAtomSetSeq

setSeverity(CheckerSeverity) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the severity of the concerning checker

setSgroup(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing s-group H

setSgroupDataFormatted(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets if the Sgroup data to be formatted.

setSgroupDataFormatted(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets if the Sgroup data to be formatted.

setSgroupend(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing s-group end H

setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.Sgroup

Sets the molecule graph.

setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Sets the molecule graph.

setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.Molecule

Sets or unsets an S-group as a parent of an atom.

setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule

Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.

setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule

Sets or unsets an S-group as a parent of an atom in reactants, products or agents.

setShapeData(ShapeData) - Method in class chemaxon.descriptors.ShapeDescriptor

setShift(double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the chemical shift.

setShift(double) - Method in class chemaxon.calculations.nmr.Shift

Sets the chemical shift.

setShiftError(double) - Method in class chemaxon.calculations.nmr.Multiplet

Sets the estimated error of the chemical shift.

setShiftError(double) - Method in class chemaxon.calculations.nmr.Shift

Sets the error (confidence interval radius) of the shift.

setShiftErrorClassification(NMRCoefficient.ErrorClassification) - Method in class chemaxon.calculations.nmr.Multiplet

Sets error classification of the chemical shift.

setShifts(Shift[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets chemical shifts.

setShowMultiMoleculeOnEditSource(boolean) - Method in class chemaxon.marvin.common.UserSettings

setSimpView(int) - Method in class chemaxon.marvin.beans.MSketchPane

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.5, replaced by MSketchPane.setBondDraggedAlong(boolean)

setSingleCellLabelShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions

Tests whether label should be shown for a single cell.

setSingleUpOrDownBond(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction

Sets the single wedge value of absolute stereo action

setSize(int) - Method in class chemaxon.marvin.view.MDocStorage

Sets the total number of entries.

setSketchAnyBond(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default any bond drawing style in the sketcher.

setSketchArrowHeadLength(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow head length.

setSketchArrowHeadWidth(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow head width.

setSketchArrowTailLength(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow tail length.

setSketchArrowTailWidth(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow tail width.

setSketchCarbonVisibility(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default carbon visibility style in the sketcher.

setSketchColorScheme(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the sketcher's default color scheme.

setSketchImplicitH(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the display method of implicit hydrogens for the sketcher.

setSketchLigandOrderVisibility(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default ligand order visibility style in the sketcher.

setSketchLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the load working directory for MarvinSketch load filechooser.

setSketchMode(int) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the sketching mode.

setSketchMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the sketcher's default 2D molecule background color.

setSketchMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the sketcher's default 3D molecule background color.

setSketchRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than UserSettings.MAX_RECENT_FILE_LIST_SIZE then the size will be the value of UserSettings.MAX_RECENT_FILE_LIST_SIZE

setSketchRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 2D sketcher.

setSketchRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 3D sketcher.

setSketchSaveWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings

Not implemented yet, don't use it.

setSkip(int, double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the distance of the (visible) head or tail from the corresponding line end point.

setSkipsToEndPoints() - Method in class chemaxon.struc.graphics.MEFlow

setSmallestRingSizeChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects smallest ring size atom query properties or not.

setSMARTS(MolAtom, String) - Static method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Sets SMARTS query string data.

setSMARTS(String) - Method in class chemaxon.struc.MolAtom

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.7, replaced by SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)

setSmartsQueryChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects SMARTS query properties or not.

setSMILESFontSize(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the SMILES font size.

setSMILESShown(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions

Set visibility of SMILES strings.

setSolventID(int, String) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Sets the name of the solvent at the provided index

setSolventRadius(double) - Method in class chemaxon.marvin.calculations.MSAPlugin

Sets solvent radius.

setSpecIsotopeSymbolPreferred(boolean) - Method in class chemaxon.struc.MolAtom

Sets special isotope symbol usage preference.

setSrgoups(List<Sgroup>) - Method in class chemaxon.checkers.result.SgroupCheckerResult

This method sets the groups property

setSSRType(SetOfSmallestRingsOption) - Method in class chemaxon.sss.search.SearchOptions

Sets which type of set of smallest rings to use for property calculations

setStandardizer(Standardizer) - Method in class chemaxon.descriptors.DescriptorGenerator

Sets the standardizer object to be used during descriptor generation.

setStandardizer(Standardizer) - Method in class chemaxon.sss.search.MarkushGenerator

Sets standardizer object of this MolSearch class, to be used for the query and target molecules, Chemical Terms configuration and re-standardization of query tautomers at tautomer searching.

setStandardizer(Standardizer) - Method in class chemaxon.sss.search.MolSearch

Sets the standardizer to be used for query and target molecules and re-standardization of query tautomers in case of tautomer substructure search.

setStandardizer(Standardizer) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the standardizer that will be used for performing standardizations.

setStartAt(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Set the index number of the molecule that is the first to be displayed.

setStartEnd(MolAtom, MPoint) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Sets the atoms.

setStartPosition(long) - Method in class chemaxon.struc.MDocument

Sets the starting position of this document in the input file.

setStartPosition(long) - Method in class chemaxon.struc.Molecule

Sets the starting position of this molecule in the input file.

setStartupSelectorShown(boolean) - Method in class chemaxon.marvin.common.UserSettings

setStepLimit(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setStepNumber(int) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the number of simulation steps.

setStepTime(double) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Sets the simulation timestep.

setStereo2Flags(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond

Sets double bond stereo information.

setStereoFontRatio(float) - Method in class chemaxon.marvin.MolPrinter

Sets the ratio of the font size of the stereo label compared to the normal atom label size.

setStereoGroupNumber(int) - Method in class chemaxon.struc.MolAtom

Sets the stereochemical group number for AND and OR groups of the enhanced stereo representation.

setStereoGroupType(int) - Method in class chemaxon.struc.MolAtom

Sets the stereochemical group type for enhanced stereo representation.

setStereoisomerismType(int) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Sets which type of stereoiseomers should be generated.

setStereoisomerType(EnumSet<StereoisomerSettings.StereoisomerType>) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Sets which types of stereoisomers should be generated.

setStereoModel(int) - Method in class chemaxon.sss.search.SearchOptions

Set stereo model option.

setStereoSearchType(int) - Method in class chemaxon.sss.search.SearchOptions

Specifies the way stereo information is considered during searching.

setStickdst(double) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the sticking distance.

setStickThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the stick thickness.

setStickThickness(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the stick diameter for ball and stick mode.

setStickThickness(double) - Method in class chemaxon.marvin.MolPrinter

Sets the 3D stick's diameter.

setStoichiometry(String) - Method in class chemaxon.standardizer.actions.ExpandAction

Sets the stoichiometry value of the action

setStoreAppliedTaskData(boolean) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

If set, then applied task data is stored and can be retrieved with methods ConcurrentStandardizerProcessor.getAppliedTaskIDs(), ConcurrentStandardizerProcessor.getAppliedTaskIndexes(), ConcurrentStandardizerProcessor.getInputMolecule().

setString(String, String) - Method in class chemaxon.struc.MPropertyContainer

Sets a property.

setStructure(String) - Method in class chemaxon.standardizer.advancedactions.TransformAction

Deprecated, for removal: This API element is subject to removal in a future version.

use TransformAction.setTransform(RxnMolecule) method instead

setStructureID(String) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Sets structure ID to be used in Markush code generation.

setSubscript(String) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the subscript.

setSubscript(String) - Method in class chemaxon.struc.Sgroup

Sets the subscript for non-superatom S-groups.

setSubsetChangable(boolean) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets whether startAt and maxSize can be changed.

setSubstitutionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects substitution count atom query properties or not.

setSubType(int) - Method in class chemaxon.struc.Sgroup

Sets polymer S-group subtype.

setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Sets the given molecule as the supergraph of this graph.

setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Sets the given molecule as the supergraph of this graph and its components.

setSupplier(Supplier<Molecule>) - Method in class chemaxon.jep.context.MolContext

setSurfaceAreaType(int) - Method in class chemaxon.marvin.calculations.MSAPlugin

Sets surface area calculation type: MSAPlugin.VAN_DER_WAALS or MSAPlugin.SOLVENT.

setSwitchOffAllProtectsForTDF(boolean) - Method in class chemaxon.sss.search.MolSearchOptions

Deprecated, for removal: This API element is subject to removal in a future version.

Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.

setSymbolTable(SymbolTable) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Use Evaluator.compile(String, Class, ConstantTable) instead.

setSymmetricalFuzzy(boolean) - Method in class chemaxon.descriptors.PFParameters

setSymmetryFiltering(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.

setSymmetryFiltering(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.

setT(int, int, String) - Method in class chemaxon.marvin.view.MDocStorage

Sets a text field in a record.

setT(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets a text field in a GridBagView table.

setTabScale(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the magnification in the molecule cells.

setTag(char) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the tag character for the footnote display.

setTags(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the tags of the action

setTailCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the tail crossing bonds.

setTakeCanonicalForm(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets whether canonical form should be taken.

setTakeCanonicalForm(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets whether canonical form should be generated.

setTakeDominantTautomers(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets whether dominant tautomers should be generated.

setTakeFullTautomerizationSpectrum(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets to consider the full tautomer distribution upon the macro pka calculation.

setTakeGenericTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets whether generic tautomer should be generated.

setTakeGenericTautomer(boolean, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

setTakeMajorContributors(boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Sets whether major contributors should be taken.

setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use logPPlugin.setConsiderTautomerization(boolean)

setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Sets to use major tautomeric form in calculation.

setTakeMajorTatomericForm(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Use pKaPlugin.setConsiderTautomerization(boolean)

setTakeMajorTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets whether major tautomer should be generated.

setTakeMostStableTautomer(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

Call TautomerizationPlugin.setTakeMajorTautomer(boolean) instead.

setTakePartialNeutralization(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets if partial neutralization prior to canonical tauotmer generation is allowed or not.

setTakeResonantStructures(boolean) - Method in class chemaxon.marvin.calculations.ChargePlugin

Sets calculation with resonant structures.

setTakeResonantStructures(boolean) - Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin

Sets calculation with resonant structures.

setTakeStandardForm(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

For internal use only.

setTarget(Molecule) - Method in class chemaxon.sss.search.MolComparator

Loads the target molecule into this comparator.

setTarget(Molecule) - Method in class chemaxon.sss.search.MolSearch

setTarget(Molecule) - Method in class chemaxon.sss.search.RGroupDecomposition

Specifies the target molecule to search in.

setTarget(Molecule) - Method in class chemaxon.sss.search.Search

Specifies the target molecule.

setTarget(Molecule) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the target structure.

setTarget(Molecule) - Method in interface com.chemaxon.search.SimpleSearcher

Sets the target structure of the searcher.

setTarget(Molecule, int[]) - Method in class chemaxon.sss.search.MolSearch

setTarget(Molecule, int[]) - Method in class chemaxon.sss.search.Search

Specifies the target molecule with excluded atoms.

setTarget(Molecule, int[]) - Method in interface com.chemaxon.search.SimpleSearcher

Sets the target structure of the searcher with excluded atoms.

setTarget(String) - Method in class chemaxon.sss.formula.FormulaSearch

Sets the chemical formula target string used to search in

setTargetAbsoluteStereo(boolean) - Method in class chemaxon.sss.search.MolSearchOptions

Sets whether the chiral flag should be ignored or not for the target molecule.

setTargetGroup(String) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setTargetGroup(String) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets the target group of standardizer action of the runner

setTargetGroups(String...) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

setTargetGroups(String...) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Sets the target groups of standardizer action of the runner

setTargetHomologyMatchingMode(TargetHomologyMatchingMode) - Method in class chemaxon.sss.search.SearchOptions

Sets the target homology matching mode option.

setTargetMolecule(Molecule) - Method in class chemaxon.marvin.alignment.MolAligner

Sets target molecule and calculates its dimension

setTargetRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

setTargetRigidForced(boolean) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

Set this molecule to be rigid in the input conformation even if it contains rotatable bonds

setTargetRigidForced(boolean) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

setTargets(Molecule[]) - Method in class chemaxon.sss.search.MarkushGenerator

Sets the targets.

setTargets(Molecule[]) - Method in class chemaxon.sss.search.RgDecompResults

setTautomerEqualityMode(TautomerEqualityMode) - Method in class chemaxon.sss.search.MolSearchOptions

Internal use only.

setTautomerSearch(int) - Method in class chemaxon.sss.search.SearchOptions

Sets if tautomers of the query should be enumerated for search.

setTCenter(int) - Method in class chemaxon.struc.graphics.MRectangle

Sets the transformed point.

setTemperature(double) - Method in class chemaxon.marvin.calculations.pKaPlugin

Sets the temperature (default: 298 Kelvin).

setTemplates(Molecule[]) - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

Sets the clean templates of the action

setTerminalBondDeletionStyle(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond deletion style.

setTerms(List<MAnalysisBoxTerm>) - Method in class chemaxon.struc.graphics.MAnalysisBox

setText(String) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the text.

setText(String) - Method in class chemaxon.struc.graphics.MTextBox

Sets the text.

setThickness(double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the line thickness.

setThreadCount(int) - Method in class chemaxon.formats.MolConverter

Sets the number of threads for concurrent processing.

setThreadCount(int) - Method in class chemaxon.formats.MolExporter

Sets the number of threads for concurrent processing.

setThreadCount(int) - Method in class chemaxon.formats.MolImporter

Sets the number of threads for concurrent processing.

setThreadCount(int) - Method in class chemaxon.marvin.io.MRecordImporter

Sets the number of threads for concurrent processing.

setThreshold(float) - Method in class chemaxon.descriptors.MDParameters

Sets the value of the threshold of the current parametrized metric.

setThrowable(Throwable) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Sets the throwable object.

setThrowExceptionOnTimeout(boolean) - Method in class chemaxon.sss.search.SearchOptions

Sets if search should throw exception upon timeout.

setTimelimit(int) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Sets the timelimit for the calculation.

setTimeLimit(double) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets an upper time limit for the canonical tautomer generation.

setTimeLimit(int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms

setTimeLimit(long) - Method in class com.chemaxon.mapper.AutoMapper

setTimeLimit(long) - Method in interface com.chemaxon.mapper.Mapper

Sets time limit for calculation.

setTimeLimit(long) - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure

Sets the maximum allowed time for MCS search.

setTimeoutInSeconds(int) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Set time out.

setTimeoutLimitMilliseconds(int) - Method in class chemaxon.sss.search.SearchOptions

The search on a single target timeouts reaching this amount of time.

setTitle(String) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the frame title.

setTitle(String) - Method in class com.chemaxon.calculations.gui.MChart

setTopLeftIndex(int) - Method in class chemaxon.marvin.beans.MViewPane

Scrolls to the specified cell.

setTopLevelContainer(Container) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the top level container (JFrame, JDialog, etc) of the pane.

setTopMargin(double) - Method in class chemaxon.struc.PageSettings

setTopMolViewer(Molecule) - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets molecule viewer in top-left corner.

setTopMolViewer(Molecule, String) - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets molecule viewer in top-left corner.

setTopologyConstraint(int) - Method in class com.chemaxon.search.mcs.buildup.BuildupMcs

Sets the maximum difference in topology the mapped part of the molecules can have.

setTopTextArea(String) - Method in class chemaxon.marvin.plugin.gui.ResultView

Sets text area in top-left corner.

setTOption(int) - Method in class chemaxon.struc.graphics.MRectangle

Sets the transformation options.

setTraditionalNitrogenAllowed(boolean) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

setTraining(String) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the user defined training.

setTrainingResults(InputStream) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets the user defined training from a stream.

setTransfer(Transferable) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Sets the Transferable which contains the Molecule that should be retrieved.

setTransfer(Transferable) - Method in interface chemaxon.marvin.modules.datatransfer.MTransferable

Sets the Transferable for importing Molecule from that.

setTransform(RxnMolecule) - Method in class chemaxon.standardizer.advancedactions.TransformAction

Sets the transformation

setTransformationEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Enable/disable transformation

setTransformer(Transformer) - Method in class chemaxon.sss.search.MolSearch

Sets the Transformer to be used for query and target standardization.

setTranslation(double, double, double) - Method in class chemaxon.struc.CTransform3D

Sets the translation components (CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).

setTranslation(DPoint3) - Method in class chemaxon.struc.CTransform3D

Sets the translation components (CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).

setTransparent(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the transparency state of the painting.

setTraverse(boolean) - Method in class chemaxon.jep.ChemJEP

Deprecated, for removal: This API element is subject to removal in a future version.

Use Evaluator.setVerbose(boolean) instead before creating the ChemJEP.

setType(int) - Method in class chemaxon.checkers.AromaticityErrorChecker

setType(int) - Method in class chemaxon.struc.graphics.MBracket

Sets the bracket type.

setType(int) - Method in class chemaxon.struc.graphics.MRArrow

Sets the type of this arrow.

setType(int) - Method in class chemaxon.struc.MolBond

Sets bond type and does valence checking for the endpoints.

setType(StructuralFrameworksPlugin.FrameworkTypes) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Set framework type to calculate.

setType(AbsoluteStereoAction.Type) - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

Sets the type of absolute stereo action

setType(AromatizeAction.Type) - Method in class chemaxon.standardizer.actions.AromatizeAction

Sets the type of aromatization

setType(ConvertDoubleBondsAction.Type) - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

Sets the type of action

setType(SetHydrogenIsotopeSymbolAction.Type) - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

Sets the type of action

setType(Clean2DAction.Type) - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

Sets the type of action

setType(Class<T>) - Method in class chemaxon.marvin.services.ServiceArgument

Sets the class of the argument

setType(String) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Sets the type value of the action

setTypes(List<String>) - Method in class chemaxon.checkers.AtomTypeChecker

Sets the checked atom types

setUndefinedRAtom(int) - Method in class chemaxon.sss.search.SearchOptions

Sets the matching behavior of an undefined R atom in the query.

setUndefinedRAtomUserDefined(boolean) - Method in class chemaxon.sss.search.SearchOptions

For internal use only!

setUndo(int) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the maximum undo depth.

setUnit(DipoleResult.Unit) - Method in class chemaxon.calculations.dipole.DipoleResult

Sets the dipole moment unit, see DipoleResult.Unit.

setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Sets NMR spectrum unit.

setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the unit type.

setUnitDisplayed(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets whether the units string should be displayed.

setUnits(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the unit of this data field.

setUnsaturationChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects unsaturation atom query properties or not.

setUpperLeftPoint(DPoint3) - Method in class chemaxon.struc.PageSettings

setURL(String) - Method in class chemaxon.marvin.services.ServiceDescriptor

Sets the service URL

setUseAllAtoms(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

setUseDefaultSalts(boolean) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

Sets whether default salt dictionary should be used

setUseDefaultSolvents(boolean) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Sets whether default solvent dictionary should be used

setUseOriginal(boolean) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

Deprecated, for removal: This API element is subject to removal in a future version.

always false: Molecule is always converted before alignment, but coordinates are written back to the original one.

setUsePMAP(boolean) - Method in class chemaxon.descriptors.PFGenerator

Omit or use pharmacophore map data optionally available in molecular structure.

setUsePMAP(String) - Method in class chemaxon.descriptors.PFParameters

Pharmacophore map data in imported Molecule-s should be used.

setUserSettings(UserSettings) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the user settings object.

setUserTypes(String) - Method in class chemaxon.marvin.calculations.logPPlugin

Sets user types.

setVagueBondLevel(int) - Method in class chemaxon.sss.search.SearchOptions

Option for less strict evaluation of query bonds (e.g.

setValenceCheckEnabled(boolean) - Method in class chemaxon.struc.MoleculeGraph

Enables or disables valence check on this molecule graph, depending on the value of the parameter b.

setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.MoleculeGraph

Sets the options for valence checking.

setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.RgMolecule

setValenceCheckState(MoleculeGraph.ValenceCheckState) - Method in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.0, replaced by MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) and MoleculeGraph.setValenceCheckEnabled(boolean).
Usage:

             // Same as setValenceCheckState(ValenceCheckState.OFF):
             setValenceCheckEnabled(false);
             // Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED):
             setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             // Same as setValenceCheckState(ValenceCheckState.FULL):
             setValenceCheckOptions(ValenceCheckOptions.GLOBAL);
             

setValenceerror(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing valence error H

setValenceError(boolean) - Method in class chemaxon.struc.MolAtom

Sets or clears the valence error flag.

setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Shows or hides valence errors

setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide valence errors

setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the visibility state of valence errors.

setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Shows or hides valence errors

setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide valence errors in MarvinView

setValenceMatching(boolean) - Method in class chemaxon.sss.search.SearchOptions

Set valence check option.

setValenceProp(int) - Method in class chemaxon.struc.MolAtom

Sets the valence property.

setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets atom valence property visibility.

setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.MolPrinter

Sets the atom valence propertiy visibility

setValid(boolean) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Sets the validity of the standardizer action.

setvalidateSgroupsAtCreation(boolean) - Method in class chemaxon.marvin.common.UserSettings

Set the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.

setValue(T) - Method in class chemaxon.marvin.services.ServiceArgument

Sets the service argument value

setVerbose(boolean) - Method in class chemaxon.jep.Evaluator

Sets verbose mode.

setVerbose(boolean) - Method in class chemaxon.sss.search.Search

For debugging purposes only.

setVerbose(boolean) - Method in class chemaxon.sss.search.SearchOptions

For debugging purposes only.

setVerify3d(boolean) - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Invalid 3D structures of generated stereoisomers are filtered.

setVerticalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the vertical alignment.

setViewAnyBond(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default any bond drawing style in the viewer.

setViewAtomMarkEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets atom mark and highlight visibility in Marvin View.

setViewCarbonVisibility(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default carbon visibility style in the viewer.

setViewColorScheme(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the viewer's default color scheme.

setViewHandlerType(int) - Method in class chemaxon.marvin.view.swing.TableOptions

Sets the view handler type.

setViewImplicitH(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the display method of implicit hydrogens for the viewer.

setViewLayout(int) - Method in class chemaxon.marvin.common.UserSettings

Set the layout of MarvinView.

setViewLigandOrderVisibility(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the default ligand order visibility style in the viewer.

setViewLoadWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the load working directory for MarvinView load filechooser.

setViewMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the default molecule background color for the 2D viewer.

setViewMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the default molecule background color for the 3D viewer.

setViewNavmode2d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the navigation mode for the 2D viewer.

setViewNavmode3d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the navigation mode for the 3D viewer.

setViewRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than 10 then the size will be 10.

setViewRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 2D viewer.

setViewRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 3D viewer.

setViewSaveWorkingDir(String) - Method in class chemaxon.marvin.common.UserSettings

Not implemented, don't use it.

setVisibleRows(int) - Method in class chemaxon.marvin.beans.MViewParams

Sets the nuber of visible rows.

setWebServiceName(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Sets the webservice name

setWedged(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing wedged H

setWeightOfMethods(double, double, double, double) - Method in class chemaxon.marvin.calculations.logDPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

This function will not be available from May 2016. Use logDPlugin.setlogPMethod(LogPMethod) instead.

setWeightOfMethods(double, double, double, double) - Method in class chemaxon.marvin.calculations.logPPlugin

Deprecated, for removal: This API element is subject to removal in a future version.

This function will not be available from May 2016. Use logPPlugin.setlogPMethod(LogPMethod) instead.

setWeights(double[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Sets the atom weights for location calculation.

setWeights(float[]) - Method in class chemaxon.descriptors.MDParameters

Sets the cell-wise weight factors for the current parametrized metric.

setWeights(float[], float[]) - Method in class chemaxon.descriptors.PFParameters

Sets the cell-wise weight factors for the current parametrized metric.

setWidth(double) - Method in class chemaxon.struc.PageSettings

setWigglyBondVisibility(boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Sets how wiggly bonds connected to double bonds are displayed.
For internal use only.

setWinScale(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the magnification in the zoom windows.

setWireThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the line thickness for wireframe mode.

setWireThickness(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond thickness in wireframe mode.

setWireThickness(double) - Method in class chemaxon.marvin.MolPrinter

Sets the line thickness for wireframe mode.

setWord(ByteBuffer, int, int) - Method in class chemaxon.marvin.io.PositionedInputStream

setWorkerThreadCount(int) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the number of worker threads.

setWsdlURI(String) - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Sets the WSDL URI

setX(double) - Method in class chemaxon.struc.MolAtom

Sets the X coordinate.

setX(double) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the X coordinate.

setXMLTokens(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the XML tokens of the action

setXState(int) - Method in class chemaxon.struc.Sgroup

Sets the expanded/contracted state.

setXState(int, int) - Method in class chemaxon.struc.Sgroup

Deprecated.

as of Marvin 6.2, use Sgroup.setXState(int) instead

setXState0(int) - Method in class chemaxon.struc.Sgroup

setXY(double, double) - Method in class chemaxon.struc.MolAtom

Sets the x and y coordinates.

setXYZ(double, double, double) - Method in class chemaxon.struc.MolAtom

Sets the coordinates.

setY(double) - Method in class chemaxon.struc.MolAtom

Sets the Y coordinate.

setY(double) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the Y coordinate.

setZ(double) - Method in class chemaxon.struc.MolAtom

Sets the Z coordinate.

setZero() - Method in class chemaxon.struc.CTransform3D

Sets all components to zero.

setZoomToScaffoldOnLoad(boolean) - Method in class chemaxon.marvin.common.UserSettings

severity() - Element in annotation interface chemaxon.checkers.CheckerInfo

Returns the severity of the checker

SEVERITY - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

severity of checker

Sg - Static variable in class chemaxon.core.ChemConst

Sgroup - Class in chemaxon.struc

Structural group representation in the molecule.

Sgroup(Molecule, int) - Constructor for class chemaxon.struc.Sgroup

Deprecated.

As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType).

Sgroup(Molecule, int, int) - Constructor for class chemaxon.struc.Sgroup

Deprecated.

As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType) and Sgroup.setXState(int).

Sgroup(Molecule, SgroupType) - Constructor for class chemaxon.struc.Sgroup

Sgroup(Molecule, SgroupType, int) - Constructor for class chemaxon.struc.Sgroup

Sgroup(Sgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.Sgroup

Copy constructor.

Sgroup(Sgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.Sgroup

Copy constructor.

SGROUP - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of an Sgroup.

SGROUP_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which is the only atom in an Sgroup.

SGROUP_SGROUP_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants

This String represents the key of cloned sgroup, original sgroup map

SGROUP_TYPE_COUNT - Static variable in class chemaxon.struc.Sgroup

Number of S-group types.

SGROUP_TYPENAMES - Static variable in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Array of S-group type names.

SgroupAtom - Class in chemaxon.struc.sgroup

S-group superatom.

SgroupAtom(SuperatomSgroup) - Constructor for class chemaxon.struc.sgroup.SgroupAtom

Constructs a superatom for a superatom type S-group.

SgroupCheckerResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.

SgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.SgroupCheckerResult

Constructor which initialize all the properties.

SGROUPEND_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which have a neighbor that is in a SuperatomSgroup.

sgroupGraph - Variable in class chemaxon.struc.Sgroup

The S-group's internal structure.

SgroupIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.SgroupIterator

Constructs an s-group iterator for the specified molecule of the factory.

sgroupList - Variable in class chemaxon.marvin.io.formats.mdl.MolImport

sgroupType - Variable in class chemaxon.struc.Sgroup

The S-group type.

SgroupType - Enum Class in chemaxon.struc

Enum of possible sgroup types.

SHAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

ShapeData - Class in chemaxon.marvin.alignment

ShapeDescriptor - Class in chemaxon.descriptors

Shape descriptor implements a 3D alignment based similarity calculation.

ShapeDescriptor() - Constructor for class chemaxon.descriptors.ShapeDescriptor

ShapeDescriptor(ShapeDescriptor) - Constructor for class chemaxon.descriptors.ShapeDescriptor

Copy constructor.

ShapeDescriptor(ShapeParameters) - Constructor for class chemaxon.descriptors.ShapeDescriptor

Creates a new instance of ShapeDescriptor according to the parameters given.

ShapeDescriptor(String) - Constructor for class chemaxon.descriptors.ShapeDescriptor

Creates a new instance of ShapeDescriptor according to the parameters given.s

ShapeGenerator - Class in chemaxon.descriptors

ShapeGenerator(AlignmentProperties.ColoringScheme) - Constructor for class chemaxon.descriptors.ShapeGenerator

ShapeParameters - Class in chemaxon.descriptors

ShapeParameters() - Constructor for class chemaxon.descriptors.ShapeParameters

ShapeParameters(File) - Constructor for class chemaxon.descriptors.ShapeParameters

ShapeParameters(String) - Constructor for class chemaxon.descriptors.ShapeParameters

Creates a new object based on a given configuration string.

Shift - Class in chemaxon.calculations.nmr

NMR chemical shift class.

Shift(int, double) - Constructor for class chemaxon.calculations.nmr.Shift

Constructor.

SHORTCUTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "shortcuts".

shortestPath(int, int) - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the shortest topological path (number of bonds) between two atoms.

shortName() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

shortName() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory

shortName() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory

Returns the name of category.

SHOW_SETS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "showSets".

showDialog() - Method in class chemaxon.marvin.view.swing.TableOptions

Bring up Table Options dialog box

showErrorDialog(String, Throwable) - Method in class chemaxon.marvin.beans.MarvinPane

Show error dialog.

showFileDialog(String, Molecule) - Method in class chemaxon.marvin.beans.MarvinPane

Shows an Open or Save file dialog.

showFileOpenDialog() - Method in class chemaxon.marvin.beans.MarvinPane

Shows file open dialog.

showFormalCharge(Set<FormulaGenerationRule>) - Static method in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Returns true if the formal charge should be shown at the end of the formula based on the given rules.

showSelectedNodes() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

showStartupSelector() - Method in class chemaxon.marvin.beans.MSketchPane

This method is used in startup time to throw up a skin selector dialog.

Si - Static variable in class chemaxon.core.ChemConst

similarity(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

similarity(AlignmentMolecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

similarity(AlignmentMolecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

similarity(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseAlignment

similarity(Molecule) - Method in interface chemaxon.marvin.alignment.PairwiseComparison

Calculates the 3D similarity between the previously set query and the target.

similarity(Molecule) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D

Similarity - Class in chemaxon.sss.screen

Calculates the similarity of two bit strings.

Similarity() - Constructor for class chemaxon.sss.screen.Similarity

SIMILARITY - Static variable in interface chemaxon.sss.SearchConstants

Similarity search.

SimilarityCalculator<T> - Class in chemaxon.descriptors

Descriptor similarity calculation can be performed using SimilarityCalculator.

SimilarityCalculator() - Constructor for class chemaxon.descriptors.SimilarityCalculator

SimilarityCalculatorFactory - Class in chemaxon.descriptors

This factory creates a similarity calculator object according to the user defined parameters.

SimilarityCalculatorFactory.Representation - Enum Class in chemaxon.descriptors

SimilarityException - Exception in chemaxon.descriptors

similarityNode - Variable in class chemaxon.descriptors.MDParameters

node holding the similarity calculations related parameters

SIMPLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType

SIMPLE_VIEW - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "simpView".

SimpleSearcher - Interface in com.chemaxon.search

Search interface for different Molecule-Molecule search types.

SimpleSearcherFactory - Class in com.chemaxon.search

Factory for creating SimpleSearcher instances.

SimpleSearcherFactory() - Constructor for class com.chemaxon.search.SimpleSearcherFactory

simplifyIncompleteReactionToMolecule() - Method in class chemaxon.struc.RxnMolecule

Simplify a reaction to a molecule if possible.

simplifyMolecule() - Method in class chemaxon.struc.MDocument

Simplifies the main molecule object if possible.

simplifyToMolecule() - Method in class chemaxon.struc.RxnMolecule

Simplifies this RxnMolecule by moving the atoms and bonds from the reactants, products, and agents to a Molecule.

Single - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type

Indicates, that the structure checker puts all structures to the output file.

SINGLE - Enum constant in enum class chemaxon.struc.BondType

Single bond type.

SINGLE - Static variable in class chemaxon.struc.MolBond

Single bond type.

SINGLE_OR_AROMATIC - Enum constant in enum class chemaxon.struc.BondType

Single or aromatic query bond type.

SINGLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond

Single or aromatic query bond type.

SINGLE_OR_DOUBLE - Enum constant in enum class chemaxon.struc.BondType

Single or double query bond type.

SINGLE_OR_DOUBLE - Static variable in class chemaxon.struc.MolBond

Single or double query bond type.

sinkIsAtom() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's sink is an atom.

sinkIsBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's sink is a bond.

sinkIsIncipBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's sink is an incipient bond.

size() - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Gets the total number of elements.

size() - Method in class chemaxon.struc.MPropertyContainer

Gets the total number of properties.

size() - Method in class chemaxon.struc.prop.MHashProp

Gets the table size.,

size() - Method in class chemaxon.struc.prop.MListProp

Gets the array size.

size(int) - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Gets the size of list at the specified level.

sizeToString(double) - Static method in class chemaxon.struc.graphics.MFont

Converts an integer or fractional size to a string.

SKC - Static variable in class chemaxon.formats.MFileFormat

SKC file format

SKETCH_ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "sketchAnyBond".

SKETCH_ARROW_HEAD_LENGTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "sketchArrowHeadLength".

SKETCH_ARROW_HEAD_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "sketchArrowHeadWidth".

SKETCH_ARROW_TAIL_LENGTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "sketchArrowTailLength".

SKETCH_ARROW_TAIL_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "sketchArrowTailWidth".

SKETCH_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "sketchCarbonVisibility".

SKETCH_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "sketchHelp".

SKETCH_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "sketchLigandOrderVisibility".

SKETCH_STARTUP_SHOWN - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

SKETCHABLE - Static variable in class chemaxon.marvin.beans.MViewPane

Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinSketch in a new window.

SketchCheckerRunner - Class in chemaxon.checkers.runner

Deprecated, for removal: This API element is subject to removal in a future version.

SketchCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.SketchCheckerRunner

Deprecated.

Initiate a SketchCheckerRunner instance which will can execute StructureChecker instances read from configurationReader

SKETCHPANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

SKETCHPANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

SketchParameterConstants - Class in chemaxon.marvin.sketch

Parameters of MarvinSketch Applet and Bean.
The parameters of the JMSketch applet can be set using the <param> HTML tag.

SKIN - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "skin".

skip(long) - Method in class chemaxon.marvin.io.PositionedInputStream

Skips over and discards n bytes of data.

SKIP - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy

In case of standardization error the output does not contain the molecule

SKIP_COORDINATE_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory

Exclude coordinate bonds from bond iteration.

SKIP_COVALENT_BONDS - Static variable in class chemaxon.util.iterator.IteratorFactory

Exclude covalent bonds from bond iteration.

SKIP_EXPLICIT_H - Static variable in class chemaxon.util.iterator.IteratorFactory

Exclude explicit hydrogens from atom iteration.

SKIP_LONE_PAIR - Static variable in class chemaxon.util.iterator.IteratorFactory

Exclude lone pairs from atom iteration.

SKIP_MULTICENTER - Static variable in class chemaxon.util.iterator.IteratorFactory

Exclude multicenters from atom iteration.

SKIP_PSEUDO_ATOM - Static variable in class chemaxon.util.iterator.IteratorFactory

Exclude pseudo atoms from atom iteration.

skipLine() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Skips the next line.

skipLine() - Method in class chemaxon.marvin.io.PositionedInputStream

Skips the next line.

skipRecord() - Method in class chemaxon.formats.MolImporter

Skips the next molecule or document instead of reading it into memory.

skipRecord() - Method in class chemaxon.marvin.io.ArrayMDocSource

Skips the next document.

skipRecord() - Method in class chemaxon.marvin.io.MDocSource

Skips the next document.

skipRecord() - Method in class chemaxon.marvin.io.MRecordImporter

Skips the next document.

skipRecord() - Method in interface chemaxon.marvin.io.MRecordReader

Skips the next record.

skipRecord() - Method in class chemaxon.marvin.plugin.PluginMDocSource

Skips the next document.

skipRecords(int, int, MProgressMonitor, int, Runnable) - Method in class chemaxon.marvin.io.MDocSource

Sm - Static variable in class chemaxon.core.ChemConst

SM_ATOM - Static variable in class chemaxon.marvin.beans.MSketchPane

Atom mode.

SM_BOND - Static variable in class chemaxon.marvin.beans.MSketchPane

Bond mode.

SM_DELETE - Static variable in class chemaxon.marvin.beans.MSketchPane

Delete mode.

SM_FLAGS_OFF - Static variable in class chemaxon.marvin.beans.MSketchPane

Offset of flags in sketch mode.

SM_MASK - Static variable in class chemaxon.marvin.beans.MSketchPane

Sketch mode mask.

SM_SELECT - Static variable in class chemaxon.marvin.beans.MSketchPane

Select mode.

SM_SELECT_LASSO - Static variable in class chemaxon.marvin.beans.MSketchPane

Lasso select mode.

SMALL_RING - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that small ring error had found in the molecule

smallestRing() - Method in class chemaxon.calculations.Ring

Identifies the smallest ring (number of atoms) in the molecule.

smallestRing() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.smallestRing()

smallestRingSize() - Method in class chemaxon.calculations.Ring

Calculates the size of the smallest ring in the molecule.

smallestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.smallestRingSize()

smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.Ring

Calculates the size of the smallest ring an atom is a member of.

smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.smallestRingSizeOfAtom(int)

smallestRingSystem() - Method in class chemaxon.calculations.Ring

Identifies the smallest ring system (number of rings) in the molecule.

smallestRingSystem() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.smallestRingSystem()

smallestRingSystemSize() - Method in class chemaxon.calculations.Ring

Calculates the size of the smallest ring system (number of rings) in the molecule.

smallestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Ring.smallestRingSystemSize()

SMARTS - Static variable in class chemaxon.formats.MFileFormat

SMARTS.

SMARTS_H_DAYLIGHT_COMP_MODE - Static variable in class chemaxon.struc.MolAtom

Option flag to express daylight-type smarts atom parsing of H.

SMARTS_H_MARVIN_COMP_MODE - Static variable in class chemaxon.struc.MolAtom

Option flag to express marvin-pre-3.5-type smarts atom parsing of H.

SmartsAtomQuerifier - Class in chemaxon.marvin.io.formats.smiles

Class for partial interpretation of smarts atoms.

SmartsAtomQuerifier() - Constructor for class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier

Creates a new SmartsAtomQuerifier object.

SMILES - Static variable in class chemaxon.formats.MFileFormat

SMILES.

SMILESRecognizer - Class in chemaxon.formats.recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

SMILESRecognizer() - Constructor for class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated.

smol() - Method in class chemaxon.struc.MoleculeGraph

Gets a Smolecule representation of this molecule.

Smolecule - Interface in chemaxon.struc

Array-based molecule interface.

Sn - Static variable in class chemaxon.core.ChemConst

SoapServiceDescriptor - Class in chemaxon.marvin.services.soap

Service descriptor of SOAP type requests.

SoapServiceDescriptor() - Constructor for class chemaxon.marvin.services.soap.SoapServiceDescriptor

SoapServiceHandler - Class in chemaxon.marvin.services.soap

Service handler for SOAP type requests.

SoapServiceHandler() - Constructor for class chemaxon.marvin.services.soap.SoapServiceHandler

SolubilityCalculator - Class in com.chemaxon.calculations.solubility

Solubility calculator.
API usage example:

SolubilityCalculator() - Constructor for class com.chemaxon.calculations.solubility.SolubilityCalculator

SolubilityCalculator(FragmentBasedSolubilityParameters) - Constructor for class com.chemaxon.calculations.solubility.SolubilityCalculator

Constructor.

SolubilityCategories - Class in com.chemaxon.calculations.solubility

Array of solubility categories.

SolubilityCategories(SolubilityCategory[], SolubilityUnit) - Constructor for class com.chemaxon.calculations.solubility.SolubilityCategories

Constructor.

SolubilityCategories.UndefinedSolubilityCategory - Class in com.chemaxon.calculations.solubility

Undefined category.

SolubilityCategory - Interface in com.chemaxon.calculations.solubility

Interface for solubility categories.

SolubilityResult - Interface in com.chemaxon.calculations.solubility

Solubility prediction result.

SolubilityUnit - Enum Class in com.chemaxon.calculations.solubility

Solubility unit.

SOLVENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that solvent had found in the molecule

SOLVENT - Static variable in class chemaxon.marvin.calculations.MSAPlugin

Surface area type: 3D solvent accessible surface area.

SOLVENT_AMBIGOUS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that more than one type of solvents had found in the molecule

SOLVENT_ID_PROPERTY - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Property key for solvent ID

SOLVENT_LIST_KEY - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Property key for solvent list modification

SolventChecker - Class in chemaxon.checkers

SolventChecker detects common solvents in multicomponent structures.

SolventChecker() - Constructor for class chemaxon.checkers.SolventChecker

Default constructor

sort(Sgroup[], int) - Static method in class chemaxon.struc.Sgroup

Sorts S-groups in parent-child or child-parent order.

SORT_CHILD_PARENT - Static variable in class chemaxon.struc.Sgroup

Parent-child sort order.

SORT_PARENT_CHILD - Static variable in class chemaxon.struc.Sgroup

Parent-child sort order.

sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Sorts bonds in the same order as they appear in another chemical graph.

sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RgMolecule

Sort edges in the same order as they appear in the specified array.

sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RxnMolecule

Sort edges in the same order as they appear in the specified array.

sortSgroupXBonds() - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.12, no replacement.
Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.

sortXBonds() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 5.12, no replacement.
Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.

SOURCE_TEXT - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the source text, as it appears in the original document.

sourceIsAtom() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's source is an atom.

sourceIsBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's source is a bond.

SPHERIC - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

SPIN - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "spin".

SPLASH_SCREEN_IMAGE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "splashScreenImage".

splitAllDisconnectedComponents() - Method in class chemaxon.struc.RxnMolecule

Replaces all disconnected reaction components by its connected fragments in the structure array.

splitComponentParts(MoleculeGraph, int) - Method in class chemaxon.struc.RxnMolecule

Finds those component parts that are contained in the molecule graph m and creates separate components from the fragments contained in m, splitting them from the previous merges.

splitDisconnectedComponent(int, int) - Method in class chemaxon.struc.RxnMolecule

Replaces a disconnected reaction component by its connected fragments in the structure array.

splitDisconnectedComponent(long) - Method in class chemaxon.struc.RxnMolecule

Replaces a disconnected reaction component by its connected fragments in the structure array.

splitFileAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil

Parses "file{options}" strings used in molecule file import.

splitFormatAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil

Parses "format:options" strings used in molecule file import and export.

Spreadsheet - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView

Sr - Static variable in class chemaxon.core.ChemConst

sringsize() - Method in class chemaxon.struc.MolAtom

Calculate the size of smallest ring containing this atom.

SRU - Enum constant in enum class chemaxon.struc.SgroupType

sssr - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

SSSR - Enum constant in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption

Smallest set of smallest rings.

SST_ALTERNATING - Static variable in class chemaxon.struc.Sgroup

Alternating polymer S-group subtype.

SST_BLOCK - Static variable in class chemaxon.struc.Sgroup

Block polymer S-group subtype.

SST_RANDOM - Static variable in class chemaxon.struc.Sgroup

Random polymer S-group subtype.

ST_AMINOACID - Static variable in class chemaxon.struc.Sgroup

Amino acid s-group type.

ST_ANY - Static variable in class chemaxon.struc.Sgroup

Any polymer S-group type.

ST_COMPONENT - Static variable in class chemaxon.struc.Sgroup

Component S-group type.

ST_COPOLYMER - Static variable in class chemaxon.struc.Sgroup

Copolymer S-group type.

ST_CROSSLINK - Static variable in class chemaxon.struc.Sgroup

Crosslink S-group type.

ST_DATA - Static variable in class chemaxon.struc.Sgroup

Data S-group type.

ST_FORMULATION - Static variable in class chemaxon.struc.Sgroup

Formulation S-group type.

ST_GENERIC - Static variable in class chemaxon.struc.Sgroup

Generic S-group type.

ST_GRAFT - Static variable in class chemaxon.struc.Sgroup

Graft S-group type.

ST_MER - Static variable in class chemaxon.struc.Sgroup

Mer S-group type.

ST_MIXTURE - Static variable in class chemaxon.struc.Sgroup

Mixture S-group type.

ST_MODIFICATION - Static variable in class chemaxon.struc.Sgroup

Modification S-group type.

ST_MONOMER - Static variable in class chemaxon.struc.Sgroup

Monomer S-group type.

ST_MULTICENTER - Static variable in class chemaxon.struc.Sgroup

Multicenter S-group type.

ST_MULTIPLE - Static variable in class chemaxon.struc.Sgroup

Multiple group S-group type.

ST_SRU - Static variable in class chemaxon.struc.Sgroup

SRU (Structural Repeating Unit: polymers and repeating units with repetition ranges) S-group type.

ST_SUPERATOM - Static variable in class chemaxon.struc.Sgroup

Superatom S-group type.

standardize() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Performs the standardization of the next input molecule, and returns the standardized molecule.

standardize() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

standardize() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Invoke a background thread which will run all standardizer actions on the given molecule

standardize(MolImporter, MolExporter, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner

Reads the molecules from the importer, standardizes them, and writes to the exporter.

standardize(Molecule) - Method in class chemaxon.descriptors.MDParameters

Standardizes the Molecule and returns the standardized form.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.AlignmentPlugin

standardize(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Prevents default standardization: does nothing.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Clears enhanced stereo information.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Standardize input molecule
Standardization currently ungroups SGroups

standardize(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).

standardize(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Calls AbstractStandardizerAction.standardize1(Molecule)
If molecule has more components AbstractStandardizerAction.standardize1(Molecule) is invoked on all components instead of the molecule itself.
If AbstractStandardizerAction.standardize1(Molecule) doesn't return a not null Change object for the molecule or for any of the components the value of the returned changes object's Changes.isModified() property is set based on whether molecule's MoleculeGraph.getGrinvCC() property value has changed during the standardization action.

standardize(Molecule) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

standardize(Molecule) - Method in class chemaxon.standardizer.Standardizer

Standardization for one input molecule: performs the standardization actions according to the XML configuration.

standardize(Molecule) - Method in interface chemaxon.standardizer.StandardizerAction

Standardizes the provided molecule.
Logs of standardization should be generated to a System.Logger, that can be collected by using StandardizerLogger.getLogger() method.

standardize1(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction

This method contains the current standardization mechanism.

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AddExplicitHydrogensAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AliasToAtomAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AliasToGroupAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AromatizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ClearIsotopesAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ClearStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ContractSgroupsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertPiMetalBondsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.DearomatizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.DisconnectMetalAtomsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ExpandAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MapAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MapReactionAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MesomerizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.NeutralizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RearrangeReactionAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAbsoluteStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAtomValuesAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAttachedDataAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveRGroupDefinitionsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveStereoCareBoxAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.SetAbsoluteStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.TautomerizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.UnmapAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.WedgeCleanAction

standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.Clean3DAction

standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.advancedactions.TransformAction

standardizeAndWait() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner

standardizeAndWait() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner

Executes all standardizer actions contained by the pre-set configuration on the given molecule and returns the list of applied changes.

StandardizedMolSearch - Class in chemaxon.sss.search

MolSearch subclass that standardizes (e.g.

StandardizedMolSearch() - Constructor for class chemaxon.sss.search.StandardizedMolSearch

Constructs a StandardizedMolSearch object.

standardizeIonicGroups(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Default standardization: nitro groups: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1] sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]

standardizer - Variable in class chemaxon.descriptors.MDParameters

transform molecules into standard form before descriptor generation

Standardizer - Class in chemaxon.standardizer

Performs the standardization determined by the XML configuration file, or simple action string configuration.
See the documentation for details: User's Guide Configuration Developer's Guide

Standardizer(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with XML configuration

Standardizer(Standardizer) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer based on an existing standardizer

Standardizer(File) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with XML configuration

Standardizer(InputStream) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with XML configuration

Standardizer(String) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with auto-recognized XML or action string configuration

Standardizer(String, String) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with auto-recognized XML or action string configuration

StandardizerAction - Interface in chemaxon.standardizer

Interface of standardizer actions.

StandardizerActionDescriptor - Class in chemaxon.standardizer

Descriptor of StandardizerAction objects.
Contains all needed interface informations.

StandardizerActionDescriptor(Class<? extends StandardizerAction>) - Constructor for class chemaxon.standardizer.StandardizerActionDescriptor

Constructs a descriptor based on standardizer action class.

StandardizerActionFactory - Class in chemaxon.standardizer

Factory of StandardizerAction objects
Initializes the list of available standardizer action based on the provided factory configuration XML files, defining the factory: Internal list: the factory configuration XML containing the definitions of internal (Chemaxon defined) standardizer actions, that should be available using the factory External list: the factory configuration XML containing the definitions of external (user defined) standardizer actions, that should be available using the factory The schema of the definition XML is defined by the StandardizerActionFactory.DEFAULT_CONFIGURATION_SCHEMA:

StandardizerActionFactory() - Constructor for class chemaxon.standardizer.StandardizerActionFactory

Default constructor.

StandardizerActionFactory(String, String) - Constructor for class chemaxon.standardizer.StandardizerActionFactory

With this constructor inner and external configuration location can be defined.

StandardizerActionFactory.Builder - Class in chemaxon.standardizer

Builder class for StandardizerActionFactory.

StandardizerActionFactory.StandardizerClassDescriptor - Class in chemaxon.standardizer

Descriptor of a standardizer class

StandardizerActionInfo - Annotation Interface in chemaxon.standardizer

Standardizer action info annotation
This annotation is responsible for adding user interface related meta data for StandardizerAction implementations

StandardizerActionRunner - Interface in chemaxon.standardizer.runner

The descendant of StandardizerActionRunner interface has to provide the functionality to run StandardizerConfiguration instances automatically on the given molecule.
As standardizer configuration may contain actions in groups, using StandardizerActionRunner.setTargetGroup(String) and StandardizerActionRunner.setTargetGroups(String...) methods, the target groups, containing the actions to be executed can be defined.
By default, in case of the provided configuration containing error(s) the runner throws IllegalArgumentException.

StandardizerActionStringReader - Class in chemaxon.standardizer.configuration.reader

An implementation of StandardizerConfigurationReader for parsing action strings
If the configuration contains references to molecules/molecule files not contained by the configuration file, the base path of the configuration must be set by the method StandardizerActionStringReader.setPath(String) before gathering the configuration.
Syntax of action strings:
<actionString>::=<actionStringEntry>(..<actionStringEntry>) *
<actionStringEntry>::=<standardizerAction>|<groupDefinitions& gt;<standardizerAction>
<groupDefinitions>::=<groupDefinition>(,<groupDefinition>)*
<groupDefinition>::=(a-zA-Z0-9)+
<standardizerAction>::=<actionName>|<actionName>< parameters>
<actionName>::=(a-zA-Z0-9)+
<parameters>::=<parameter>(:<parameter>)*
<parameter>::=<key>| '<extendedKey>'|<key>=<value>|<key>='<extendedValu e & g t ; '
<key>::=(a-zA-Z0-9)+
<value>::=(anything\{.':,"})*
<extendedKey>::=(anything\{'" })*
<extendedValue>::=(anything\{'"})*

StandardizerActionStringReader(String) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Default constructor of the reader.

StandardizerActionStringReader(String, StandardizerActionFactory) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader

Constructor with custom standardizer action factory

StandardizerClassDescriptor() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Initializes an empty standardizer class descriptor

StandardizerClassDescriptor(String, String, String, String) - Constructor for class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Initializes a standardizer class descriptor

STANDARDIZERCONFIG_XML - Static variable in class chemaxon.standardizer.StandardizerActionFactory

Chemaxon's default standardizer action configuration file name

StandardizerConfiguration - Class in chemaxon.standardizer.configuration

Standardizer configuration class.
Contains a list of StandardizerAction instances.

StandardizerConfiguration() - Constructor for class chemaxon.standardizer.configuration.StandardizerConfiguration

standardizerConfigurationNode - Variable in class chemaxon.descriptors.MDParameters

node defining the Standardizer configuration

StandardizerConfigurationReader - Interface in chemaxon.standardizer.configuration.reader

This interface is provided for classes which can read the configuration of StandardizerActionRunner
Configuration error
There are 2 kinds of configuration errors for execution configuration.

StandardizerResult - Class in chemaxon.standardizer.concurrent

Result of a standardization process for a molecule

StandardizerResult(Molecule, Molecule, List<Changes>, List<StandardizerAction>) - Constructor for class chemaxon.standardizer.concurrent.StandardizerResult

Initializes a standardizer result for a successful execution

StandardizerResult(Molecule, Molecule, List<StandardizerAction>) - Constructor for class chemaxon.standardizer.concurrent.StandardizerResult

Initializes a standardizer result for a successful execution

StandardizerResult(Molecule, Exception) - Constructor for class chemaxon.standardizer.concurrent.StandardizerResult

Initializes a standardizer result for an error

StandardizerRunner - Class in chemaxon.standardizer.concurrent

Concurrent executor of the standardizer

StandardizerRunner.ErrorHandlingPolicy - Enum Class in chemaxon.standardizer.concurrent

Policy for error handling

StandardizerUtil - Class in chemaxon.standardizer

Utility class for standardizer
Functionalities of old standardizer can be simulated using this class.

StandardizerUtil() - Constructor for class chemaxon.standardizer.StandardizerUtil

StandardizerXMLReader - Class in chemaxon.standardizer.configuration.reader

XML Configuration reader for standardizer configurations.

StandardizerXMLReader(InputStream) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerXMLReader

Initiate an StandardizerXMLReader instance with the given inputSteam with the configuration

StandardizerXMLReader(InputStream, StandardizerActionFactory) - Constructor for class chemaxon.standardizer.configuration.reader.StandardizerXMLReader

Initiate an StandardizerXMLReader instance with the given inputSteam with the configuration

StandardUpperBoundCalculator - Class in com.chemaxon.search.mcs.upperbound

This class implements a max-weight matching-based upper bound calculator for the MCS problem.

StandardUpperBoundCalculator() - Constructor for class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator

STAR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that star atom had found in the molecule

STAR - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the star atom.

StarAtomChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting so called star atoms having "*" as atomic symbol.

StarAtomChecker() - Constructor for class chemaxon.checkers.StarAtomChecker

Default constructor

start() - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface

start(MDocSource, String) - Method in class chemaxon.marvin.view.swing.TableSupport

Starts loading molecules.

startElement(String, String, String, Attributes) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter

startEMFGenerator() - Static method in class chemaxon.util.ImageExportUtil

Starts the initialization of the .NET based EMF generator on a background thread.

startGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream

Deprecated, for removal: This API element is subject to removal in a future version.

startNow(MDocSource, String) - Method in class chemaxon.marvin.view.swing.TableSupport

Starts loading molecules immediately.

STATICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin

pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)

STATUS_BAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "statusBar".

STEP_DEFAULT - Static variable in class chemaxon.marvin.calculations.AlignmentPlugin

stepWedge() - Method in class chemaxon.struc.MolBond

Set the bond from 0 to MolBond.UP or UP to MolBond.DOWN.

stereo(int) - Method in class chemaxon.calculations.stereo.Stereochemistry

Calculates absolute stereo configuration of the given atom.

stereo(int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.stereo(int)

stereo(int, int) - Method in class chemaxon.calculations.stereo.Stereochemistry

Calculates absolute stereo configuration of the given double bond.

stereo(int, int) - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.stereo(int, int)

STEREO_CARE_BOX - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing stereo search markers in the molecule

STEREO_DIASTEREOMER - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for "diastereomer" stereo search type.

STEREO_ENANTIOMER - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for "enantiomer" stereo search type.

STEREO_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for "exact" stereo search type.

STEREO_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for "ignore" stereo search type.

STEREO_INVERSION_RETENTION_MARK - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing stereo inversion/retention marks in the molecule/reaction

STEREO_MASK - Static variable in class chemaxon.struc.MolBond

Single and double bond stereo mask.

STEREO_MODEL_COMPREHENSIVE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant of the comprehensive stereo search model, which combines the advantages of local and global models.

STEREO_MODEL_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

For markush search in all cases and for non-markush duplicate search in query tables SearchConstants.STEREO_MODEL_LOCAL, for non-markush duplicate search (with the exception of query tables) SearchConstants.STEREO_MODEL_GLOBAL.

STEREO_MODEL_GLOBAL - Static variable in interface chemaxon.sss.SearchConstants

Option value constant of the global stereo search model, which considers global stereo information (global parity, global double bond stereo configuration, etc.).

STEREO_MODEL_LOCAL - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for the local stereo search model, which only considers local stereo information (local parity, local double bond stereo configuration, etc.).

STEREO_SPECIFIC - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for "specific" stereo search type.

STEREO1_MASK - Static variable in class chemaxon.struc.MolBond

Single bond stereo mask.

STEREO2_CARE - Static variable in class chemaxon.struc.MolBond

Cis/trans info of this bond is taken care of during the SSS process if this flag is set - used only for query bonds.

StereoActivePart - Class in chemaxon.struc

Stereo active molecule part with stereo active atom index and its ligands which takes part in the stereo description.

StereoActivePart(int, int[]) - Constructor for class chemaxon.struc.StereoActivePart

Creates a new stereo active part.

StereoAnalysis - Class in com.chemaxon.calculations.stereoanal

The stereo analysis module is able to calculate stereochemical descriptors for a molecule, giving an analysis in terms of the stereochemical properties.
API usage example:

StereoAnalysis(Molecule) - Constructor for class com.chemaxon.calculations.stereoanal.StereoAnalysis

Creates an analysis.

StereoAnalysis(Molecule, String) - Constructor for class com.chemaxon.calculations.stereoanal.StereoAnalysis

Creates an analysis.

StereoCareBoxChecker - Class in chemaxon.checkers

Checker to find molecules containing Stereo Care Boxes.

StereoCareBoxChecker() - Constructor for class chemaxon.checkers.StereoCareBoxChecker

Creates a stereo care box checker.

StereoCenter - Interface in com.chemaxon.calculations.stereoanal.stereocenters

Interface for stereo centers.

StereoCenterVisitor - Interface in com.chemaxon.calculations.stereoanal.filters

Visitor interface for stereo centers.

StereoCheckUtility - Class in chemaxon.checkers

Deprecated, for removal: This API element is subject to removal in a future version.

Will be removed from the public API.

StereoCheckUtility() - Constructor for class chemaxon.checkers.StereoCheckUtility

Deprecated.

Stereochemistry - Class in chemaxon.calculations.stereo

Central class for accessing functions analyzing the topology of a molecule.

Stereochemistry() - Constructor for class chemaxon.calculations.stereo.Stereochemistry

stereoClean() - Method in class chemaxon.struc.MoleculeGraph

Reset the wedges of the molecule, based on the actual parity information in 2D, remove wedges in 3D.

stereoClean() - Method in class chemaxon.struc.RgMolecule

Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.

stereoClean() - Method in class chemaxon.struc.RxnMolecule

Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.

StereoConstants - Interface in chemaxon.struc

Constants for atom parity and double bond stereo.

StereoConstants - Interface in com.chemaxon.calculations.stereoanal

Wrapper interface for stereo constants.

StereoConstants.EnhancedStereoType - Enum Class in com.chemaxon.calculations.stereoanal

Enhanced stereo flags.

StereoConstants.StereoValue - Interface in com.chemaxon.calculations.stereoanal

Deprecated, for removal: This API element is subject to removal in a future version.

Check the implementing enums for details.

StereoConstants.StereoValue.AtropStereo - Enum Class in com.chemaxon.calculations.stereoanal

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue.

StereoConstants.StereoValue.AxialStereo - Enum Class in com.chemaxon.calculations.stereoanal

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue.

StereoConstants.StereoValue.CisTransStereo - Enum Class in com.chemaxon.calculations.stereoanal

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue.

StereoConstants.StereoValue.TetrahedralStereo - Enum Class in com.chemaxon.calculations.stereoanal

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue.

StereoConstants.Type - Enum Class in com.chemaxon.calculations.stereoanal

Stereo center type.

stereoDoubleBondCount() - Method in class chemaxon.calculations.stereo.Stereochemistry

Calculates the number of stereo double bonds.

stereoDoubleBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Deprecated, for removal: This API element is subject to removal in a future version.

as of release 5.5, replaced by Stereochemistry.stereoDoubleBondCount()

StereoInversionRetentionMarkChecker - Class in chemaxon.checkers

Detects reaction inversion/retention marks on atoms.

StereoInversionRetentionMarkChecker() - Constructor for class chemaxon.checkers.StereoInversionRetentionMarkChecker

Default constructor

STEREOISOMER_DOUBLEBOND - Enum constant in enum class chemaxon.calculator.CalculatorTag

STEREOISOMER_TETRAHEDRAL - Enum constant in enum class chemaxon.calculator.CalculatorTag

StereoisomerEnumeration - Class in com.chemaxon.calculations.stereoisomers

Enumerates stereoisomers of the specified molecule.

StereoisomerEnumeration(Molecule) - Constructor for class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

Constructs a StereoisomerEnumeration object with default settings.

StereoisomerEnumeration(Molecule, StereoisomerSettings) - Constructor for class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

Construct new StereoisomerEnumeration object.

StereoisomerEnumeration(Molecule, StereoisomerSettings, String) - Constructor for class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

Construct new StereoisomerEnumeration object.

StereoisomerPlugin - Class in chemaxon.marvin.calculations

Deprecated.

StereoisomerPlugin() - Constructor for class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

StereoisomerSettings - Class in com.chemaxon.calculations.stereoisomers

Settings class for StereoisomerEnumeration.

StereoisomerSettings.StereoisomerType - Enum Class in com.chemaxon.calculations.stereoisomers

Types of stereoisomers.

stereoisomerTypes() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Returns the type of generated stereoisomers.

stericEffectIndex(int) - Method in class chemaxon.calculations.TopologyAnalyser

Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.

STGRP_ABS - Static variable in interface chemaxon.struc.StereoConstants

Absolute stereo group type for enhanced stereo representation.

STGRP_AND - Static variable in interface chemaxon.struc.StereoConstants

AND stereo group type for enhanced stereo representation.

STGRP_NONE - Static variable in interface chemaxon.struc.StereoConstants

Empty stereo group type setting meaning no enhanced stereo label.

STGRP_OR - Static variable in interface chemaxon.struc.StereoConstants

OR stereo group type for enhanced stereo representation.

STICK_DISTANCE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "stickdst".

STICK_THICKNESS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "stickThickness".

Sticky(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky

Copy constructor.

Sticky(MPolyline, int) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky

Constructor.

Sticky(MRectangle, int) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky

Constructor.

Sticky(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky

Copy constructor.

STOICHIOMETRY_KEY - Static variable in class chemaxon.standardizer.actions.ExpandAction

Key of type for parsing and property changes

stop() - Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface

stop() - Method in class chemaxon.sss.search.MolSearch

stop() - Method in class chemaxon.sss.search.Search

Tries to stop the running search as fast as possible.

storageSizeChanged(MDocStorage, int, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener

Storage size changed.

storageSizeFinalized(MDocStorage) - Method in interface chemaxon.marvin.view.MDocStorage.Listener

Final storage size determined.

store() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Stores a new result item.

storeDoc(MDocument, int, String) - Method in class chemaxon.marvin.view.MDocStorage

Store new document and free the oldest accessed if the number of documents is too much to fit in memory.

storeInDocument(NoStructure, MDocument) - Static method in class chemaxon.struc.NoStructure

Puts the given NoStructe into the document.

storeMainDoc(MDocument, int) - Method in class chemaxon.marvin.view.MDocStorage

Store new document and free the oldest accessed if the number of documents is too much to fit in memory.

storeTemporaryObject(String, Object) - Method in class chemaxon.struc.MolAtom

Stores an object temporarily.

STRAIGHT_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents molecules containing "either" double bonds.

StraightDoubleBondChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting double bonds in molecule which can be either "E" or "Z".

StraightDoubleBondChecker() - Constructor for class chemaxon.checkers.StraightDoubleBondChecker

Constructs EitherDoubleBondChecker instance

stringBuffer - Variable in class chemaxon.marvin.io.MolExportModule

This buffer can contain the molecule file contents, in case of a text format.

stringToArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler

stringToScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler

stringValue() - Method in class chemaxon.struc.prop.MStringProp

Gets the string value.

StripSaltsAction - Class in chemaxon.standardizer.advancedactions

Strip salts standardizer action

StripSaltsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.StripSaltsAction

Initializes strip salts action

StrucFPConfig - Class in chemaxon.sss.screen

Utility class for assembling and parsing structural FP configurations.

StrucFPConfig() - Constructor for class chemaxon.sss.screen.StrucFPConfig

StructuralFrameworksPlugin - Class in chemaxon.marvin.calculations

Plugin class to calculate Bemis-Murcko and other structural scaffolds of input molecules.

StructuralFrameworksPlugin() - Constructor for class chemaxon.marvin.calculations.StructuralFrameworksPlugin

StructuralFrameworksPlugin.FrameworkTypes - Enum Class in chemaxon.marvin.calculations

FrameworkTypes represents the available calculations

StructuralFrameworksPlugin.VerbosePrinter - Interface in chemaxon.marvin.calculations

Verbose printer specification

STRUCTURE_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction

Key of query molecule for parsing and property change

StructureCheck - Class in chemaxon.checkers

This class contains the command line interface for running inner StructureChecker and StructureFixer instances.

StructureChecker - Interface in chemaxon.checkers

General interface describing functions that are available for a chemical structure checker.

StructureCheckerDescriptor - Class in chemaxon.checkers

Descriptor for StructureChecker

StructureCheckerDescriptor(Class<? extends StructureChecker>) - Constructor for class chemaxon.checkers.StructureCheckerDescriptor

Constructs a descriptor based on checker class.

StructureCheckerErrorType - Enum Class in chemaxon.checkers

Enum containing possible error types for structure checkers.

StructureCheckerFactory - Class in chemaxon.checkers

Deprecated.

use CheckerFixerFactory instead

StructureCheckerFactory() - Constructor for class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Please consider using StructureCheckerFactory.getInstance() instead of calling this constructor directly.

Default constructor. Default configurations will be read.

StructureCheckerFactory(InputStream, InputStream) - Constructor for class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Please consider using StructureCheckerFactory.getInstance(String, String) instead of calling this constructor directly.

With this constructor inner and external configuration location can be defined.

StructureCheckerFactory(String, String) - Constructor for class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Please consider using StructureCheckerFactory.getInstance(String, String) instead of calling this constructor directly.

With this constructor inner and external configuration location can be defined.

StructureCheckerResult - Interface in chemaxon.checkers.result

An instance of StructureCheckerResult identifies a molecule problem

StructureCheckerUtility - Class in chemaxon.checkers

Utility to handle core features

StructureCheckerUtility() - Constructor for class chemaxon.checkers.StructureCheckerUtility

StructureCheckOptions - Class in chemaxon.checkers

Options descriptor for structure checker command line interface

StructureCheckOptions() - Constructor for class chemaxon.checkers.StructureCheckOptions

StructureCheckOptions.Mode - Enum Class in chemaxon.checkers

The mode of the structure check

StructureCheckOptions.ModeConverter - Class in chemaxon.checkers

Converter for Mode enumeration.

StructureCheckOptions.Type - Enum Class in chemaxon.checkers

The output type of the structure check

StructureCheckOptions.TypeConverter - Class in chemaxon.checkers

Converter for Type enumeration.

StructureFixer - Interface in chemaxon.fixers

A StructureFixer can fix a Molecule problem identified by a StructureCheckerResult

StructureFixerDescriptor - Class in chemaxon.fixers

Descriptor class for StructureFixer classes.

StructureFixerDescriptor(Class<? extends StructureFixer>) - Constructor for class chemaxon.fixers.StructureFixerDescriptor

Constructs a descriptor based on fixer class.

StructureFixerFactory - Class in chemaxon.fixers

Deprecated.

use CheckerFixerFactory instead

StructureFixerFactory() - Constructor for class chemaxon.fixers.StructureFixerFactory

Deprecated.

Default constructor.

StructureFixerFactory(InputStream, InputStream) - Constructor for class chemaxon.fixers.StructureFixerFactory

Deprecated.

Parameterized constructor.

StructureFixerFactory(String) - Constructor for class chemaxon.fixers.StructureFixerFactory

Deprecated.

Parameterized constructor.

StructureFixerFactory(String, String) - Constructor for class chemaxon.fixers.StructureFixerFactory

Deprecated.

Parameterized constructor.

structureFormat - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

The structure format used to represent hits converted from other sources than names (OSR, embedded structures, ...).

structureFormat(String) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

SUBFORMULA - Static variable in class chemaxon.sss.formula.FormulaSearch

Constant value specifying the sub formula search type.

SubjectToRemoval - Annotation Interface in com.chemaxon.common.annotations

Denotes that an entity has been deprecated and is subject to removal in a release following the specified date.

substring(int) - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets a substring.

substring(int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets a substring of the document.

substring(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets a substring.

substring(int, int) - Method in class chemaxon.struc.graphics.MTextDocument

Gets a substring of the document.

SUBSTRUCTURE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that the needed substructure had found

SUBSTRUCTURE - Enum constant in enum class chemaxon.descriptors.MetricsType

SUBSTRUCTURE - Static variable in interface chemaxon.sss.SearchConstants

Substructure search that applies both screening and atom-by-atom search.

SUBSTRUCTURE_NOFIX - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that the needed substructure had found but no data will be available for the fix in the result

SubstructureChecker - Class in chemaxon.checkers

This descendant of AbstractStructureChecker is responsible for detecting substructures in a Molecule instance.

SubstructureChecker() - Constructor for class chemaxon.checkers.SubstructureChecker

Default constructor.

SubstructureChecker(String) - Constructor for class chemaxon.checkers.SubstructureChecker

Parameterized constructor.

SubstructureChecker(Map<String, String>) - Constructor for class chemaxon.checkers.SubstructureChecker

Parameterized constructor.

SubstructureCheckerResult - Class in chemaxon.checkers.result

SubstructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<int[]>, String) - Constructor for class chemaxon.checkers.result.SubstructureCheckerResult

Constructor which initialize all the properties.

SubstructureFixer - Class in chemaxon.fixers

Fixer to fix substructure issues.

SubstructureFixer() - Constructor for class chemaxon.fixers.SubstructureFixer

subTask(String, long) - Method in interface chemaxon.util.progress.ProgressObserver

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

subtract(DPoint3) - Method in class chemaxon.struc.DPoint3

Subtract the given v2 vector from this one.

subtract(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3

Calculates the difference of the two vectors

sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.MoleculeGraph

For internal use only.

sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.RgMolecule

For internal use only.

sumDistanceSquare(MoleculeGraph, DPoint3) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the sum of the distance square for each atom from a point.

sumNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator

sumOfRadicals() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis

Calculates the sum of the radicals of all atoms of the molecule.

SUPERATOM - Enum constant in enum class chemaxon.struc.SgroupType

SuperatomSgroup - Class in chemaxon.struc.sgroup

Superatom S-group.

SuperatomSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Constructs a superatom S-group in expanded state.

SuperatomSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Constructs a superatom S-group.

SuperatomSgroup(SuperatomSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Copy constructor.

superGraph - Variable in class chemaxon.struc.MoleculeGraph

Parent of all parents.

SUPERSTRUCTURE - Enum constant in enum class chemaxon.descriptors.MetricsType

SUPERSTRUCTURE - Static variable in interface chemaxon.sss.SearchConstants

Superstructure search (Value=6)

support - Variable in class chemaxon.standardizer.AbstractStandardizerAction

SURE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

SURE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

svFuzzyIncrements - Variable in class chemaxon.descriptors.PFParameters

Fuzzy smoothing values for smoothing with user defined smoothing vector.

SVG - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat

SVG - Static variable in class chemaxon.formats.MFileFormat

Scalable Vector Graphics.

swap() - Method in class chemaxon.struc.MolBond

Change orientation.

swapAtoms(int, int) - Method in class chemaxon.struc.SelectionMolecule

Swap two atoms.

swapHeadTail() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Swaps the head and tail bonds of this sru if both are set.

SwingUtil - Class in chemaxon.marvin.util

Swing utility functions.

SwingUtil() - Constructor for class chemaxon.marvin.util.SwingUtil

switchToDeterminate(long) - Method in interface chemaxon.util.progress.ProgressObserver

Notifies that the remaining amount of work units to complete this task is known.

SYBYLMOL - Static variable in class chemaxon.formats.MFileFormat

Tripos SYBYL molfiles.

SYM_CX - Static variable in class chemaxon.struc.MolAtom

Atom symbol string for CxSMILES export.

SYM_EXPLH - Static variable in class chemaxon.struc.MolAtom

Atom symbol string contains explicit H count if this flag is set.

SYM_IMPLH - Static variable in class chemaxon.struc.MolAtom

Atom symbol string contains implicit H count is shown flag is set.

SYM_MOLEX - Static variable in class chemaxon.struc.MolAtom

Atom symbol string for Molfile export.

SYM_NEUTRAL - Static variable in class chemaxon.struc.MolAtom

Atom symbol string does not contain the charge if this flag is set.

SYM_SMARTS - Static variable in class chemaxon.struc.MolAtom

Atom symbol string for SMILES export.

SYM_SQBRACKETS - Static variable in class chemaxon.struc.MolAtom

Atom symbol is shown in square brackets if this flag is set.

symbolOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the element symbol for the specified atomic number.

symbolOf(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the special element symbol for the specified atomic and mass numbers.

SYN - Static variable in interface chemaxon.struc.StereoConstants

Non-CIP stereodescriptor, syn (relative configuration).

szegedIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Szeged index of the molecule.

T

T_BRACES - Static variable in class chemaxon.struc.graphics.MBracket

Braces.

T_CHEVRONS - Static variable in class chemaxon.struc.graphics.MBracket

Chevrons.

T_DOUBLE - Static variable in class chemaxon.struc.graphics.MBracket

The bracket has two sides.

T_NOROT - Static variable in class chemaxon.struc.graphics.MRectangle

Disable rotation.

T_ROUND - Static variable in class chemaxon.struc.graphics.MBracket

Round bracket type (parenthesis).

T_SINGLE - Static variable in class chemaxon.struc.graphics.MBracket

The bracket has one side.

T_SQUARE - Static variable in class chemaxon.struc.graphics.MBracket

Square bracket type.

Ta - Static variable in class chemaxon.core.ChemConst

TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "tabScale".

TableOptions - Class in chemaxon.marvin.view.swing

SDF table options for MarvinView.

TableSupport - Class in chemaxon.marvin.view.swing

Viewer table support class.

TaggedCalculator - Interface in chemaxon.calculator

Base interface for calculator objects that can report a set of optional tags, which are used primarily to identify the calculator in configuration files.

TaggedCalculatorInputChecker - Interface in chemaxon.calculator

Instances of this interface are used by calculators to check if they can process an input molecule.

tags() - Method in class chemaxon.calculations.dipole.DipoleCalculator

tags() - Method in class chemaxon.calculations.nmr.NMRCalculator

tags() - Method in interface chemaxon.calculator.TaggedCalculator

Returns the set of tags reported by this calculator.

tags() - Method in class chemaxon.marvin.calculations.ConformerPlugin

tags() - Method in class chemaxon.marvin.calculations.GeometryPlugin

tags() - Method in class chemaxon.marvin.calculations.HBDAPlugin

tags() - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

tags() - Method in class chemaxon.marvin.calculations.MSAPlugin

tags() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

tags() - Method in class chemaxon.marvin.calculations.ResonancePlugin

tags() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

tags() - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

tags() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the tags of the action as a string, divided by comma characters

tags() - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

TAGS - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

tags of action

TAIL - Static variable in class chemaxon.struc.graphics.MPolyline

Arrow tail (feather).

tanimoto() - Method in class chemaxon.marvin.alignment.Alignment

Calculates the atomic colored volume Tanimoto similarity of two 3D molecules.

tanimoto(float[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates Tanimoto dissimilarity for floating point values.

tanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics

Calculates Tanimoto dissimilarity for floating point values.

Tanimoto() - Method in class chemaxon.sss.screen.Similarity

Deprecated, for removal: This API element is subject to removal in a future version.

TANIMOTO - Enum constant in enum class chemaxon.descriptors.MetricsType

target - Variable in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

The target molecule.

target - Variable in class chemaxon.sss.search.MolComparator

TargetHomologyMatchingMode - Enum Class in chemaxon.sss.search.options

Option to control homology matching on target side.

targetMol - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Target molecule (it is neither cloned nor modified).

targetSearchData - Variable in class chemaxon.sss.search.MolComparator

TaskScheduler - Interface in chemaxon.marvin.view

Generic task scheduler interface.

TAUTOMER_SEARCH_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for indicating that tautomer duplicate search option is not explicitly set.

TAUTOMER_SEARCH_OFF - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for switching tautomer searching off.

TAUTOMER_SEARCH_ON - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for switching tautomer searching on.

TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.

TautomerEqualityMode - Enum Class in chemaxon.sss.search.options

TAUTOMERIZATION_CANONICAL - Enum constant in enum class chemaxon.calculator.CalculatorTag

TAUTOMERIZATION_DOMINANTS - Enum constant in enum class chemaxon.calculator.CalculatorTag

TAUTOMERIZATION_GENERIC - Enum constant in enum class chemaxon.calculator.CalculatorTag

TAUTOMERIZATION_MAJOR - Enum constant in enum class chemaxon.calculator.CalculatorTag

TautomerizationPlugin - Class in chemaxon.marvin.calculations

Plugin class for generating tautomer structures.

TautomerizationPlugin() - Constructor for class chemaxon.marvin.calculations.TautomerizationPlugin

Constructor.

TautomerizeAction - Class in chemaxon.standardizer.actions

Tautomerize standardizer action

TautomerizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.TautomerizeAction

Initializes the action

TautomerizeAction.TautomerForm - Enum Class in chemaxon.standardizer.actions

TautomerTransformationMode - Enum Class in chemaxon.sss.search.options

Tb - Static variable in class chemaxon.core.ChemConst

Tc - Static variable in class chemaxon.core.ChemConst

Te - Static variable in class chemaxon.core.ChemConst

tell() - Method in class chemaxon.formats.MolImporter

Returns the current file offset.

TEMPLATE_FILE_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction

Key of template file for parsing and property change

TEMPLATE_TOOLBAR_CUSTOMIZABLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "templateToolbarCustomizable".

TEMPLATEBASED - Enum constant in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Template based clean

TEMPLATES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "tmpls".

TEMPLATES_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction

Key for templates property change

temporaryObjects - Variable in class chemaxon.struc.MDocument

testEncoding(String) - Static method in class chemaxon.formats.MFileFormatUtil

Tests whether the given charset name is supported by this JVM

testLine(String) - Static method in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

testLine(String) - Static method in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

testRecord(String) - Static method in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated, for removal: This API element is subject to removal in a future version.

TETRAHEDRAL - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType

TETRAHEDRAL - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type

Tetrahedral stereo center.

TETRAHEDRAL - Enum constant in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType

Tetrahedral stereoisomers.

TETRAHEDRAL - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

TetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral

Filter for tetrahedral centers.

TetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter

TetrahedralStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters

Tetrahedral stereo center implementation.

TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Constructs a new instance of tetrahedral stereo center.

TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue, EnhancedStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Constructs a new instance of tetrahedral stereo center.

TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue, EnhancedStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Constructs a new instance of tetrahedral stereo center with attached data.

TetrahedralStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue, Optional<EnhancedStereo>, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Constructs a new instance of tetrahedral stereo center with attached data.

TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by TetrahedralStereoCenter(AtomSelection, TetrahedralStereoIUPACValue).

TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, EnhancedStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by TetrahedralStereoCenter(AtomSelection, TetrahedralStereoIUPACValue, EnhancedStereo).

TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, EnhancedStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by TetrahedralStereoCenter(AtomSelection, TetrahedralStereoIUPACValue, EnhancedStereo, List).

TetrahedralStereoCenter(AtomSelection, StereoConstants.StereoValue.TetrahedralStereo, Optional<EnhancedStereo>, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by TetrahedralStereoCenter(AtomSelection, TetrahedralStereoIUPACValue, Optional, List).

tetrahedralStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the tetrahedral stereogenic centers.

tetrahedralStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the tetrahedral stereogenic centers (with attached data).

TetrahedralStereoDescriptor - Class in chemaxon.struc

TetrahedralStereoDescriptor(CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue, StereoActivePart) - Constructor for class chemaxon.struc.TetrahedralStereoDescriptor

TetrahedralStereoDescriptor(CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue, StereoActivePart, int) - Constructor for class chemaxon.struc.TetrahedralStereoDescriptor

TEXT - Static variable in class chemaxon.formats.MolExporter

Use this flag to write text files with OS dependent line separators.

TEXT - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Property display type: display in text.

TEXTMODE - Static variable in class chemaxon.formats.MdlCompressor

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 3.1, there is no possibility to do that

Th - Static variable in class chemaxon.core.ChemConst

theAtoms - Variable in class chemaxon.struc.MoleculeGraph

The atoms (nodes).

theBonds - Variable in class chemaxon.struc.MolAtom

The bonds.

theBonds - Variable in class chemaxon.struc.MoleculeGraph

The bonds (edges).

THICKNESS_SET_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Thickness is set flag.

THREE_DIM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that 3d coordinates had found in the molecule

ThreeDimensionChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atoms having non-zero Z coordinates.

ThreeDimensionChecker() - Constructor for class chemaxon.checkers.ThreeDimensionChecker

Default constructor

thresholds - Variable in class chemaxon.descriptors.MDParameters

dissimilarity thresholds values

Ti - Static variable in class chemaxon.core.ChemConst

TIFF - Static variable in class chemaxon.formats.MFileFormat

Tagged Image File Format.

timeLimit - Variable in class com.chemaxon.search.mcs.MaxCommonSubstructure

Time limit in milliseconds (-1 means disabled).

timeoutLimitMilliseconds - Variable in class chemaxon.sss.search.SearchOptions

The search on a single target timeouts reaching this number of milliseconds.

title - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The result frame title.

Tl - Static variable in class chemaxon.core.ChemConst

Tm - Static variable in class chemaxon.core.ChemConst

toBinaryString() - Method in class chemaxon.descriptors.ChemicalFingerprint

Converts the fingerprint into a 0,1 string.

toBinaryString() - Method in class chemaxon.descriptors.ECFP

Converts the fingerprint into a fixed-length 0,1 string.

toBinaryString() - Method in class chemaxon.descriptors.MolecularDescriptor

Creates the binary string representation of a MolecularDescriptor object.

toBinaryString() - Method in class chemaxon.descriptors.ReactionFingerprint

Converts the fingerprint into a 0,1 string.

toBinaryString() - Method in class chemaxon.descriptors.ShapeDescriptor

toBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter

Returns a binary representation of the given molecule.

toBinFormat(String) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by MolExporter.toBinFormat(Molecule, String).

toBitSet() - Method in class chemaxon.descriptors.ECFP

Returns a bit vector storing the "folded" binary representation of the fingerprint.

toData() - Method in class chemaxon.descriptors.BCUT

Converts a BCUT object into a byte array.

toData() - Method in class chemaxon.descriptors.ChemicalFingerprint

Converts a chemical fingerprint object into a byte array.

toData() - Method in class chemaxon.descriptors.CustomDescriptor

Converts a CustomDescriptor object into a byte array.

toData() - Method in class chemaxon.descriptors.ECFP

Converts an ECFP object into a byte array.

toData() - Method in class chemaxon.descriptors.MolecularDescriptor

Converts the internal (memory) representation of a MolecularDescriptor instance into an external format that can be stored in a database.

toData() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Converts a PharmacophoreFingerprint object into a byte array.

toData() - Method in class chemaxon.descriptors.ReactionFingerprint

Converts a reaction fingerprint object into a byte array.

toData() - Method in class chemaxon.descriptors.ScalarDescriptor

Converts a ScalarDescriptor object into an array of bytes.

toData() - Method in class chemaxon.descriptors.ShapeDescriptor

toData() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

Deprecated.

use ShapeData.toData() instead.

toData() - Method in class chemaxon.marvin.alignment.ShapeData

Serializes the current object to a byte array

toDecimalString() - Method in class chemaxon.descriptors.BCUT

Converts the BCUT descriptor into a tab separated string.

toDecimalString() - Method in class chemaxon.descriptors.ChemicalFingerprint

Converts the fingerprint into a tab separated string.

toDecimalString() - Method in class chemaxon.descriptors.CustomDescriptor

Converts the descriptor into a readable string of decimal numbers (float or integer, depending on descriptor type).

toDecimalString() - Method in class chemaxon.descriptors.ECFP

Converts the ECFP fingerprint into a tab separated string.

toDecimalString() - Method in class chemaxon.descriptors.MolecularDescriptor

Creates the string representation of a MolecularDescriptor object.

toDecimalString() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Converts the fingerprint into a string of decial numbers.

toDecimalString() - Method in class chemaxon.descriptors.ReactionFingerprint

Converts the fingerprint into a tab separated string.

toDecimalString() - Method in class chemaxon.descriptors.ScalarDescriptor

Converts the descriptor value into a readable string.

toDecimalString() - Method in class chemaxon.descriptors.ShapeDescriptor

toFeatureSet() - Method in class chemaxon.descriptors.ECFP

Deprecated, for removal: This API element is subject to removal in a future version.

As of JChem 5.4.1, replaced by ECFP.toIdentiferSet().

toFloatArray() - Method in class chemaxon.descriptors.BCUT

Creates the float array representation of a BCUT descriptor object.

toFloatArray() - Method in class chemaxon.descriptors.ChemicalFingerprint

Creates the float array representation of the fingerprint.

toFloatArray() - Method in class chemaxon.descriptors.CustomDescriptor

Creates the float array representation of a CustomDescriptor object.

toFloatArray() - Method in class chemaxon.descriptors.ECFP

Creates the float array representation of a ECFP fingerprint object.

toFloatArray() - Method in class chemaxon.descriptors.MolecularDescriptor

Creates the float array representation of a MolecularDescriptor object.

toFloatArray() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Creates the float array representation of a MolecularDescriptor object.

toFloatArray() - Method in class chemaxon.descriptors.ReactionFingerprint

Creates the float array representation of the fingerprint.

toFloatArray() - Method in class chemaxon.descriptors.ScalarDescriptor

Creates the float array representation of the descriptor.

toFloatArray() - Method in class chemaxon.descriptors.ShapeDescriptor

toFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter

Returns a string representation of the given molecule.

toFormat(String) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by MolExporter.toFormat(Molecule, String).

toHistogramString(String, boolean) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Creates the string representation of the fingerprint.

toIdentiferSet() - Method in class chemaxon.descriptors.ECFP

Converts the fingerprint to a set of Integer identifiers.

toIntArray() - Method in class chemaxon.descriptors.ECFP

Converts the fingerprint to an array of int identifiers.

token - Variable in exception chemaxon.naming.NamePrefixException

toList() - Method in class chemaxon.sss.search.MolSearchOptions

toList() - Method in class chemaxon.sss.search.SearchOptions

Returns the text representation of this options object as a list of "optionname:optionvalue" strings.

toMolecule() - Method in class chemaxon.marvin.alignment.MMPAlignmentResult

Creates a single two-fragment molecule from the reference and aligned molecule.

toMolecule() - Method in class chemaxon.marvin.alignment.ShapeData

toObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter

Returns a String, byte[] or Image representation of the given molecule.

toObject(String) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by MolExporter.toObject(Molecule, String).

TOOLBAR_FLOATABLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "toolbarFloatable".

TOOLBAR_TEMPLATES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "ttmpls".

topLevelContainer - Static variable in class chemaxon.marvin.beans.MarvinPane

The top level container of the pane

toPoint2D() - Method in class chemaxon.struc.DPoint3

TOPOLOGY_CHAIN - Static variable in class chemaxon.struc.MolBond

Bond is in a chain.

TOPOLOGY_MASK - Static variable in class chemaxon.struc.MolBond

Bond topology mask.

TOPOLOGY_RING - Static variable in class chemaxon.struc.MolBond

Bond is in a ring.

TopologyAnalyser - Class in chemaxon.calculations

Central class for accessing functions analysing the topology of a molecule.

TopologyAnalyser() - Constructor for class chemaxon.calculations.TopologyAnalyser

TopologyAnalyserPlugin - Class in chemaxon.marvin.calculations

Calculates topological data.

TopologyAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Constructor.

toString() - Method in class chemaxon.calculations.nmr.Multiplet

toString() - Method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus

toString() - Method in class chemaxon.calculations.nmr.Shift

toString() - Method in class chemaxon.checkers.AbstractStructureChecker

toString() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

toString() - Method in enum class chemaxon.checkers.FixMode

toString() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

toString() - Method in class chemaxon.checkers.StructureCheckerDescriptor

toString() - Method in class chemaxon.checkers.SubstructureChecker

toString() - Method in class chemaxon.checkers.util.AtomLabels

toString() - Method in class chemaxon.checkers.util.DataExclusionList

toString() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

toString() - Method in class chemaxon.descriptors.BCUT

Converts the descriptor into a readable string.

toString() - Method in class chemaxon.descriptors.BCUTParameters

Returns the XML configuration in a string.

toString() - Method in class chemaxon.descriptors.ChemicalFingerprint

Converts the fingerprint into a readable string.

toString() - Method in class chemaxon.descriptors.CustomDescriptor

Converts the descriptor into a readable string.

toString() - Method in class chemaxon.descriptors.ECFP

Converts the fingerprint into a readable string.

toString() - Method in class chemaxon.descriptors.MDParameters

Returns the parameter values in string.

toString() - Method in class chemaxon.descriptors.MolecularDescriptor

Creates the string representation of a MolecularDescriptor object.

toString() - Method in class chemaxon.descriptors.PFParameters

Returns the XML configuration in a string.

toString() - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Converts the fingerprint into a readable string.

toString() - Method in class chemaxon.descriptors.ReactionFingerprint

Converts the fingerprint into a readable string.

toString() - Method in class chemaxon.descriptors.ScalarDescriptor

Converts the descriptor value into a readable string.

toString() - Method in class chemaxon.descriptors.scalars.HBParameters

Returns the XML configuration in a string.

toString() - Method in class chemaxon.descriptors.scalars.LDParameters

Returns the XML configuration in a string.

toString() - Method in class chemaxon.descriptors.ShapeDescriptor

toString() - Method in class chemaxon.fixers.StructureFixerDescriptor

toString() - Method in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

toString() - Method in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption

toString() - Method in class chemaxon.formats.GeneralExportOptions

Returns the text representation of the builder.

toString() - Method in class chemaxon.formats.MFileFormat

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.formats.recognizer.RecognizerList

Deprecated.

Gets the string representation of the list.

toString() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

toString() - Method in class chemaxon.marvin.alignment.atrop.BondInfo

toString() - Method in class chemaxon.marvin.alignment.atrop.DihedralScanStep

toString() - Method in class chemaxon.marvin.alignment.Pharmacophore3D

toString() - Method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

toString() - Method in class chemaxon.marvin.io.Encoding

Converts the encoding object to string.

toString() - Method in class chemaxon.marvin.io.MRecordReader.Position

toString() - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

toString() - Method in class chemaxon.marvin.services.DynamicArgument

toString() - Method in class chemaxon.marvin.services.ServiceArgument

toString() - Method in class chemaxon.marvin.services.ServiceDescriptor

toString() - Method in class chemaxon.marvin.swing.MAction

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.marvin.util.OptionDescriptor

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.sss.search.MarkushFeature

Deprecated.

toString() - Method in enum class chemaxon.sss.search.options.HaltOnErrorOption

Returns the string representation.

toString() - Method in enum class chemaxon.sss.search.options.HomologyTranslationOption

toString() - Method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

toString() - Method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption

toString() - Method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

toString() - Method in class chemaxon.sss.search.SearchHit

toString() - Method in class chemaxon.sss.search.SearchOptions

Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)

toString() - Method in class chemaxon.standardizer.AbstractStandardizerAction

toString() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

toString() - Method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

toString() - Method in class chemaxon.standardizer.actions.AbstractSgroupAction

toString() - Method in class chemaxon.standardizer.actions.AliasToGroupAction

toString() - Method in class chemaxon.standardizer.actions.AromatizeAction

toString() - Method in enum class chemaxon.standardizer.actions.AromatizeAction.Type

toString() - Method in class chemaxon.standardizer.actions.ClearStereoAction

toString() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

toString() - Method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

toString() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

toString() - Method in class chemaxon.standardizer.actions.ExpandAction

toString() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

toString() - Method in class chemaxon.standardizer.actions.MapAction

toString() - Method in class chemaxon.standardizer.actions.MapReactionAction

toString() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

toString() - Method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

toString() - Method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

toString() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

toString() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

toString() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

toString() - Method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

toString() - Method in class chemaxon.standardizer.actions.TautomerizeAction

toString() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

toString() - Method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

toString() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

toString() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition

toString() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

toString() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

toString() - Method in class chemaxon.standardizer.advancedactions.TransformAction

toString() - Method in class chemaxon.standardizer.Changes

toString() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration

toString() - Method in class chemaxon.standardizer.StandardizerActionDescriptor

toString() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

toString() - Method in class chemaxon.struc.BicycloStereoDescriptor

toString() - Method in class chemaxon.struc.CTransform3D

Gets a string representation of the matrix.

toString() - Method in class chemaxon.struc.DPoint3

Gets a string representation of the point

toString() - Method in class chemaxon.struc.graphics.MAtomSetPoint

toString() - Method in class chemaxon.struc.graphics.MElectron

toString() - Method in class chemaxon.struc.graphics.MFont

toString() - Method in class chemaxon.struc.graphics.MMidPoint

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.graphics.MRectanglePoint

toString() - Method in class chemaxon.struc.graphics.MTextAttributes

Returns the string representation of the attributes.

toString() - Method in class chemaxon.struc.graphics.MTextDocument.Portion

Gets the string representation of the portion.

toString() - Method in class chemaxon.struc.graphics.MTextDocument

Gets the string representation of the document.

toString() - Method in class chemaxon.struc.MDocument

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.MObject

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.MolAtom

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.MolBond

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.MoleculeGraph

Overrides MoleculeGraph.toString() to ease debugging.

toString() - Method in class chemaxon.struc.MPoint

toString() - Method in class chemaxon.struc.MProp

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.prop.MBooleanProp

toString() - Method in class chemaxon.struc.prop.MDoubleArrayProp

toString() - Method in class chemaxon.struc.prop.MDoubleProp

toString() - Method in class chemaxon.struc.prop.MFontProp

toString() - Method in class chemaxon.struc.prop.MHashProp

toString() - Method in class chemaxon.struc.prop.MHCoords3DProp

toString() - Method in class chemaxon.struc.prop.MIntegerArrayProp

toString() - Method in class chemaxon.struc.prop.MIntegerProp

toString() - Method in class chemaxon.struc.prop.MListProp

toString() - Method in class chemaxon.struc.prop.MMoleculeProp

String representation of this object: number of atoms, number of bonds.

toString() - Method in class chemaxon.struc.prop.MObjectProp

Create the serialized object base64 string representation.

toString() - Method in class chemaxon.struc.prop.MStringProp

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.RgMolecule

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.RgroupBridgeId

toString() - Method in class chemaxon.struc.RxnMolecule

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.sgroup.AttachmentPoint

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.Sgroup

Overrides Object.toString() to ease debugging.

toString() - Method in class chemaxon.struc.StereoActivePart

toString() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor

toString() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory

toString() - Method in class com.chemaxon.calculations.stereoanal.ErrorReport

toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Creates a string representation.

toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter

toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter

toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter

toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup

toString() - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter

toString() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

toString(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Returns a string representation of the group.

toString(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Returns a string representation of the group.

toString(int) - Method in class chemaxon.struc.Sgroup

Gets a string representation of the S-group.

toString(Object) - Static method in class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

Was only intended for internal use, will be removed.

toString(Object, int) - Static method in class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

Was only intended for internal use, will be removed.

toString(Object, DecimalFormat) - Static method in class chemaxon.jep.Evaluator

Deprecated, for removal: This API element is subject to removal in a future version.

Was only intended for internal use, will be removed.

toString(String) - Method in class chemaxon.sss.search.SearchOptions

Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)

toString(String, boolean) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Creates the string representation of the pharmacophore fingerprint.

toString(Node) - Method in class chemaxon.descriptors.MDParameters

Returns parts of the parameter values in string.

TOWARDS_EITHER_BRIDGE - Static variable in class chemaxon.struc.BicycloStereoDescriptor

Direction of the ligand is not defined, it can be oriented towards both of the bridges (e.g.

TOWARDS_HIGHER_BRIDGE - Static variable in class chemaxon.struc.BicycloStereoDescriptor

The ligand is towards the bridge with the higher index.

TOWARDS_LOWER_BRIDGE - Static variable in class chemaxon.struc.BicycloStereoDescriptor

The ligand is towards the bridge with the lower index.

TOXIC - Enum constant in enum class com.chemaxon.calculations.admet.HergClass

TPSA - Class in chemaxon.descriptors.scalars

Implements TPSA (Topological Polar Surface Area) value as a scalar descriptor.

TPSA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction

Topological polar surface area.

TPSA - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Topological polar surface area.

TPSA() - Constructor for class chemaxon.descriptors.scalars.TPSA

Creates a new, empty logD descriptor.

TPSA(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.TPSA

Copy constructor.

TPSA(SDParameters) - Constructor for class chemaxon.descriptors.scalars.TPSA

Creates a new instance according to the parameters given.

TPSA(String) - Constructor for class chemaxon.descriptors.scalars.TPSA

Creates a new instance according to the parameters given.

TPSAPlugin - Class in chemaxon.marvin.calculations

Plugin class for TPSA (topological polar surface area) calculation.

TPSAPlugin() - Constructor for class chemaxon.marvin.calculations.TPSAPlugin

Constructor.

TRANS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue

2 dimension: The rigid part's maximal indexed ligands placed in different half-plane according to the rigid part.
0 dimension: TRANS stereo value was set on the double bond for it's maximal indexed ligands.

TRANS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue.E.

TRANS - Static variable in interface chemaxon.struc.StereoConstants

Trans double bond.

TransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans

Filter for TRANS double bonds.

TransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter

transDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the TRANS double bonds.

transfer - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

The Transferable which represents the clipboard data.

TRANSFER_BUTTON_ICON - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "transferButtonIcon".

TRANSFER_BUTTON_TEXT - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "transferButtonText".

TRANSFER_BUTTON_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "transferButtonVisible".

TransferableDescriptor - Class in chemaxon.marvin.modules.datatransfer

Data object to store lookup information for MTransferable objects.

TransferableDescriptor(String, String, Integer, Integer, boolean, boolean) - Constructor for class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Deprecated.

since 5.3.3 new descriptor parameter added.

TransferableDescriptor(String, String, Integer, Integer, boolean, boolean, boolean) - Constructor for class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Constructs a TransferableDescriptor object.

transform(CTransform3D) - Method in class chemaxon.struc.MDocument

Transforms all object's coordinates.

transform(CTransform3D) - Method in class chemaxon.struc.MoleculeGraph

Apply a transformation matrix to the atomic coordinates.

transform(CTransform3D) - Method in interface chemaxon.struc.MTransformable

Transformation.

transform(CTransform3D) - Method in class chemaxon.struc.NoStructure

Transforms the location of the object

transform(CTransform3D) - Method in class chemaxon.struc.prop.MHCoords3DProp

Transforms the coordinates.

transform(CTransform3D) - Method in class chemaxon.struc.SelectionMolecule

Apply a transformation matrix to the atomic coordinates.

transform(CTransform3D, boolean) - Method in class chemaxon.struc.MolAtom

Apply a transformation matrix to the coordinates.

transform(CTransform3D, boolean) - Method in class chemaxon.struc.Molecule

Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.

transform(CTransform3D, boolean) - Method in class chemaxon.struc.MoleculeGraph

Apply a transformation matrix to the atomic coordinates.

transform(CTransform3D, boolean) - Method in class chemaxon.struc.RgMolecule

Apply a transformation matrix to the atomic coordinates.

transform(CTransform3D, boolean) - Method in class chemaxon.struc.RxnMolecule

Apply a transformation matrix to the atomic coordinates and the reaction arrow.

transform(CTransform3D, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom

Apply a transformation matrix to the coordinates.

transform(CTransform3D, int) - Method in class chemaxon.struc.MDocument

Transforms all object's coordinates.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Does not perform any operation.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MBracket

Transforms the bracket.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct

Transforms all points.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Does not perform any operation.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MMidPoint

Transforms all points.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Transforms all points.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MNameTextBox

Transforms all points, scales the arrow head widths and lengths.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Transforms all points, scales the arrow head widths and lengths.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Transforms the rectangle.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint

Transforms all points.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.graphics.MTextBox

Transforms all points and scales the font size.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MDocument

Transforms all object's coordinates.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MObject

Transforms the object.

transform(CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MPoint

Transforms all points.

transform(CTransform3D, CTransform3D, int, CTransform3D) - Method in class chemaxon.struc.MDocument

Transforms all object's coordinates.

transform(DPoint3) - Method in class chemaxon.struc.CTransform3D

Transforms a point.

transform(Molecule) - Method in interface chemaxon.standardizer.ConcurrentStandardizerProcessor.MolTransformer

Transforms and returns the molecule (the transformed input molecule is returned, no new molecule object is created).

transform(Molecule) - Method in interface com.chemaxon.search.transformation.Transformer

Transforms a Molecule.

transform(Molecule) - Method in enum class com.chemaxon.search.transformation.transformers.Aromatizer

TRANSFORM_DISTORT - Static variable in class chemaxon.struc.MObject

Distorting transformations are allowed.

TransformAction - Class in chemaxon.standardizer.advancedactions

Transformation standardizer action

TransformAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.TransformAction

Initializes the action with parameters

TRANSFORMATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

TransformationException - Exception in com.chemaxon.search.transformation

Exception thrown during transformation.

TransformationException() - Constructor for exception com.chemaxon.search.transformation.TransformationException

TransformationException(String) - Constructor for exception com.chemaxon.search.transformation.TransformationException

TransformationException(String, Throwable) - Constructor for exception com.chemaxon.search.transformation.TransformationException

TransformationException(Throwable) - Constructor for exception com.chemaxon.search.transformation.TransformationException

transformByParent(CTransform3D, boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Applies a transformation matrix to the Data Sgroup coordinates.

transformByParent(CTransform3D, boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Applies a transformation matrix to the Sgroup coordinates.

transformByParent(CTransform3D, boolean) - Method in class chemaxon.struc.Sgroup

Applies a transformation matrix to the coordinates.

transformCT(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond

Transform cis/trans stereo information into the `reference frame' of this bond.

Transformer - Interface in com.chemaxon.search.transformation

Transformer.

TRANSFORMER_SET_DIM_0 - Static variable in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Transformer: sets the molecule dimension to 0.

TransformerFactory - Class in com.chemaxon.search.transformation

Creates Molecule Transformer objects.

TransformerFactory() - Constructor for class com.chemaxon.search.transformation.TransformerFactory

transformReactionArrow(CTransform3D) - Method in class chemaxon.struc.RxnMolecule

Apply a transformation matrix to the reaction arrow.

transformTo2D() - Method in class chemaxon.struc.graphics.MRectangle

Rotate to the XY plane.

TRANSLATE_ROTATE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType

Translate and rotate only as a rigid body.

TRANSLATE_ROTATE_FLEXIBLE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType

Translate and rotate, and tweak rotatable bonds to adapt conformation.

TRANSLATE_ROTATE_FLEXIBLE_EXTRA - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType

As of AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).

TRIPLE - Enum constant in enum class chemaxon.struc.BondType

Triple bond type.

TRIPLE - Static variable in class chemaxon.struc.MolBond

Triple bond type.

tripletIndex(int, int, int) - Method in class chemaxon.descriptors.PFParameters

Calculates the index of a feature pair and distance triplet in the linearised representation of histograms.

TRIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Trivalent radical center.

TRIVALENT_DOUBLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Trivalent radical center with doublet electronic configuration.

TRIVALENT_QUARTET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical

Trivalent radical center with quartet electronic configuration.

TRUE - Static variable in class chemaxon.jep.ChemJEP

Logical result value: TRUE.

TRUE - Static variable in interface chemaxon.jep.CustomFunction

TRUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

TRUE - Static variable in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated.

tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.CubeRecognizer

Deprecated.

tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated.

tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated.

tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.Recognizer

Checks whether the parameter line can be part of a valid (format specified) file on the given file position.

tryToRecognize(String, int) - Method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated.

tryToRecognize(String, int, RecognizerList) - Method in class chemaxon.formats.recognizer.Recognizer

Deprecated, for removal: This API element is subject to removal in a future version.

Not used in recognition and will be removed. Implement Recognizer.tryToRecognize(String, int) instead.

Ts - Static variable in class chemaxon.core.ChemConst

tversky(float[], float, float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates Tversky dissimilarity for floating point values.

tversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates Tversky dissimilarity index for integer values.

TVERSKY - Enum constant in enum class chemaxon.descriptors.MetricsType

tverskyA - Variable in class chemaxon.descriptors.MDParameters

alpha values for tversky dissimilarity

tverskyB - Variable in class chemaxon.descriptors.MDParameters

beta values for tversky dissimilarity

twicesumbonds(boolean, boolean) - Method in class chemaxon.struc.MolAtom

Calculates the total number of bonding electrons, excluding implicit hydrogens.

TWO_HEADED_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule

Two headed double reaction arrow type.

TWO_HEADED_SINGLE - Static variable in class chemaxon.struc.RxnMolecule

Two headed single reaction arrow type.

TXT - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

type - Variable in class chemaxon.checkers.StructureCheckOptions

The output type of the structure check (one or two files)

type - Variable in class chemaxon.marvin.services.ServiceArgument

type of the argument

TYPE - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the type of source for the structure.

TYPE_3D_COORDS - Static variable in class chemaxon.struc.MProp

TYPE_ARRAY_BYTE - Static variable in class chemaxon.struc.MProp

TYPE_ARRAY_DOUBLE - Static variable in class chemaxon.struc.MProp

TYPE_ARRAY_INTEGER - Static variable in class chemaxon.struc.MProp

TYPE_BOOLEAN - Static variable in class chemaxon.struc.MProp

TYPE_CAS - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a CAS Registry Number^®.

TYPE_CDX - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is an embedded ChemDraw structure.

TYPE_COLLECTION_HASH - Static variable in class chemaxon.struc.MProp

TYPE_COLLECTION_LIST - Static variable in class chemaxon.struc.MProp

TYPE_COMMON - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a common name.

TYPE_CONFORMER_DESCRIPTOR - Static variable in class chemaxon.struc.MProp

TYPE_COUNT - Static variable in class chemaxon.struc.RxnMolecule

Number of structure types.

TYPE_DISTR - Static variable in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Type constant for microspecies distribution.

TYPE_DISTR - Static variable in class chemaxon.marvin.calculations.pKaPlugin

Type constant for microspecies distribution.

TYPE_DOUBLE - Static variable in class chemaxon.struc.MProp

TYPE_EC - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is an EC Number.

TYPE_FONT - Static variable in class chemaxon.struc.MProp

TYPE_GENERIC - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a generic name, for instance "C1-C4 alkyl".

TYPE_INCHI - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is an InChI string.

TYPE_INTEGER - Static variable in class chemaxon.struc.MProp

TYPE_ION - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is an ion abbreviation, for instance K+ or Ca2+.

TYPE_KEY - Static variable in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

Key of type for parsing and property change

TYPE_KEY - Static variable in class chemaxon.standardizer.actions.AromatizeAction

Key of type for parsing and property change

TYPE_KEY - Static variable in class chemaxon.standardizer.actions.ClearStereoAction

Key of type for parsing

TYPE_KEY - Static variable in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

Key of type for parsing and property change

TYPE_KEY - Static variable in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

Key of type for parsing and property change

TYPE_KEY - Static variable in class chemaxon.standardizer.advancedactions.Clean2DAction

Key of type for parsing and property change

TYPE_MASK - Static variable in class chemaxon.struc.MolBond

The lowest bits of the flags that store the bond type.

TYPE_MASK - Static variable in class chemaxon.struc.RxnMolecule

Component type mask.

TYPE_MDOCUMENT_PROP - Static variable in class chemaxon.struc.MProp

TYPE_MOLECULE - Static variable in class chemaxon.struc.MProp

TYPE_MRV - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is an embedded Chemaxon MRV structure.

TYPE_OBJECT - Static variable in class chemaxon.struc.MProp

TYPE_OSR - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a structure image recognized by Optical Structure Recognition.

TYPE_PEPTIDE - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a peptide notation, for instance Val-Gly-Ser-Ala.

TYPE_SMILES - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a SMILES string.

TYPE_STRING - Static variable in class chemaxon.struc.MProp

TYPE_SYMYX - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is an embedded Symyx/ISIS draw structure.

TYPE_SYSTEMATIC - Static variable in class chemaxon.naming.document.DocumentToStructure

Possible value for the DocumentToStructure.TYPE property: the source is a systematic name.

TYPE_VOLUMETRIC_DATA - Static variable in class chemaxon.struc.MProp

TypeConverter() - Constructor for class chemaxon.checkers.StructureCheckOptions.TypeConverter

typeLabel(int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

types - Variable in class chemaxon.checkers.AtomTypeChecker

A List of String which represents the types should be checked in the molecule

U

U - Static variable in class chemaxon.core.ChemConst

UI_DISABLED_GROUP_TYPES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

UNBALANCED_REACTION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing reactions scheme having more atoms on one side of the reaction arrow than on the other.

UnbalancedReactionChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting reaction schemes having more atoms on one side of the reaction arrow than on the other.

UnbalancedReactionChecker() - Constructor for class chemaxon.checkers.UnbalancedReactionChecker

Creates a new UnbalancedReactionChecker instance.

UNDECIDED - Static variable in class chemaxon.jep.ChemJEP

Logical result value: UNDECIDED.

UNDECIDED - Static variable in interface chemaxon.jep.CustomFunction

UNDECIDED - Static variable in interface chemaxon.nfunk.jep.function.PostfixMathCommandI

Deprecated.

UNDEF_R_MATCHING_ALL - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

UNDEF_R_MATCHING_GROUP - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

UNDEF_R_MATCHING_GROUP_H - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

UNDEF_R_MATCHING_GROUP_H_EMPTY - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

UNDEF_R_MATCHING_UNDEF_R - Static variable in interface chemaxon.sss.SearchConstants

Option value constant.

UndefinedSolubilityCategory() - Constructor for class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory

UNDETACH_BY_X - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "undetachByX".

undo() - Method in class chemaxon.marvin.beans.MSketchPane

Invokes an undo command.

UNDO - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "undo".

UngroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which ungroups all abbreviated groups in the molecule

UngroupFixer() - Constructor for class chemaxon.fixers.UngroupFixer

ungroupSgroup(int) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.

ungroupSgroup(int, int) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.

ungroupSgroup(Sgroup) - Method in class chemaxon.struc.Molecule

Ungroups the specified S-group and expands it if it is an Expandable S-group.

ungroupSgroup(Sgroup, int) - Method in class chemaxon.struc.Molecule

Expand and ungroup the specified S-group.

ungroupSgroups() - Method in class chemaxon.struc.Molecule

Expands and ungroups all S-groups.

ungroupSgroups(int) - Method in class chemaxon.struc.Molecule

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 6.3. use Molecule.ungroupSgroups(EnumSet) instead.

ungroupSgroups(EnumSet<SgroupType>) - Method in class chemaxon.struc.Molecule

Ungroups all S-groups of the specified types in this molecule.

UngroupSgroupsAction - Class in chemaxon.standardizer.actions

Standardizer action un-groups s-groups of the target molecule

UngroupSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.UngroupSgroupsAction

Initializes the action

unhighlight(MObject) - Method in class chemaxon.struc.MDocument

Unhighlights an object.

unhighlightAll() - Method in class chemaxon.struc.MDocument

Unhighlights all objects.

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue

2 dimension: the maximal indexed ligand's bonds angle is close to 180 degrees.
0 dimension: no stereo configuration was set on the double bond, or the rigid part is not just one double bond.

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

UNKNOWN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue

UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue.UNKNOWN.

UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue.UNKNOWN.

UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue.UNKNOWN.

UNKNOWN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue.UNKNOWN.

UnknownAtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop

Filter for unknown atrop stereo centers.

UnknownAtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter

unknownAtropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the UNKNOWN atrop stereocenters.

UnknownAxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial

Filter for unknown axial centers.

UnknownAxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter

unknownAxialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the UNKNOWN axial stereocenters.

unknownResolvedStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the unknown, resolved tetrahedral stereogenic centers.

unknownResolvedStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the unknown, resolved tetrahedral stereogenic centers (with attached data).

UnknownResolvedTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral

Filter for unknown, resolved tetrahedral centers.

UnknownResolvedTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter

unmap(Molecule) - Static method in class com.chemaxon.mapper.AutoMapper

Remove atom maps from the given structure

UnmapAction - Class in chemaxon.standardizer.actions

Unmap reaction standardizer action

UnmapAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.UnmapAction

Initializes the action

unorderedIterator() - Method in class chemaxon.struc.prop.MCollectionProp

Gets an unordered iterator for the entries.

unorderedIterator() - Method in class chemaxon.struc.prop.MHashProp

Gets an iterator for the entries.

unorderedIterator() - Method in class chemaxon.struc.prop.MListProp

Gets an iterator for the entries.

unresolvedStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the unresolved tetrahedral stereogenic centers.

unresolvedStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis

Calculates the unresolved tetrahedral stereogenic centers (with attached data).

UnresolvedTetrahedralFilter - Class in com.chemaxon.calculations.stereoanal.filters.tetrahedral

Filter for unresolved tetrahedral centers.

UnresolvedTetrahedralFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter

unRgroupAtoms(Set<?>) - Method in class chemaxon.struc.RgMolecule

Ungroup R-groups consisting of the specified atoms and make them be part of root.

unselectContents() - Method in class chemaxon.struc.graphics.MChemicalStruct

Unselects atoms.

unselectContents() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Unselects atoms.

unselectContents() - Method in class chemaxon.struc.graphics.MPolyline

Unselects the points.

unselectContents() - Method in class chemaxon.struc.graphics.MTextBox

Unselects text.

unselectContents() - Method in class chemaxon.struc.MObject

Unselects sub-objects.

unSelectInDocument(MDocument) - Static method in class chemaxon.struc.NoStructure

Removes the selection from all NoStructure labels in the document.

UNSPECIFIED_AROMATICITY - Static variable in class chemaxon.struc.MolAtom

Atom aromaticity is not specified explicitly.

UNSUPPORTED - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

UNUSED_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that molecule with unused R-group definition found

UnusedRGroupChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting unused R-group definitions.

UnusedRGroupChecker() - Constructor for class chemaxon.checkers.UnusedRGroupChecker

Initializes the checker

UP - Static variable in class chemaxon.struc.MolBond

Single bond up flag.

updateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated.

as of Marvin 6.2, use SuperatomSgroup.calculateAttachmentPoints() instead

updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.graphics.MBracket

updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Calculate the bounding rectangle.

updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.graphics.MReactionSign

updateBoundingRect(double[], CTransform3D) - Method in class chemaxon.struc.MObject

Calculate the bounding rectangle.

updateBoundingRect(double[], CTransform3D, double) - Method in class chemaxon.struc.MObject

Calculate the bounding rectangle.

updateComponentRoles() - Method in class chemaxon.struc.RxnMolecule

Updates fragment roles in the molecule.

updateDifLoc(DPoint3) - Method in class chemaxon.struc.graphics.MElectron

updateDifLoc(DPoint3[]) - Method in class chemaxon.struc.graphics.MElectronContainer

updateDim(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Updates the dimensions when fusing two structures.

updateFields(MDocument) - Method in class chemaxon.marvin.view.swing.TableOptions

Update fields of SDF table

updateFields(MDocument[]) - Method in class chemaxon.marvin.view.swing.TableOptions

Update fields of SDF table

updateStatistics(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator

Updates statistics gathered on fingerprints generated.

updateStatistics(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeGenerator

updateSubLevel(double[], double, int) - Method in class chemaxon.struc.graphics.MTextDocument

UpperBoundCalculator - Interface in com.chemaxon.search.mcs.upperbound

An interface for providing upper bound calculation for MaxCommonSubstructure (MCS) search.

URL - Static variable in class chemaxon.marvin.services.ServiceDescriptor

Property key for service URL as String

USE_DEFAULT_SALTS_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction

Property key for use default salts modification

USE_DEFAULT_SOLVENTS_KEY - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

Property key for use default solvent modification

USE_DO_LABEL - Static variable in class chemaxon.marvin.swing.MAction

Use short `do' label instead of name for the created menu item.

USE_WARNINGS - Static variable in class chemaxon.marvin.common.ParameterConstants

Constant key to set wether the user wants to see warnings or not.

USE_WHAT_LABEL - Static variable in class chemaxon.marvin.swing.MAction

Use short `what' label instead of name for the created menu item.

useCorrectionLibrary(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin

Deprecated.

Use pKaPlugin.setCorrectionLibrary(String)

USED_JARS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "usedJars".

USEFUL - Static variable in class chemaxon.sss.search.MolComparator

Describes that the MolComparator should be used with the current search object and the current query, regardless of the target.

useOnlyFirstAtomInStereoCalculation - Variable in class chemaxon.struc.MoleculeGraph

useOnlyFirstAtomInStereoCalculation(boolean) - Method in class chemaxon.struc.MoleculeGraph

Set how parity module should interpret wedes.

useOpticalCharacterRecognition - Variable in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions

Whether to use Optical Character Recognition on images.

useOpticalCharacterRecognition(Boolean) - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

usePopups(boolean) - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

USER_CHECKERS_CONFIG_PATH - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader

Deprecated, for removal: This API element is subject to removal in a future version.

Configuration file URL can be set in MarvinSketch preferences, and stored in UserSettings.

USER_DEFINED - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod

User defined logP calculation method.

USER_DEFINED_CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Users checker configuration file name

USER_DEFINED_CHECKERCONFIG_XML - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory

Users checker configuration file name

USER_DEFINED_STANDARDIZERCONFIG_XML - Static variable in class chemaxon.standardizer.StandardizerActionFactory

Users standardizer action configuration file name

USER_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader

path to user-defined standardizer action configuration list

UserSettings - Class in chemaxon.marvin.common

Represents the settings of the MarvinSketch and MarvinView applications.

UserSettings() - Constructor for class chemaxon.marvin.common.UserSettings

Construct a UserSettings object based on the default configuration, and the marvin.properties file stored in the chemaxon settings directory in the home directory of the user.

UserSettings(UserSettings) - Constructor for class chemaxon.marvin.common.UserSettings

Copy consturctor.

UserSettings(InputStream) - Constructor for class chemaxon.marvin.common.UserSettings

UserSettings(String) - Constructor for class chemaxon.marvin.common.UserSettings

Construct a UserSettings object based on the default configuration, and the file stored in the chemaxon settings directory in the home of the user.

UUID - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

V

V - Static variable in class chemaxon.core.ChemConst

VAGUE_BOND_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for vague bond level HALF.

VAGUE_BOND_LEVEL_HALF - Static variable in interface chemaxon.sss.SearchConstants

Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1.

VAGUE_BOND_LEVEL1 - Static variable in interface chemaxon.sss.SearchConstants

Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries.

VAGUE_BOND_LEVEL2 - Static variable in interface chemaxon.sss.SearchConstants

Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search.

VAGUE_BOND_LEVEL3 - Static variable in interface chemaxon.sss.SearchConstants

Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search.

VAGUE_BOND_LEVEL4 - Static variable in interface chemaxon.sss.SearchConstants

Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search.

VAGUE_BOND_OFF - Static variable in interface chemaxon.sss.SearchConstants

Option value constant to disable vague bond matching.

VALENCE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that valence error had found in the molecule

VALENCE_CHECK - Static variable in class chemaxon.struc.MoleculeGraph

Valence check calculation bit in flags.

VALENCE_CHECK_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph

Deprecated, for removal: This API element is subject to removal in a future version.

As of Marvin 6.0, replaced by ValenceCheckOptions.

VALENCE_CHECK_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "valenceCheckEnabled".

VALENCE_CHECKED - Static variable in class chemaxon.struc.MolAtom

Valence checked if this flag is set.

VALENCE_ERROR - Static variable in class chemaxon.struc.MolAtom

The atom has valence error if this flag is set.

VALENCE_ERROR_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "valenceErrorVisible".

VALENCE_ERROR_VISIBLE_IN_VIEW - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "valenceErrorVisibleInView".

VALENCE_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type representing that an atom has a valence property set.

VALENCE_PROPERTY_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "valencePropertyVisible".

valenceCheck() - Method in class chemaxon.struc.MolAtom

Valence checking.

valenceCheck() - Method in class chemaxon.struc.MoleculeGraph

Check valence and query property errors for atoms.

valenceCheck(List<MolAtom>) - Method in class chemaxon.struc.MoleculeGraph

Check valence and query property errors.

ValenceCheckOptions - Class in chemaxon.core.calculations.valencecheck

Class created to make valence calculation configurable.

ValenceCheckOptions(boolean, boolean) - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions

Deprecated, for removal: This API element is subject to removal in a future version.

since Marvin 6.2, Use ValenceCheckOptions.Builder for building ValenceCheckOptions.

ValenceCheckOptions.Builder - Class in chemaxon.core.calculations.valencecheck

Builder for ValenceCheckOptions.

VALENCEERROR_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom(s) connected to an atom which have valence error.

ValenceErrorChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atoms with invalid valences.

ValenceErrorChecker() - Constructor for class chemaxon.checkers.ValenceErrorChecker

Default constructor

ValenceErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ValenceErrorChecker

Parameterized constructor.

ValenceFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which fixes valence problem in the molecule if it is possible with removing explicit hydrogens or by adding charge

ValenceFixer() - Constructor for class chemaxon.fixers.ValenceFixer

ValencePropertyChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atoms having an explicitly set valence property.

ValencePropertyChecker() - Constructor for class chemaxon.checkers.ValencePropertyChecker

Creates a new ValencePropertyChecker instance.

ValencePropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ValencePropertyChecker

Creates a new ValencePropertyChecker instance.

value - Variable in class chemaxon.marvin.services.ServiceArgument

value of the argument

value() - Method in class chemaxon.calculations.bbb.BBB.Property

value() - Method in class chemaxon.calculations.cnsmpo.CnsMpo.Property

value() - Element in annotation interface chemaxon.fixers.Fixes

The error type values

value() - Element in annotation interface chemaxon.fixers.FixesExternal

The error code values

value() - Element in annotation interface chemaxon.jep.ChemContext.ProvidesFunctionContainer

valueOf(int) - Static method in enum class com.chemaxon.search.AromatizationMethod

Gets the aromatization method corresponding to the given int code.

valueOf(String) - Static method in enum class chemaxon.calculations.bbb.BBBFunction

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.calculations.dipole.DipoleResult.Unit

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.calculator.CalculatorTag

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.checkers.CheckerSeverity

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.checkers.FixMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckerErrorType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckOptions.Mode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckOptions.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.common.swing.io.output.FileSaveResult

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.descriptors.MetricsType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.calculations.LogPMethod

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.collecting.Consent

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.io.MolImportModule.PreferredView

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.HaltOnErrorOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.HomologyTranslationOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.TautomerEqualityMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.sss.search.options.TautomerTransformationMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.AtomProperty.Radical

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.BondType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.SgroupType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class chemaxon.struc.stereo.EZConfiguration

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.admet.HergClass

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.solubility.SolubilityUnit

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo

Deprecated.

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo

Deprecated.

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated.

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo

Deprecated.

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.common.annotations.RemovalDate

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.mapper.Mapper.MappingStyle

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.search.AromatizationMethod

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.search.mcs.RingHandlingMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.search.mcs.SearchMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.chemaxon.search.transformation.transformers.Aromatizer

Returns the enum constant of this class with the specified name.

values() - Static method in enum class chemaxon.calculations.bbb.BBBFunction

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.calculations.dipole.DipoleResult.Unit

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.calculator.CalculatorTag

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.checkers.CheckerSeverity

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.checkers.FixMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.checkers.StructureCheckerErrorType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.checkers.StructureCheckOptions.Mode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.checkers.StructureCheckOptions.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.common.swing.io.output.FileSaveResult

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.descriptors.MetricsType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.NodeType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AlignmentProperties

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.calculations.LogPMethod

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.collecting.Consent

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.io.MolImportModule.PreferredView

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.marvin.services.json.JsonServiceDescriptor.Method

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.ImageFormat

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.HaltOnErrorOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.HomologyTranslationOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.TautomerEqualityMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.sss.search.options.TautomerTransformationMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.advancedactions.Clean2DAction.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.AtomProperty.Radical

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.BondType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.SgroupType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class chemaxon.struc.stereo.EZConfiguration

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.admet.HergClass

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.solubility.SolubilityUnit

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo

Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo

Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo

Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.common.annotations.RemovalDate

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.mapper.Mapper.MappingStyle

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.search.AromatizationMethod

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.search.mcs.RingHandlingMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.search.mcs.SearchMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.chemaxon.search.transformation.transformers.Aromatizer

Returns an array containing the constants of this enum class, in the order they are declared.

VAN_DER_WAALS - Static variable in class chemaxon.marvin.calculations.MSAPlugin

Surface area type: 3D van der Waals surface area.

VARARG - Static variable in interface chemaxon.jep.ChemContext

A possible value for ChemContext.ProvidesFunction.maxParameterCount(), signaling that there is no maximum.

VARARG - Static variable in interface chemaxon.jep.CustomFunction

The multiplicity that marks a function vararg.

verbose - Variable in class chemaxon.sss.search.SearchOptions

For debugging purposes.

verbose(Object) - Method in interface chemaxon.marvin.calculations.StructuralFrameworksPlugin.VerbosePrinter

Log a verbose message

verify3d() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Returns true if 3D structure will be checked for a valid stereo conformation.

verifyParameters() - Method in class chemaxon.marvin.plugin.gui.ParameterPanel

Verifies parameters on the parameter panel.

verifyParameters() - Method in interface com.chemaxon.calculations.gui.ParameterPanelHandler

Verifies parameters on the parameter panel.

VERSION - Static variable in class chemaxon.marvin.beans.MarvinPane

Marvin version.

VersionInfo - Class in com.chemaxon.version

Provides version information of Chemaxon products.

VersionInfo() - Constructor for class com.chemaxon.version.VersionInfo

VH_AUTO - Static variable in class chemaxon.marvin.view.swing.TableOptions

Automatic view selection.

VH_GRIDBAG - Static variable in class chemaxon.marvin.view.swing.TableOptions

Molecule matrix view.

VH_SPREADSHEET - Static variable in class chemaxon.marvin.view.swing.TableOptions

Record oriented view.

VIEW_ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "viewAnyBond".

VIEW_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "viewCarbonVisibility".

VIEW_EXPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants

Deprecated, for removal: This API element is subject to removal in a future version.

As of release 5.3, this feature is deprecated and has no replacement. It will be removed in a future version of Marvin.

VIEW_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "viewHelp".

VIEW_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "viewLigandOrderVisibility".

VIEW_NAVIGATION_MODE_2D - Static variable in class chemaxon.marvin.common.ParameterConstants

VIEW_NAVIGATION_MODE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants

VIEW_ONLY - Static variable in class chemaxon.marvin.beans.MViewPane

Editing mode identifier meaning the structures cannot be edited.

VIEW_ONLY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "viewonly".

VIEW_PANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.view.ViewParameterConstants

VIEW_PANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.view.ViewParameterConstants

ViewParameterConstants - Class in chemaxon.marvin.view

Parameters of MarvinView Applet and Bean.
The parameters of the JMView applet can be set using the <param> HTML tag.

VISIBLE_COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "visibleCols".

VISIBLE_ROWS - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "visibleRows".

visitAt(AtropStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor

Visits atrop stereo centers.

visitAx(AxialStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor

Visits axial stereo centers.

visitCT(CisTransStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor

Visits cis-trans stereo centers.

visitTH(TetrahedralStereoCenter) - Method in interface com.chemaxon.calculations.stereoanal.filters.StereoCenterVisitor

Visits tetrahedral stereo centers.

VMN - Static variable in class chemaxon.formats.MFileFormat

W

W - Static variable in class chemaxon.core.ChemConst

waitForAll() - Method in interface chemaxon.marvin.view.TaskScheduler

Waits for all tasks to finish.

WARNING - Enum constant in enum class chemaxon.checkers.CheckerSeverity

This severity level should used for StructureChecker implementations which search for problematic features in a Molecule

warningMsgOn - Static variable in class chemaxon.marvin.calculations.TautomerizationPlugin

WAVY - Static variable in class chemaxon.struc.MolBond

Single bond wavy flag.

WedgeCleanAction - Class in chemaxon.standardizer.actions

Wedge clean standardizer action

WedgeCleanAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.WedgeCleanAction

Initializes the action

WedgeCleanFixer - Class in chemaxon.fixers

Deprecated.

WedgeCleanFixer() - Constructor for class chemaxon.fixers.WedgeCleanFixer

Deprecated.

WEDGED_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom(s) with wedge bonds.

WedgeErrorChecker - Class in chemaxon.checkers

Deprecated.

WedgeErrorChecker() - Constructor for class chemaxon.checkers.WedgeErrorChecker

Deprecated.

Default constructor

WEIGHT - Static variable in class chemaxon.marvin.alignment.MinMaxDistance

weightedAsymmetricEuclidean(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric Euclidean distance.

weightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric Euclidean distance.

weightedAsymmetricNormalizedEuclidean(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric normalized Euclidean distance.

weightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted asymmetric normalized Euclidean distance.

weightedEuclidean(float[], float[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted Euclidean distance.

weightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted Euclidean distance.

weightedNormalizedEuclidean(float[], float[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted normalized Euclidean distance.

weightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics

Calculates the weighted normalized Euclidean distance.

weights - Variable in class chemaxon.descriptors.MDParameters

weights for parametrized metrics

wienerIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.

wienerPolarity() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.

WIGGLY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents that wiggly bond had found in the molecule

WIGGLY - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Wiggly double bond type

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue

Equals to CIS | TRANS

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue

WIGGLY - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue

WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue.WIGGLY.

WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue.WIGGLY.

WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue.WIGGLY.

WIGGLY - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo

Deprecated, for removal: This API element is subject to removal in a future version.

Replaced by CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue.WIGGLY.

WIGGLY_BOND_TETRAHEDRAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType

Error type represents molecules having wiggly bonds on tetrahedral stereo centers

WigglyBondChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting wiggly bonds on tetrahedral stereo centers.

WigglyBondChecker() - Constructor for class chemaxon.checkers.WigglyBondChecker

Initializes a wiggly bond checker

WigglyDoubleBondChecker - Class in chemaxon.checkers

A descendant of BondChecker detecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.

WigglyDoubleBondChecker() - Constructor for class chemaxon.checkers.WigglyDoubleBondChecker

Default constructor

WigglyDoubleBondFixer - Class in chemaxon.fixers

Deprecated, for removal: This API element is subject to removal in a future version.

use ConvertToCrossedDoubleBondFixer

WigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.WigglyDoubleBondFixer

Deprecated.

WINDOW_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants

Identifier of parameter: "winScale".

windowActivated(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Do nothing.

windowActivated(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

windowClosed(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Do nothing.

windowClosed(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

windowClosing(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Close the window.

windowClosing(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Close the window.

windowDeactivated(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Do nothing.

windowDeactivated(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

windowDeiconified(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Do nothing.

windowDeiconified(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

windowIconified(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Do nothing.

windowIconified(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

windowOpened(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Do nothing.

windowOpened(WindowEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView

Do nothing.

WIRE_THICKNESS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "wireThickness".

withoutType(int, int) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

WORD_SEPARATORS - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Word separators used to form multi-line text if the text is too long.

wordLength() - Method in class chemaxon.marvin.io.Encoding

Gets the word length in bytes.

worked(long) - Method in interface chemaxon.util.progress.ProgressObserver

Notifies that a given number of work units has been completed.

workUnit(String) - Method in interface chemaxon.util.progress.ProgressObserver

Deprecated, for removal: This API element is subject to removal in a future version.

No longer used, will be removed.

wrapTextAndSetActualPoints(CTransform3D, double) - Method in class chemaxon.struc.graphics.MReactionSign

wrapTextAndSetActualPoints(CTransform3D, double) - Method in class chemaxon.struc.graphics.MTextBox

write(Molecule) - Method in class chemaxon.formats.MolExporter

Writes a molecule into the stream.

write(String) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter

write16doubles(ObjectOutput) - Method in class chemaxon.struc.CTransform3D

Writes the 4x4 matrix components as double precision floating point numbers.

write16floats(ObjectOutput) - Method in class chemaxon.struc.CTransform3D

Writes the 4x4 matrix components as single precision floating point numbers.

writeConfiguration(OutputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory

Writes the factory configuration to the output stream

writeConfiguration(OutputStream) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory

Writes the factory configuration to the output stream

writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MarvinPane

Saves object state.

writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MSketch

Saves the sketcher's state.

writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MSketchPane

Saves object state.

writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MView

Saves the viewer's state.

writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MViewPane

Saves object state.

writeExternal(ObjectOutput) - Method in class chemaxon.marvin.io.Encoding

Saves object state.

writeExternal(ObjectOutput) - Method in class chemaxon.struc.CTransform3D

Serializes a transformation matrix.

writeExternal(ObjectOutput) - Method in class chemaxon.struc.DPoint3

Serializes a 3D point.

writeExternal(ObjectOutput) - Method in class chemaxon.struc.graphics.MTextAttributes

writeExternal(ObjectOutput) - Method in class chemaxon.struc.graphics.MTextDocument

Saves the document.

writeExternal(ObjectOutput) - Method in class chemaxon.struc.MPropertyContainer

Saves the property container's state.

writeExternal(ObjectOutput) - Method in class chemaxon.struc.PageSettings

writeMetricParameter(ArrayList, String, int, boolean) - Method in class chemaxon.descriptors.MDParameters

Writes a given parameter of the specified metric into the corresponding tree node.

writeMol(ObjectOutput, Molecule) - Static method in class chemaxon.marvin.beans.MarvinPane

writeServiceDescriptors(List<ServiceDescriptor>, OutputStream) - Method in interface chemaxon.marvin.services.ServiceDescriptorWriter

Writes the descriptors to the specified output

WSDL - Static variable in class chemaxon.marvin.services.soap.SoapServiceDescriptor

Property key for Service descriptor as String

X

x - Variable in class chemaxon.struc.DPoint3

The x coordinate.

xCoordinate - Variable in class chemaxon.struc.MolAtom

X coordinate.

Xe - Static variable in class chemaxon.core.ChemConst

XML - Enum constant in enum class chemaxon.naming.document.annotate.DocumentAnnotator.DocumentType

XML_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

xml token of the action

XMLBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader

A descendant of ConfigurationReader which can read CheckerRunner configuration described Chemaxon's own checker configuration XML format (schema in jar: chemaxon/checkers/runner/configuration /reader/resoruce/checkerconfiguation.xsd)

XMLBasedConfigurationReader(InputStream) - Constructor for class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader

Initiate an XMLBasedConfigurationReader instance with the given inputSteam with the configuration

XMLBasedConfigurationReader(InputStream, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader

Initiate an XMLBasedConfigurationReader instance with the given inputSteam with the configuration

XMLRPCServiceDescriptor - Class in chemaxon.marvin.services.xmlrpcservice

ServiceDescriptor implementation for XML-RPC services.

XMLRPCServiceDescriptor() - Constructor for class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor

XMLRPCServiceHandler - Class in chemaxon.marvin.services.xmlrpcservice

ServiceHandler implementation for XML-RPC Services.

XMLRPCServiceHandler() - Constructor for class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceHandler

XmlToHtmlConverter - Class in chemaxon.naming.document.annotate

This class implements the default conversion from XML to HTML.

XmlToHtmlConverter() - Constructor for class chemaxon.naming.document.annotate.XmlToHtmlConverter

xmlToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo

Returns the XML tokens of the action as a string, divided by comma characters

XSTATE_C - Static variable in class chemaxon.struc.Sgroup

S-group is contracted (useful only in GUI!).

XSTATE_NONE - Static variable in class chemaxon.struc.Sgroup

S-group is in an undetermined state.

XSTATE_X - Static variable in class chemaxon.struc.Sgroup

S-group is expanded.

XSTATE_XC - Static variable in class chemaxon.struc.Sgroup

S-group is expanded but its atoms have the same coordinates as in contracted state.

xyz - Variable in class chemaxon.descriptors.PFParameters

The calculateXYZ() methods (in PharmacophoreFingerprint sub-classes) calculate three numbers (denoted by x,y and z), but methods in java cannot have output parameters.

XYZ - Static variable in class chemaxon.formats.MFileFormat

XYZ files.

Y

y - Variable in class chemaxon.struc.DPoint3

The y coordinate.

Y - Static variable in class chemaxon.core.ChemConst

Yb - Static variable in class chemaxon.core.ChemConst

yCoordinate - Variable in class chemaxon.struc.MolAtom

Y coordinate.

YES - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption

Stop on any errors during the search.

Z

z - Variable in class chemaxon.struc.DPoint3

The z coordinate.

Z - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue

Z - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration

Z_OR_UNSPEC - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration

zCoordinate - Variable in class chemaxon.struc.MolAtom

Z coordinate.

ZERO_BASED_ATOM_INDEXING - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier for parameter: "zeroBasedAtomIndexing" See Parameters and Events documentation.

ZERO_VECTOR - Static variable in class chemaxon.struc.DPoint3

Zn - Static variable in class chemaxon.core.ChemConst

ZOOM_TO_SCAFFOLD_ON_LOAD - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "zoomToScaffoldOnLoad".

Zr - Static variable in class chemaxon.core.ChemConst

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