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A

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

All identifiers.

A_ALL - Static variable in interface chemaxon.struc.Smolecule

Use all atom and bond property arrays.

A_ASTEREO - Static variable in interface chemaxon.struc.Smolecule

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

A_ATOMMAP - Static variable in interface chemaxon.struc.Smolecule

Use atom type array.

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

Identifier of the font's bold subattribute.

A_BOND - Static variable in interface chemaxon.struc.Smolecule

Use arrays to store bonds.

A_CHARGE - Static variable in interface chemaxon.struc.Smolecule

Use charge array.

A_CHIRALITY - Static variable in interface chemaxon.struc.Smolecule

Chirality.

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

Identifier of the x shift attribute.

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

Identifier of the y shift attribute.

A_EXPLH - Static variable in interface chemaxon.struc.Smolecule

Use explicit Hydrogen count array.

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

Identifier of the font attribute.

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

All font bits.

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

Identifier of the font family subattribute.

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

Identifier of the font size subattribute.

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

Identifier of the color attribute.

A_HYBRIDIZATION - Static variable in interface chemaxon.struc.Smolecule

Use hybridization state array.

A_IMPLH - Static variable in interface chemaxon.struc.Smolecule

Use implicit Hydrogen count array.

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

Identifier of the font's italic subattribute.

A_MASSNO - Static variable in interface chemaxon.struc.Smolecule

Use mass number array.

A_PARITY - Static variable in interface chemaxon.struc.Smolecule

Atom parity.

A_RADICAL - Static variable in interface chemaxon.struc.Smolecule

Use radical array.

A_RGROUP - Static variable in interface chemaxon.struc.Smolecule

Use R-group ID array.

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

Identifier of the font scale attribute.

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

Identifier of the subscript/superscript level attribute.

A_VALENCE - Static variable in interface chemaxon.struc.Smolecule

Use valence array.

AAMAP_MASK - Static variable in class chemaxon.struc.MolAtom

Atom map mask in flags.

AAMAP_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom-atom mapping number.

AAMAP_OFF - Static variable in class chemaxon.struc.MolAtom

Atom map offset in flags.

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

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

Property Key of the abbreviated group modification

ABBREVGROUP - Static variable in class chemaxon.formats.MFileFormat

Chemaxon SMILES Abbreviated Groups.

AbbrevGroupRecognizer - Class in chemaxon.formats.recognizer

Deprecated.

as of Marvin 2014.07.21.0 intended for internal use only

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

Deprecated.

ABBREVIATED_GROUP - chemaxon.checkers.StructureCheckerErrorType

Error type represents that abbreviated groups had found in the molecule

ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED - chemaxon.checkers.StructureCheckerErrorType

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

ABBREVIATED_GROUP_WITH_ONLY_EXPANDED - 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 - com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

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

ABS_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Absolute stereoconfiguration label visibility flag.

ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABSENT_CHIRAL_FLAG - 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.

use AddChiralFlagFixer

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

Deprecated.

ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Show absolute stereo label.

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

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

ABSOLUTE_STEREO_CONFIGURATION - chemaxon.checkers.StructureCheckerErrorType

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

AbsoluteStereoAction - Class in chemaxon.standardizer.actions

Deprecated.

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 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.

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

AbstractShapeComparator<T extends ShapeDescriptor> - Class in com.chemaxon.descriptors.alignment

AbstractShapeComparator(DescriptorGenerator<T>) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeComparator

AbstractShapeGenerator<D extends ShapeDescriptor,P extends AbstractShapeGeneratorParameter> - Class in com.chemaxon.descriptors.alignment

AbstractShapeGenerator(P) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGenerator

AbstractShapeGeneratorParameter - Class in com.chemaxon.descriptors.alignment

Helper class without the requested getDescriptorGenerator method.

AbstractShapeGeneratorParameter(AtomTyping) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter

AbstractStandardizerAction - Class in chemaxon.standardizer

Abstract implementation of the StandardizerAction.

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

Initializes the functionality of the abstract implementation.

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

Abstract class for Filter interface.

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

AbstractStructureChecker - Class in chemaxon.checkers

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

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

Constructor to create a Structure checker instance with the given errorType

AbstractStructureFixer - Class in chemaxon.fixers

This class is the default abstract implementation of StructureFixer interface

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

Constructor to create a Structure fixer

Ac - Static variable in class chemaxon.core.ChemConst

accept(Molecule) - Method in class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter

Accepts molecule if the number of R-group attachments in the molecule is exactly the attachment count specified in the constructor of this filter.

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

Returns true if molecule is accepted by the filter.

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

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

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

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

Accepts visitors.

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

accept(T) - Method in interface com.chemaxon.calculations.io.Sink

Deprecated.

ACCEPT_ONLY_SAME - chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase

Accepted - chemaxon.checkers.StructureCheckOptions.Type

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

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

Acceptor sign displayed in GUI.

ACCEPTOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint

ACCORD - Static variable in class chemaxon.formats.MFileFormat

ACCORD file format

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

ACCURATE - chemaxon.marvin.alignment.AlignmentAccuracyMode

Atomic contribution with correction terms.

ACCURATE - chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy

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

Constant denoting acidic pKa.

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

Deprecated.

Key of type for parsing and property change

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

Action handler.

ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

action string token of the checker

ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor

action string tokens of the fixer

ACTIONSTRING_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

action string token of the action

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

An implementation of ConfigurationReader for parsing action strings

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

Default constructor

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

Deprecated.

use ActionStringBasedConfigurationReader(String, CheckerFixerFactory) instead

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

Constructor with custom checker factory

actionStringToken() - Method in annotation type chemaxon.checkers.CheckerInfo

Returns the action string token of the checker

actionStringToken() - Method in annotation type chemaxon.fixers.FixerInfo

Returns the action string token of the fixer.

actionStringToken() - Method in annotation type chemaxon.standardizer.StandardizerActionInfo

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

activateContainerCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

The containing cell of the GraphicComponent will be the active cell of the scene.

active - Variable in class chemaxon.marvin.space.GraphicComponent

Is this component selected or not.

adaptiveSPHEX(int, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion

Sphere exclusion clustering with sphere radius inference.

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

Add a name to structure converter.

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

Adds a standardizer action class descriptor to the factory

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

Add the given point to this one.

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

Calculates the sum of the two vectors

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

Adds an atom to the molecule.

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

Adds an atom to the root structure.

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

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

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

Adds an atom to the molecule.

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

Adds a new atom to the S-group.

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

Adds a new atom to the S-group.

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

Adds a new atom to the S-group.

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

Adds an atom to the molecule.

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

Add a bond if it had not been already added.

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

Adds a bond to the molecule.

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

Adds a bond to the molecule.

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

Adds a bond to the root structure.

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

Adds a bond to a reactant, product, agent.

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

Adds a bond to the graph.

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

Add an edge if it had not been already added.

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

Add a bond to the molecule.

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

Add a bond to the molecule.

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

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

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

Adds an element.

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

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

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

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

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

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

ADD - chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Add absolute stereo

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

Identifier of parameter: "addRemoveHatomsEnabled".

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

Adds an action to the configuration

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

Adds an action listener.

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

Adds an action listener.

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

Adds actions to the configuration

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

Adds an action to the group

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

Adds an action to a list of groups

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

Adds atoms to the "added atom" list.

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

Adds atoms to the "added atom" list.

addAtom(int) - Method in interface chemaxon.struc.WSmolecule

Adds an atom.

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

Adds an atom to the "added atom" list.

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

Adds an atom to the "added atom" list.

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

Adds an atom from another Smolecule.

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

Adds an atom.

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

Adds an atom.

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

Adds an atom.

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

Adds an alignment constraint between the reference and aligned molecule.

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

Adds an alignment constraint between the reference and aligned molecule.

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

Adds all atoms and bonds to the specified molecule.

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

Adds an atom to a fragment.

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

Adds an atom to a fragment.

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

Adds an atom to a fragment.

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

Adds an atom to a fragment.

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

Adds an atom to the molecule.

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

Adds an atom without setting its parentGraph and index fields.

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

Adds an atom without setting its parentGraph and index fields.

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

Adds a new free attachment point for an atom.

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

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

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

Adds a new free attachment point.

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

Adds the attribute names to the specified list.

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

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

Adds the attribute names to the specified vector.

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

Adds the attribute names to the specified list.

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

Adds the attribute names to the specified vector.

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

Adds the attribute names to the specified list.

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

Adds the attribute names to the specified list.

addBond(int, int, int) - Method in interface chemaxon.struc.WSmolecule

Adds a bond.

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

Adds a bond.

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

Adds a bond.

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

Adds a bond.

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

Adds a bond without setting its parentGraph and index fields.

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

Adds a bracket to this S-group.

addCanvas(Container) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace viewer to the container.

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

Adds attribute names to the specified list.

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

Adds attribute names to the specified list.

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

Adds a central atom to this sgroup.

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

Adds a character to the text.

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

Adds a checker mark to the document.

addChildCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

Add a cluster to another cluster as a child cluster.

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

Adds a child S-group.

AddChiralFlagFixer - Class in chemaxon.fixers

Absent chiral flag fixer.

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

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

Add a comparator to the search object.

addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell

Adds a new component to this cell.

addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

Adds a component to the active or to the first cell.

addComponent(GraphicComponent, int) - Method in class chemaxon.marvin.space.GraphicScene

Adds a component to the cell having the given index.

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

Adds a reactant, product or agent.

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

Adds a reactant, product or agent.

addComponentToEmptyCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

Adds a component to an empty cell.

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

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

addCoordinateSystem(int) - Method in class chemaxon.marvin.space.GraphicScene

Adds a dummy graphic component that represents the coordinate system.

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

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

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

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

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

Adds a line to the data stored in the field.

addDataPoint(double, double) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot

Add new point to put.

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

Add a new step.

addDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent

Forces the component to set all drawing property stored in drawProperties, and leaves the old settings which are not overidden.

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

Deprecated.

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

             Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
             

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

Deprecated.

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

             Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
             

AddExplicitHydrogensAction - Class in chemaxon.standardizer.actions

Hydrogenization standardizer action

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

Initializes the action

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

Deprecated.

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

             Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
             

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

Adds a new function to the parser.

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

Adds a group definition to the group list of the action

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

Adds a group to the list defined by its abbreviation

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

Deprecated.

since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph) instead

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

Deprecated.

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

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

Deprecated.

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

addHeavyAtomLimitChecker(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Creates an input checker by calling CalculatorInputChecker.heavyAtomLimit(int) and adds it to this plugin.

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

Adds the help menu to a parent menu.

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

Adds HTML link handling to an editor pane.

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

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

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

Adds an input file.

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

Deprecated.

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

Adds an input stream.

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

Deprecated.

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

Adds an input file.

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

Deprecated.

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

Adds the specified input checker to this plugin.

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

Defines a label component inside the MarvinView table.

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

Defines a label component inside the MarvinView table.

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

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

Adds a listener if it is not yet added.

addListToDelete(int) - Method in class chemaxon.marvin.space.GraphicScene

Adds a gl list id to the deletion list

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

Deprecated.

since Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead

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

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

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

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

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

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

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

addMenuBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace menubar to the container.

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

Adds a menubar change listener.

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

Defines a molecule viewer component inside the MarvinView table.

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

Defines a molecule viewer component inside the MarvinView table.

addMolecule(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds a Molecule object to the actual cell of the viewer.

addMolecule(Molecule) - Method in class com.chemaxon.clustering.common.MolInputBuilder

Add a new structure.

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

Add molecule to align

addMolecule(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.

addMolecules(Collection<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder

Add multiple structures.

addMolecules(Iterator<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder

Add multiple structures.

addMolecules(Iterator<? extends Molecule>, StandardizerWrapper) - Method in class com.chemaxon.clustering.common.MolInputBuilder

Add multiple structures with preprocessing.

addMoleculeTo(Molecule, int) - Method in class chemaxon.marvin.space.MSpaceEasy

Makes the given cell to be the active cell, and adds the molecule to it.

addMoleculeToEmptyCell(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.

addMoleculeToEmptyCell(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.

addMoleculeWithoutChange(Molecule, boolean) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds a Molecule object to the actual cell of the viewer and resets the view only if required.

addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder

Allocate a new cluster.

addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

Allocate a new cluster.

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

User may define extra weights between colors defined at setColoringScheme.

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

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

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

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

Point added to a document.

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

Point added to a document.

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

Called when the object is added to a document.

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

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

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

Adds an object to the document.

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

Adds an object to the document.

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

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

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

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

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

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

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

Expands the set of parametrized metrics with a new item.

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

Adds a ParametrizedMetric node to the DOM tree.

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

Adds the ParametrizedMetrics node to the DOM tree.

addPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)

addPopupMenu() - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace popup menu to the JPanel.

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.

addReactionStep(List<Molecule>, List<Molecule>, List<Molecule>, MRArrow, int) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

Deprecated without replacement. The method had no effect.

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

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

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

Adds an R-group member.

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

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

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

Adds a definition member to an R-group bridge.

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

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

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

Adds a salt to the salt list of the action

addSelectionPanel(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace selection panel to the container.

addSelectionPanelAndProgressBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace selection panel to the container.

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

Adds an S-group to this object.

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

Adds an S-group to this object.

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

Adds an S-group to this object.

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

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

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

Adds S-groups to this object and its parent.

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

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

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

Adds a solvent to the solvent list of the action

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

Changes terminal carbon atoms to star atoms (*).

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

Adds a string to the text.

addStructuresToCluster(Collection<Integer>, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder

Add multiple structures to a cluster.

addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder

Set a structure to be a part of a cluster as a leaf.

addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

Add a structure to a cluster as an immediate leaf.

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

Add a thread-local name to structure converter.

addToolBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace toolbar to the container.

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

Deprecated.

Not used.

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

Adds the selected NoStrutures from the document to the selectionDocument

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

Add an element to marvinsketch's recent file list

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

Add an element to marvinview's recent file list

addTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler

Add a TransferableDescriptor to the MTransferable Registry.

addTransferable(String, String, Integer, Integer, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler

Deprecated.

use ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) instead.

addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler

Add a TransferableDescriptor to the registry, and constructing it by the given parameters.

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

Adds the given user-defined comparator to the search.

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

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

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

Checks whether the molecule has multiple chiral centres

AdvancedCheckerRunner - Class in chemaxon.checkers.runner

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

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

Constructs CheckerRunner with more advanced fixing capabilities.

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

Constructs CheckerRunner with more advanced fixing capabilities.

AdvancedCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner

Constructs CheckerRunner with more advanced fixing capabilities.

Ag - Static variable in class chemaxon.core.ChemConst

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

AGENTS - Static variable in class chemaxon.struc.RxnMolecule

"Agent" structure type.

Al - Static variable in class chemaxon.core.ChemConst

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

the alias of the argument

alias() - Method in annotation type chemaxon.checkers.Persistent

Returns the alias name of the annotated property

ALIAS - chemaxon.checkers.StructureCheckerErrorType

Error type represents that alias values had found in the molecule

ALIAS_ATOM - chemaxon.checkers.StructureCheckerErrorType

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

ALIAS_GROUP - chemaxon.checkers.StructureCheckerErrorType

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

ALIAS_NONE - 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.util.MolAligner

Execute best alignment based on hit map provided earlier

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

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

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

Rigid alignment on the user defined atom index

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

Align the given molecule to the reference.

ALIGN_AS_IS - 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 - chemaxon.descriptors.SimilarityCalculatorFactory.Representation

ALIGNMENT - Static variable in class chemaxon.license.LicenseManager

Identifier of product: Alignment

AlignmentAccuracyMode - Enum in chemaxon.marvin.alignment

Settings for the representation of a molecular shape.

AlignmentMolecule - Class in chemaxon.marvin.alignment

AlignmentMoleculeFactory - Class in chemaxon.marvin.alignment

Creates an AlignmentMolecule form a Molecule based on the settings.

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

AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.marvin.alignment

AlignmentPlugin - Class in chemaxon.marvin.calculations

Plugin layer for the AlignmentAPI

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

AlignmentProperties - Enum in chemaxon.marvin.alignment

AlignmentProperties.ColoringScheme - Enum in chemaxon.marvin.alignment

AlignmentProperties.ColorNotSpecifiedCase - Enum in chemaxon.marvin.alignment

AlignmentProperties.DegreeOfFreedomType - Enum in chemaxon.marvin.alignment

AlignmentProperties.FlexibilityMode - Enum in chemaxon.marvin.alignment

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

AlignmentProperties.NodeType - Enum in chemaxon.marvin.alignment

AlignmentProperties.OrientationType - Enum in chemaxon.marvin.alignment

AlignOnPairedAtoms - Class in chemaxon.marvin.alignment

Overlays two molecules using the user defined atom pairs
Example:

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

AlignRigidEasy - Class in chemaxon.marvin.alignment

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

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

ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aliphatic query atom.

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

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

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

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

Deprecated.

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

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

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

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

Deprecated.

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

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

Calculates the number of aliphatic ring systems of the molecule.

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

Deprecated.

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

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

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

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

Deprecated.

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

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

Identifies the aliphatic rings in the molecule.

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

Deprecated.

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

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

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

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

Deprecated.

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

ALL - chemaxon.sss.search.options.HomologyTranslationOption

All atoms can have translation.

ALL - chemaxon.sss.search.options.TargetHomologyMatchingMode

ALL_H - Static variable in class chemaxon.struc.MolAtom

Include any Hydrogen atom.

ALL_MATCH_AMBIG - 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 - chemaxon.marvin.alignment.AlignmentProperties.OrientationType

allringsystems - chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

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

All stereo centers of molecule.

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

All stereo centers with attached data.

Am - Static variable in class chemaxon.core.ChemConst

ambient - Static variable in class chemaxon.marvin.space.monitor.Control

AMBIGUOUS - com.chemaxon.search.transformation.transformers.Aromatizer

AMBIGUOUS_AROMATIC_ATOMS_IGNORED - chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

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

             molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             

AMINOACID - chemaxon.struc.SgroupType

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

Identifier of parameter: "aminoAcidBondColoringEnabled".

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

and(StandardizerWrapper) - Method in interface com.chemaxon.overlap.io.StandardizerWrapper

Create a new wrapper representing an additional step.

AND - com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType

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

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

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

Set of enhanced stereo flags.

ANGLE_STEP - Static variable in class chemaxon.struc.MolAtom

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

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

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

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

AngleMonitor - Class in chemaxon.marvin.space.monitor

Monitor for measuring angle between 3 components, the first 2 determines a line, the second 2 another.

AngleMonitor() - Constructor for class chemaxon.marvin.space.monitor.AngleMonitor

Creates a new instance of AngleMonitor

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

Identifier of parameter: "animate".

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

Identifier of parameter: "animDelay".

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

Identifier of parameter: "animFPS".

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

Identifier of parameter: "animSync".

ANIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint

ANTI - Static variable in interface chemaxon.struc.StereoConstants

Non-CIP stereodescriptor, anti (relative configuration).

ANY - chemaxon.struc.SgroupType

ANY - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the any atom A.

ANY - Static variable in class chemaxon.struc.MolBond

Any bond type.

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

anybond_auto - chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues

ANYBOND_AUTO - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

ANYBOND_AUTO_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

anybond_dashed - chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues

ANYBOND_DASHED - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

ANYBOND_DASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

ANYBOND_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

ANYBOND_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

anybond_solid - chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues

ANYBOND_SOLID - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

ANYBOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

ANYBOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

Use AnyBondStyle instead.

anyBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the drawing style for ANY bonds.

AnyBondStyle - Enum in chemaxon.marvin.paint.constants

Holds the values for the possible rendering styles for Any bonds.

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

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

anyCancelled(CancelObserver...) - Static method in class com.chemaxon.calculations.common.ProgressObservers

Returns a cancel observer which cancels when any of the specified observer is cancelled.

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

Appends a set of changes to the already existing changes.

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

Append text to end of document.

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

Append a character n times to the string buffer.

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

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

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

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

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

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

appendLongAsBinaryString(StringBuilder, long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness

Convert 64 bit long to binary string.

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

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

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

Extends internal data with a new parametrized metric.

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

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

Appends the pH text.

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

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

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

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

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

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

apply(BinaryVectorMetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory.ToLinenote

apply(MetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.MetricFactory.ToLinenote

APPLY_DEPTH_CUE - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

As of Marvin 5.4.1, replaced by DispOptConsts.AUTOMATIC_FOG

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

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

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

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

Ar - Static variable in class chemaxon.core.ChemConst

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

The default arc angle of the Braces Rectangle in degrees.

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

The default arc angle of the Rounded Rectangle in degrees.

areArrowsAndLikelyTheSame(MPolyline, MPolyline) - Static method in class chemaxon.marvin.modules.reaction.ReactionEditUtils

Compares type and checks perfect equality of location.

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

Gets the attachment points visibility.

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

Checks whether the child S-groups are visible.

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

Checks whether the child S-groups are visible.

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

Obtain monomer transformation information.

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

Tests whether two atoms are connected.

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

Are popup menus enabled?

areRGroupsHidden() - Method in class chemaxon.marvin.io.image.ImageExporter

ARO_R - chemaxon.calculations.bbb.BBBFunction

Number of aromatic rings.

AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph

Aromatization type for ambiguous 5-membered rings.

AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph

Basic aromatization.

AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph

Huckel aromatization.

AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph

General (Daylight conform) aromatization.

AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph

Loose aromatization.

AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph

Substructure aromatization.

AROMATIC - Static variable in class chemaxon.struc.MolAtom

Aromatic query atom.

AROMATIC - Static variable in class chemaxon.struc.MolBond

Aromatic bond type.

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

AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aromatic or aliphatic query atom.

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

AROMATIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint

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

Calculates the number of all aromatic atoms in the molecule.

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

Deprecated.

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

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

Calculates the number of all aromatic bonds in the molecule.

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

Deprecated.

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

AROMATICITY - chemaxon.checkers.StructureCheckerErrorType

Error type represents that aromaticity problem had found in the molecule

AromaticityCheckerResult - Class in chemaxon.checkers.result

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

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

Constructor which initialize all the properties.

AromaticityErrorChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting aromatization problems.

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

Default constructor.

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

Parameterized constructor.

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

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

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

Deprecated.

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

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

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

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

Deprecated.

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

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

Identifies the aromatic rings in the molecule.

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

Deprecated.

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

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

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

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

Deprecated.

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

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

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

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

Aromatize molecule using the default general aromatization method.

aromatize(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 in chemaxon.standardizer.actions

Type of aromatization

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

Aromatize or dearomatize molecules in all cells.

aromatizeBasic() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers

Wrap basic aromatization.

aromatizeGeneral() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers

Wrap general aromatization.

aromatizeLoose() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers

Wrap loose aromatization.

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

Aromatizer transformer.

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

Deprecated.

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

             CleanUtil.arrangeComponents(molecule, true, true);
             

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

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

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

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

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

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

arrangeCrossingBonds(MolBond, Molecule, boolean) - Static method in class chemaxon.marvin.util.MoleculeUtil

Deprecated.

as of Marvin 5.11.1 use MoleculeGraph.setBond(int, MolBond)

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

Arrange data attached to DataSgroup.

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

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

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

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

Arranges reaction components nicely

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

Arrange data attached to DataSgroup.

arrangeRgroupMembers(RgMolecule) - Method in class chemaxon.marvin.util.MolFragLoader

Arranges R-group definition member coordinates.

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

Arrange sgroup brackets in the molecule.

ArrayMDocSource - Class in chemaxon.marvin.io

MDocSource implementation for an array of documents or molecules.

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

Creates a document source for an array of documents.

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

Creates a document source for an array of molecules.

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

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

ARROW - chemaxon.marvin.io.image.ImageExporter.LineType

ARROW - chemaxon.marvin.paint.constants.CoordinateBondStyle

Arrow is used when rendering Coordinate bonds.

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

Arrow points back.

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

Crossed arrow flag.

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

Curved arrow flag.

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

Dashed arrow flag.

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

Equilibrium arrow flag.

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

Mask for the equilibrium and retrosynthetic arrow flags.

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

Mask for the curved, dashed and crosed arrow flags.

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

Only the left half of the arrow head is drawn.

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

Unshifted mask of the half arrow option bits in flags.

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

Only the right half of the arrow head is drawn.

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

Retrosynthetic arrow flag.

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

Arrow flags.

As - Static variable in class chemaxon.core.ChemConst

ASK - chemaxon.checkers.FixMode

on problem requests user interaction

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

associate(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent

The given component will depend on this component.

associatedComponents - Variable in class chemaxon.marvin.space.GraphicComponent

Strores components that depend on this component.

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

Calculates the number of atoms having four different ligands.

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

Deprecated.

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

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

Retrieves the indexes of atom having four different ligands.

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

Deprecated.

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

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

Calculates the asymmetric Euclidean distance.

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

Calculates the asymmetric Euclidean distance.

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

Calculates the asymmetric normalized Euclidean distance.

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

Calculates the asymmetric normalized Euclidean distance.

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

Calculates the asymmetric Tanimoto dissimilarity for floating point values.

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

Calculates the asymmetric Tanimoto dissimilarity for floating point values.

asymmetricXYZSum - Variable in class chemaxon.descriptors.PFParameters

Stores last calculatred asymmetric Tanimoto sum.

asymmetryFactors - Variable in class chemaxon.descriptors.MDParameters

asymmetry ratio of parametrized asymmetric metrics

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

Callback interface for asynchronous service calls

At - Static variable in class chemaxon.core.ChemConst

ATMAP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Show atom mapping flag.

ATNUM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Show atom numbers flag.

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

The atom whose the neighbours are processed.

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

Calculation domain type: calculation refers to atoms.

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

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

ATOM_COUNT - 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 - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Sets the atom font.

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

Identifier of parameter: "atomFontSize".

ATOM_MAP - chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom maps had found in the molecule

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

Identifier of parameter: "atomMappingVisible".

ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Displays atom mapping.

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

Identifier of parameter: "atomNumberingType".

ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Atom numbering type

ATOM_NUMBERS - chemaxon.marvin.io.image.ImageExporter.AtomNumberingType

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

Deprecated.

in 6.2.0 use atomNumberingType parameter instead.

ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Displays atom numbers.

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

Identifier of parameter: "atomPropertiesVisible".

ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

ATOM_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by mapping atom based property values to the surface.

ATOM_QUERY_PROPERTY - 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 - 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 - chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme

ATOM_VALUE - chemaxon.checkers.StructureCheckerErrorType

Error type represents that atom values had found in the molecule

atomA - Variable in class chemaxon.marvin.space.monitor.DihedralControl

atomAndBondColors(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Set the atom and bond colors.

atomB - Variable in class chemaxon.marvin.space.monitor.DihedralControl

AtomChecker - Class in chemaxon.checkers

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

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

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

AtomContext - Class in chemaxon.jep.context

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

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

Constructor.

atomCount - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent

atomCount - Variable in class chemaxon.struc.MoleculeGraph

The number of atoms.

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

Calculates the number of atoms in the molecule.

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

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

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

Calculates the number of atoms in the molecule.

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

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

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

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

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

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

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

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

ATOMCOUNT - chemaxon.standardizer.actions.RemoveFragmentAction.Measurement

Atom count of the molecule

atomFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Atom font type.

AtomIdentifier - Class in chemaxon.reaction

The identifier of an atom in the input of the reaction.

AtomIdentifier(int, int) - Constructor for class chemaxon.reaction.AtomIdentifier

Initializes an atom identifier based on the input molecules of the reaction.

AtomIdentifier(int, int, int) - Constructor for class chemaxon.reaction.AtomIdentifier

Initializes an atom identifier based on the input molecules of the reaction.

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

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

atomLabelSize(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the atom label font size.

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

Expansion type: atom list.

AtomMapChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atom maps.

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

Default constructor

atomMapMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder

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

Sets whether atom map numbers should be considered in search.

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

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

Array of atom - atom mapping.

atomMapping() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Displays atom mapping.

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

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

atomNumber() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Displays atom numbers.

atomNumberType(ImageExporter.AtomNumberingType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the type of atom numbering: Atom numbers or IUPAC numbering.

AtomProperty - Class in chemaxon.marvin.space

The AtomProperty class provides access to chemical properties of Molecule atoms by atom index.

AtomProperty - Class in chemaxon.struc

Class for storing atom property enumerations.

AtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty

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

AtomProperty.MoleculeAtomProperty - Class in chemaxon.marvin.space

AtomProperty.Radical - Enum in chemaxon.struc

Enumeration of the supported radicals.

AtomProperty.SmoleculeAtomProperty - Class in chemaxon.marvin.space

AtomQueryPropertyChecker - Class in chemaxon.checkers

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

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

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

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

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

AtomQueryPropertyCheckerResult - Class in chemaxon.checkers.result

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

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

Constructor which initialize all the properties.

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

Provides a list view of the atoms in the molecule.

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

Selection which contains atom indexes.

AtomSelection(int[], int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Deprecated.

AtomSelection(int, int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection

Deprecated.

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

Constructs an AtomSelection from lists.

atomSet - Variable in class chemaxon.struc.Sgroup

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

ATOMSIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Prefix of atom label font size parameter.

ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants

Either stereo atom type.

ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants

Stereo atom type mask.

ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants

No stereo atom type specified.

ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants

Specific stereo atom type.

AtomTypeChecker - Class in chemaxon.checkers

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

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

Default constructor.

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

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

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

Parameterized constructor.

atomTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder

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

Sets whether atom types should be considered in search.

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

AtomTyping - Enum in com.chemaxon.descriptors.alignment

Settings for shape associated atom typing.

atomTypizer(EcfpAtomTypizers) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder

Set atom typizer to use.

AtomValueChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting atoms with atom value.

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

Default constructor.

ATPROP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Show atom properties flag.

ATROP - chemaxon.struc.CIPStereoDescriptorIface.CIPType

ATROP - 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 - 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 in chemaxon.marvin.alignment

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

Atrop stereo center implementation.

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

Constructs a new instance of axial stereo center.

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

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

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

Deprecated.

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

Deprecated.

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

Calculates the atrop stereocenters.

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

Calculates the atrop stereocenters with attached data.

AtropStereoDescriptor - Class in chemaxon.struc

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

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

ATSYM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Show atom symbols in 3D flag.

ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom

S-group attachment point on first and second site.

ATTACH_NONE - Static variable in class chemaxon.struc.MolAtom

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

ATTACH_UNKNOWN - Static variable in class chemaxon.struc.MolAtom

S-group attachment point information

ATTACH1 - Static variable in class chemaxon.struc.MolAtom

S-group attachment point on first site.

ATTACH2 - Static variable in class chemaxon.struc.MolAtom

S-group attachment point on second site.

ATTACHED_DATA - chemaxon.checkers.StructureCheckerErrorType

Error type represents that attached data had found in the molecule

ATTACHED_DATA_MATCH_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for exact match of attached data.

ATTACHED_DATA_MATCH_GENERAL - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for general match of attached data.

ATTACHED_DATA_MATCH_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for ignoring attached data.

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

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

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

Creates an AttachedData class.

AttachedDataChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting attached data in the molecule.

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

Default constructor.

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

Parameterized constructor.

ATTACHMENT_ATOM - Static variable in interface chemaxon.sss.SearchConstants

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

ATTACHMENT_LABEL - Static variable in interface chemaxon.sss.SearchConstants

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

ATTACHMENT_MAP - Static variable in interface chemaxon.sss.SearchConstants

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

ATTACHMENT_NONE - Static variable in interface chemaxon.sss.SearchConstants

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

ATTACHMENT_POINT - Static variable in interface chemaxon.sss.SearchConstants

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

ATTACHMENT_RLABEL - Static variable in interface chemaxon.sss.SearchConstants

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

Au - Static variable in class chemaxon.core.ChemConst

AUTO - chemaxon.marvin.paint.constants.AnyBondStyle

Automatically decide whether Dashed or Solid rendering is used.

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

Automatic check for structures.

AUTO_RESOLUTION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent

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

Identifier of parameter: "autoscale".

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

Identifier of parameter: "autoTabScale".

AUTO_UNGROUP - Static variable in class chemaxon.struc.MoleculeGraph

Automatic ungroup bit in flags.

autoGzip(InputStream) - Static method in class com.chemaxon.calculations.util.CmdlineUtils

Detect gzipped InputStream.

AutoMapper - Class in com.chemaxon.mapper

AutoMapper is a tool that performs automated chemical reaction mapping.

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

Initializes an AutoMapper object

AutoMapper.Options - Class in com.chemaxon.mapper

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

AUTOMATIC_FOG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

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

Identifier of parameter: "automaticFogEnabled".

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

Identifier of parameter: "automaticReactionEnabled".

automaticSettingOfGridSize - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent

AverageLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage

AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat

Image object (java.awt.Image).

AXIAL - chemaxon.struc.CIPStereoDescriptorIface.CIPType

AXIAL - com.chemaxon.calculations.stereoanal.StereoConstants.Type

Axial stereo center (eg.

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

Filter for axial stereo centers.

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

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

Axial stereo center implementation.

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

Constructs a new instance of axial stereo center.

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

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

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

Deprecated.

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

Deprecated.

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

Calculates the axial stereocenters.

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

Calculates the axial stereocenters with attached data.

AxialStereoDescriptor - Class in chemaxon.struc

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

B

B - Static variable in class chemaxon.core.ChemConst

B_FACTOR_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent

Ba - Static variable in class chemaxon.core.ChemConst

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

Identifier of parameter: "background".

BACKGROUND_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label

BACKGROUND_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label

backgroundColor - Variable in class chemaxon.marvin.space.monitor.Label

backgroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label

backgroundColorMode - Variable in class chemaxon.marvin.space.monitor.Label

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

Identifier of parameter: "bgloadEnabled".

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

Identifier of parameter: "bgload".

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

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

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

BALL_AND_STICK - chemaxon.marvin.io.image.ImageExporter.Rendering

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

Identifier of parameter: "ballRadius".

ballPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent

ballRadius - Variable in class chemaxon.marvin.space.MoleculeComponent

ballRadius(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the ball radius in ball and stick mode.

BALLRADIUS - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Ball radius for ball and stick mode.

ballstick - chemaxon.marvin.io.image.ImageExportParamConstants.renderingValues

BALLSTICK - chemaxon.marvin.paint.constants.RenderingStyle

Stick rendering style with balls at atoms

BALLSTICK - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

use RenderingStyle instead.

BALLSTICK_RENDERING_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

use RenderingStyle instead.

BASE64 - Static variable in class chemaxon.formats.MFileFormat

BASE64 encoded file.

BaseColor16 - chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues

16 base colors defined with a palette, image data contains 2 bits/pixel

BaseColor256 - chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues

256 colors defined with a palette, image data contains 2 bits/pixel

BaseShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment

BaseShapeComparatorParameter(AlignmentProperties.FlexibilityMode, ShapeFunction, Optional<Integer>) - Constructor for class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter

BASIC - chemaxon.standardizer.actions.AromatizeAction.Type

Basic aromatization

BASIC - 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 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 - chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

BemisMurckoClustering - Class in com.chemaxon.clustering.framework

Convenience utilities for using Bemis-Murcko clustering.

bemismurckoloose - chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

bgColor(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the background color.

bgColorAlpha(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the background color with alpha value.

Bh - Static variable in class chemaxon.core.ChemConst

Bi - Static variable in class chemaxon.core.ChemConst

BIG_ENDIAN - com.chemaxon.descriptors.common.BinaryVectors.Endianness

Decreasing numeric significance with increasing addresses/indices.

BINARY_COMMONPART - com.chemaxon.descriptors.metrics.BinaryMetrics

Commonly set bits.

BINARY_COMMONPART_NORMALIZED - com.chemaxon.descriptors.metrics.BinaryMetrics

Common set bit ratio.

BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters

descriptor type constants

BINARY_DICE - com.chemaxon.descriptors.metrics.BinaryMetrics

Dice's similarity measure.

BINARY_EUCLIDEAN - com.chemaxon.descriptors.metrics.BinaryMetrics

Euclidean distance.

BINARY_EUCLIDEAN_NORMALIZED - com.chemaxon.descriptors.metrics.BinaryMetrics

Normalized Euclidean distance.

BINARY_TANIMOTO - com.chemaxon.descriptors.metrics.BinaryMetrics

Tanimoto coefficient.

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

Calculates the asymmetric Euclidean distance of binary descriptors.

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

Calculates the asymmetric normalized Euclidean distance of binary descriptors.

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

Calculates the asymmetric normalized Euclidean distance of binary descriptors.

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

Calculates asymmetric Tanimoto dissimilarity for binary descriptors.

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

Calculates asymmetricTanimoto dissimilarity for binary descriptors.

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

Calculates the Euclidean distance of two binary descriptors.

BinaryMetrics - Enum in com.chemaxon.descriptors.metrics

Simple metrics suitable for finite length binary vectors.

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

Calculates the normalized Euclidean distance of two binary descriptors.

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

Calculates the normalized Euclidean distance of two binary descriptors.

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

Calculates Tanimoto dissimilarity for binary descriptors.

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

Calculates Tanimoto dissimilarity for binary descriptors.

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

Calculates Tversky dissimilarity for binary descriptors.

BinaryVectorComparator - Interface in com.chemaxon.descriptors.metrics

Basic functionality for finite binary vector based calculations.

BinaryVectorComparator.Util - Class in com.chemaxon.descriptors.metrics

Simple consistency check utility.

BinaryVectorDescriptor - Interface in com.chemaxon.descriptors.common

BinaryVectorDescriptor is a Descriptor which holds a fixed length binary fingerprint.

BinaryVectorMetricFactory<C> - Interface in com.chemaxon.descriptors.metrics

Represents available metrics for binary vector based descriptors.

BinaryVectorMetricFactory.ToLinenote<C> - Class in com.chemaxon.descriptors.metrics

Utility for creating a default linenote.

BinaryVectors - Class in com.chemaxon.descriptors.common

Utility methods related to bit string descriptors.

BinaryVectors.Endianness - Enum in com.chemaxon.descriptors.common

Order of components in packed representations.

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

Calculates the weighted asymmetric Euclidean distance of binary descriptors.

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

Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.

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

Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.

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

Calculates the weighted Euclidean distance of binary descriptors.

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

Calculates the weighted normalized Euclidean distance of binary descriptors.

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

Calculates the weighted normalized Euclidean distance of binary descriptors.

bitsPerPattern(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder

Set bits per pattern.

Bk - Static variable in class chemaxon.core.ChemConst

BlackWhite - chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues

Black and white colors defined with a palette, image data contains 1 bit/pixel

BlackWhiteGray - chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues

Black, white, light, and dark gray colors defined with a palette, image data contains 2 bits/pixel

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

Constant storing the blue rgb value (the basic pKa result color).

BOLD - Static variable in class chemaxon.struc.graphics.MFont

Bold font style.

BOLD - Static variable in class chemaxon.struc.MolBond

"Bold" attribute of the bond.

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

Identifier of parameter: "boldBondWidth".

BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Prefix of bold bond width parameter.

bond - Variable in class chemaxon.marvin.space.monitor.DihedralControl

BOND_ANGLE - chemaxon.checkers.StructureCheckerErrorType

Error type represents that bond angle problem had found in the molecule

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

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

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

Identifier of parameter: "bondDraggedAlong".

BOND_DRAW_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent

BOND_DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent

BOND_DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent

BOND_FACING - Static variable in class chemaxon.marvin.space.MoleculeComponent

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

Identifier of parameter: "bondHashSpacing".

BOND_HASH_SPACING - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Prefix of bondHashSpacing parameter.

BOND_LENGTH - chemaxon.checkers.StructureCheckerErrorType

Error type represents that bond length problem had found in the molecule

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

Identifier of parameter: "bondLength".

BOND_LENGTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Prefix of bond length parameter.

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

Identifier of parameter: "bondLengthVisible".

BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Show bond lengths.

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

Identifier of parameter: "bondSet".

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

Identifier of parameter: "bondSetColor".

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

Identifier of parameter: "bondSpacing".

BondAngleChecker - Class in chemaxon.checkers

Bond Angle Checker detects wrong bond angles in 2D structures.

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

Default constructor

BondAngleChecker(double) - Constructor for class chemaxon.checkers.BondAngleChecker

Deprecated.

Not used.

BondAngleCheckerResult - Class in chemaxon.checkers.result

Bond angle checker result.

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

Constructor which initialize all the properties.

BondAngleFixer - Class in chemaxon.fixers

Bond Angle Fixer fixes wrong bond angles in 2D structures.

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

BondChecker - Class in chemaxon.checkers

Descentants of the abstract BondChecker class detect bond related problems.

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

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

bondCount - Variable in class chemaxon.struc.MolAtom

Number of bonds.

bondCount - Variable in class chemaxon.struc.MoleculeGraph

The number of bonds.

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

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

bondCount(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder

Set bond count to consider.

bondDistance - Variable in class chemaxon.marvin.space.MoleculeComponent

bondFacing - Variable in class chemaxon.marvin.space.MoleculeComponent

bondHashSpacing() - Method in class chemaxon.marvin.io.image.ImageExporter

bondHashSpacing(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

The spacing of the hash in hashed bonds in C-C bond length units.

BondInfo - Class in chemaxon.marvin.alignment.atrop

Encapsulates bond info.

BondInfo(int, int, int) - Constructor for class chemaxon.marvin.alignment.atrop.BondInfo

Construct.

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

Constructs an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.

BONDLEN_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Show bond lengths flag.

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

Calculate the regular bond length for the unified structure.

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

Calculates the regular bond length.

BondLengthChecker - Class in chemaxon.checkers

Bond Length Checker detects bonds with wrong length in 2D structures.

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

Default constructor

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

Deprecated.

Checker has no parameters.

BondLengthCheckerResult - Class in chemaxon.checkers.result

Bond angle checker result.

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

Constructor which initialize all the properties.

BondLengthFixer - Class in chemaxon.fixers

Bond Length Fixer fixes bonds with wrong length in 2D structures.

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

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

Expansion type: bond list.

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

Constructs an iterator to process the bonds connecting to the specified atom.

bondRadius - Variable in class chemaxon.marvin.space.MoleculeComponent

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

Provides a list view of the connected bonds of the atom.

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

Provides a list view of the bonds in the molecule.

bondSkipped(BondInfo, String) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener

Called when visited bond is skipped.

bondSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent

BondTable - Class in chemaxon.core.util

Provides easy lookup of bonds between pair of atoms in a molecule graph.

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

Determines the type of a bond (aromatic bonds are automatically recognized)

bondTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder

bondTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder

Sets whether bond types should be considered in search.

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

bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom

Calculates the average of the bond unit vectors pointing out of this atom.

bondWidth - Variable in class chemaxon.marvin.space.MoleculeComponent

bondWidth(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the width of the double bond.

BONDWIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Prefix of bond width parameter.

BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor

Boolean option.

BOOLEAN - com.chemaxon.apidiscovery.ParameterWrapper.ParameterType

A boolean parameter (primitive type).

booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp

Gets the boolean value.

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

Identifier of parameter: "border".

BORDER_MODE_BRIGHTER_FOREGROUND - Static variable in class chemaxon.marvin.space.monitor.Label

BORDER_MODE_FOREGROUND_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label

BORDER_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label

BORDER_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label

borderColor - Variable in class chemaxon.marvin.space.monitor.Label

borderColorChanged - Variable in class chemaxon.marvin.space.monitor.Label

borderColorMode - Variable in class chemaxon.marvin.space.monitor.Label

BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

boundingBox - Variable in class chemaxon.marvin.space.GraphicComponent

The smallest box containing the graphic component.

BoundingBox - Class in chemaxon.marvin.space

Class for representing a bounding box of any component in the 3D space.

BoundingBox() - Constructor for class chemaxon.marvin.space.BoundingBox

Creates a new instance of BoundingBox but does not set anything.

BoundingBox(float, float, float, float, float, float) - Constructor for class chemaxon.marvin.space.BoundingBox

Creates a bounding box with the given coordinates, computes the center and radius of the box.

Br - Static variable in class chemaxon.core.ChemConst

brackets - Variable in class chemaxon.struc.Sgroup

BRACKETS - chemaxon.checkers.StructureCheckerErrorType

Error type representing that the molecule contains brackets (S-groups).

BracketsChecker - Class in chemaxon.checkers

Detects brackets (S-groups) in molecules.

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

Default constructor.

BRIDGEHEAD_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which is connected to a bridgehead atom.

brightness - Variable in class chemaxon.descriptors.ChemicalFingerprint

number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less pausible)

brightness - Variable in class chemaxon.descriptors.ECFP

The number of bits set in the binary vector storage

brightness - Variable in class chemaxon.descriptors.ReactionFingerprint

number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)

btab - Variable in class chemaxon.struc.MoleculeGraph

Bond table.

bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream

Reads a character and writes into the buffer.

build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder

build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

build() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

Builds a ValenceCheckOptions object.

build() - Method in class chemaxon.formats.MolConverter.Builder

Builds the MolConverter.

build() - Method in class chemaxon.formats.MolConverter.Options

Deprecated.

build() - Method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.marvin.io.image.exporter.JpegExporter.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.marvin.io.image.exporter.PngExporter.Builder

Builds an unmodifiable export option.

build() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Builds an unmodifiable export option.

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

build() - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder

Builds a StandardizerActionFactory based on the previously added InputStream instances

build() - Method in interface com.chemaxon.apidiscovery.interfaces.ParameterBuilder

Constructs an immutable instance of T.

build() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder

Build immutable clustering representation.

build() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

Build the immutable clustering representation.

build() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder

build() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder

build() - Method in class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder

Build a new instance of MaccsParameters.

build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder

build() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder

build() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder

build() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder

build() - Method in class com.chemaxon.search.MatchingOptions.Builder

Creates a search options object with the settings specified by this builder instance.

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

build(IDBasedAssignerBuilder) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

Build an immutable snapshot of the clustering.

build(DescriptorGenerator<D>, DescriptorComparator<D>) - Method in class com.chemaxon.clustering.common.MolInputBuilder

Build immutable input descriptor.

buildButtonBar() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog

buildContentPanel() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog

builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter

Creates a builder for this class.

builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter

Creates a builder for this class.

builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter

Creates a builder for this class.

builder() - Static method in class chemaxon.marvin.io.image.exporter.JpegExporter

Creates a builder for this class.

builder() - Static method in class chemaxon.marvin.io.image.exporter.MsbmpExporter

Creates a builder for this class.

builder() - Static method in class chemaxon.marvin.io.image.exporter.PngExporter

Creates a builder for this class.

Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder

Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder

Builder() - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

Builder() - Constructor for class chemaxon.formats.MolConverter.Builder

Constructs an empty Builder object.

Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder

Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder

Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder

Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder

Builder() - Constructor for class chemaxon.marvin.io.image.exporter.JpegExporter.Builder

Builder() - Constructor for class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder

Builder() - Constructor for class chemaxon.marvin.io.image.exporter.PngExporter.Builder

Builder() - Constructor for class chemaxon.marvin.io.image.ImageExporter.Builder

Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder

Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder

Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder

Constructor with default settings.

Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder

Constructor with default settings.

Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder

Constructor mandated by descriptors API contracts.

Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder

Constructor with default settings.

Builder() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder

Instantiate builder with default values.

Builder() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder

Constructor with default settings.

Builder() - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder

Constructor with default settings.

Builder() - Constructor for class com.chemaxon.search.MatchingOptions.Builder

Creates a Builder object with the default settings.

Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder

Creates a Builder object with the default settings.

Builder(double, double) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder

Instantiate with weights.

Builder(CfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder

Constructor based on a parameter object.

Builder(EcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder

Constructor based on a parameter object.

Builder(MaccsParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder

Constructor mandated by descriptors API contracts.

Builder(PfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder

Constructor based on a parameter object.

Builder(TverskyParameters) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder

Instantiate builder based on an actual parameter instance.

Builder(BvParameters) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder

Construct to represent the state of a parameter object instance.

Builder(FvParameters) - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder

Construct to represent the state of a parameter object instance.

Builder(MatchingOptions) - Constructor for class com.chemaxon.search.MatchingOptions.Builder

Creates a Builder object containing the settings of the given search options object.

Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder

Creates a Builder object containing the settings of the given search options object.

builderClass() - Method in annotation type com.chemaxon.apidiscovery.annotations.BuilderClass

Associated builder class for this immutable object.

BuilderClass - Annotation Type in com.chemaxon.apidiscovery.annotations

This annotation gives information about the associated ParameterBuilder for this class.

BuildupMcs - Class in com.chemaxon.search.mcs.buildup

Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.

BuildupMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.buildup.BuildupMcs

Creates a new BuildupMcs object with the given search options.

BUILT_IN_CHAIN_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in chain colors.

BUILT_IN_CPK_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in cpk colors.

BUILT_IN_RAINBOW_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in rainbow colors.

BUILT_IN_RESIDUE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in residue colors.

BUILT_IN_SECONDARY_STRUCTURE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in secondary structure colors.

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

Identifier of parameter: "buttonmenubar".

BvGenerator - Interface in com.chemaxon.descriptors.vectors.binary

Generator for generic binary vector descriptors.

BvParameters - Class in com.chemaxon.descriptors.vectors.binary

Parameters for generic binary vector descriptor.

BvParameters() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters

Construct with default values.

BvParameters(BvParameters.Builder) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters

Constructor based on a builder.

BvParameters.Builder - Class in com.chemaxon.descriptors.vectors.binary

Builder for BvParameters.

BvParameters.ConstructBvGenerator - Interface in com.chemaxon.descriptors.vectors.binary

Interface representing BvGenerator implementation constructor

BvParameters.StringFormat - Enum in com.chemaxon.descriptors.vectors.binary

Fingerprint textual representation.

BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure

For internal usage only.

BYTES_IN_INT - Static variable in class com.chemaxon.descriptors.common.BinaryVectors

Number of bytes in an int.

BYTES_IN_LONG - Static variable in class com.chemaxon.descriptors.common.BinaryVectors

Number of bytes in a long.

C

C - Static variable in class chemaxon.core.ChemConst

C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter

Close the underlying stream.

C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter

Flush the output stream and force any buffered output bytes to be written out.

C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator

Name of the 13C chemical shift atom property.

C13 - chemaxon.calculations.nmr.NMRSpectrum.Nucleus

13C NMR

Ca - Static variable in class chemaxon.core.ChemConst

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

Identifier of parameter: "cacheMols".

CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for clearing all cached info.

CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in aromatization.

CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for cacheMemory.

CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in graph invariant calculation.

CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in parity calculation.

CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in sssr.

CACHE_REMOVE_TABS - Static variable in class chemaxon.struc.MoleculeGraph

Cache remove option to clear ctab and btab.

cacheMemory - Variable in class chemaxon.struc.MoleculeGraph

calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates a "badness" value for the atomic coordinates.

calcBitCount(int) - Static method in class chemaxon.descriptors.Metrics

Counts the number of bits set (1) in the integer parameter.

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

Counts the number of bits set (1) in a bit vector.

calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the bracket endpoints from the base line of the bracket.

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

Calculates the geometrical center.

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

Calculates the geometrical center.

calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument

Calculates the geometrical center.

calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint

Calculates the geometrical center.

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

Calculates the graph invariants with the assumption that hydrogens are removed.

calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the division point of a segment with a given ratio.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator

Calculate and store in freqCount[] absolute frequency counts per cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator

Calculate and store in freqCount[] absolute frequency counts per cells.

calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

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

Calculates the molecule height.

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

Calculates and sets hybridazation state for each atom.

calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the logD value at fixed pH.

calcMaxDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance

calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance

Calculates the minimum distance between two atoms in the molecule.

calcOrderFromLength() - Method in class chemaxon.struc.MolBond

Calculate the bond order from the atomic distances.

calcOrderFromValence() - Method in class chemaxon.struc.MolBond

Calculate bond order from the types and charges of the two atoms.

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

Calculates the outer rectangle.

calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the outer rectangle.

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

Calculates the center of the outer rectangle.

calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the center of the outer rectangle.

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

Calculator rgb offset.

calcSimplePolymerBracket(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates the points of a simple polymer bracket that belongs to a bond.

calcStereo2() - Method in class chemaxon.struc.MolBond

Computes the stereochemistry of the bond based on the atomic coordinates.

calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond

Computes the stereochemistry of the bond based on the atomic coordinates.

calcStereo2(MolAtom, MolAtom, MolAtom, MolAtom) - Static method in class chemaxon.struc.MolBond

Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates.

calculate() - Method in class chemaxon.marvin.alignment.MMPAlignment

Runs the MCS alignment calculation on the two structures of the constructor.

calculate(int[]) - Method in class chemaxon.util.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 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 chemaxon.calculations.cnsmpo.CnsMpoFunction

Calculates the CNS MPO property and its score.

calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator

calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator

Calculates NMR spectrum for the given input molecule.

calculate(Molecule) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Run the atropisomer calculation.

calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator

calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator

calculate(Molecule, Molecule, McsSearchOptions) - Method in interface com.chemaxon.search.mcs.upperbound.UpperBoundCalculator

Returns an upper bound for the number of bonds the Maximum Common Substructure of the given molecules may contain.

calculate(Molecule, SubProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Run the atropisomer calculation.

calculate(Molecule, SubProgressObserver, DihedralScanListener) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector

Run the atropisomer calculation.

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

Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.

calculateBinaryVectorDissimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator

Calculate represented dissimilarity score from binary vector parameters.

calculateBinaryVectorDissimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters

calculateBinaryVectorSimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator

Calculate represented similarity score from binary vector parameters.

calculateBinaryVectorSimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters

calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator

calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.

calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator

calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.

calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator

Calculates the stereo descriptors of the given molecule.

calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Calculates the coordinates during expand and contract.

calculateCosAFromScalarMul(MolBond, MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper

Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.

calculateDarkness() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor

Calculate the darkness of this fingerprint.

calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator

calculateDissimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator

Compare two descriptors in serialized form.

calculateDissimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator

Compare two descriptors.

calculateDissimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator

calculateDissimilarityMatrix(DissimilarityInput, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm

Distance matrix calculation.

calculateFloatVectorDissimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator

Calculate dissimilarity.

calculateFloatVectorSimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator

Deprecated.

In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation

calculateIntrinsicSolubility(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates intrinsic solubility.

calculatePhDependentSolubility(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubility.

calculatePhDependentSolubility(Molecule, double[]) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubilities.

calculatePhDependentSolubility(Molecule, double, double, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubilities.

calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator

calculateSimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator

Compare two descriptors in serialized form.

calculateSimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator

Compare two descriptors.

calculateSimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator

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

Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.

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

Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.

CALCULATIONS_PACK - Static variable in class chemaxon.license.LicenseManager

Identifier of product: Calculations Pack

CalculatorError - Interface in chemaxon.calculator

An error that might occur when a calculator is initialized.

CalculatorInputChecker - Interface in chemaxon.calculator

Instances of this interface are used by calculators to check if they can process an input molecule.

CalculatorPlugin - Class in chemaxon.marvin.plugin

Common base class for calculator plugins.

CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin

Constructor.

CalculatorPlugin(Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin

Constructor.

CalculatorPlugin(Consumer<Molecule>, Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin

Constructor.

CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin

CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin

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

This class has been moved to a new package, import and use it from its new location: CalculatorPluginDisplay

CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.gui

Common base class for calculator plugin displays.

CalculatorPluginDisplay() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginDisplay

Deprecated.

CalculatorPluginDisplay() - Constructor for class com.chemaxon.calculations.gui.CalculatorPluginDisplay

CalculatorPluginOutput<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin

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

This class has been moved to a new package, import and use it from its new location: CalculatorPluginOutput

CalculatorPluginOutput<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.cli

Class providing plugin output in table form.

CalculatorPluginOutput() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput

Deprecated.

CalculatorPluginOutput() - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput

Default constructor.

CalculatorPluginOutput(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput

Deprecated.

CalculatorPluginOutput(CalculatorPlugin) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput

Constructor that sets plugin.

CalculatorPluginService<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin

Base class for types that implement a functionality related to a specific CalculatorPlugin.

CalculatorPluginService() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginService

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

Calculates the molecule width.

call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit

Performs the calculation and returns the result returned by PluginWorkUnit.getResult().

call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit

Performs the calculation and returns the result returned by ReusablePluginWorkUnit.getResult().

callback(String, Object) - Method in interface chemaxon.jep.ChemContext

Implements CallbackIface.

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

Delegates CallbackIface.callback(String, Object) to the context.

callback(String, Object) - Method in class chemaxon.jep.context.AtomContext

Implements CallbackIface.

callback(String, Object) - Method in class chemaxon.jep.context.MolContext

Implements CallbackIface.

callback(String, Object) - Method in class chemaxon.jep.context.ReactionContext

Implements CallbackIface.

callback(String, Object) - Method in class chemaxon.marvin.space.GraphicScene

callback(String, Object) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent

callback(String, Object) - Method in class chemaxon.marvin.space.MSpaceEasy

Callback function to make avoiding direct calls easier.

callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.marvin.services.ServiceHandler

Performs thread-safe asynchronous service call.

callService(DT, Object...) - Method in class chemaxon.marvin.services.ServiceHandler

Performs a service call.

CAN_BE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Deprecated.

Line can be in the given format.

CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer

Deprecated.

Line can be in the given format.

canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated.

Tests whether a string can be one-letter-abbreviated peptide name.
A valid name contains only uppercase letters.

canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer

Deprecated.

Tests whether a string can be three-letter-abbreviated peptide name.

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

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

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

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

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

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

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

Determines whether the given bond can be a CIS/TRANS or not.

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

Tests whether an object of this class can be a reaction component.

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

Tests whether an object of this class can be a reaction component.

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

Tests whether an object of this class can be a reaction component.

canBeSMARTS(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated.

Tests whether a string can be SMARTS.

canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer

Deprecated.

Tests whether a string can be SMILES.

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

Stops the background thread

cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment

Cancel the ongoing calculation

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

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

Stops the background thread

CancelObserver - Interface in com.chemaxon.calculations.common

Callback to propagate cancel requests into long running tasks.

canHandle(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory

Returns true if this factory can handle the given xml.

CANONICAL - chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.

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

Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).

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

Deprecated.

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

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

Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).

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

Deprecated.

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

CARBON_VIS_INCHAIN - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Carbon-visibility is switched on in chain.

CARBON_VIS_INCHAIN_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

String constant for switching on carbon-visibility in chain.

CARBON_VIS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Carbon-visibility mask.

CARBON_VIS_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Carbon-visibility is switched off.

CARBON_VIS_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

String constant for switching off carbon-visibility.

CARBON_VIS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Carbon-visibility offset.

CARBON_VIS_ON - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Carbon-visibility is switched on.

CARBON_VIS_ON_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

String constant for switching on carbon-visibility.

CARBON_VIS_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Array of carbon-visibility styles.

carbonDisplay(ImageExporter.CarbonDisplay) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Show the atom labels on carbon atoms.

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

Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).

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

Deprecated.

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

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

Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).

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

Deprecated.

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

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

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).

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

Deprecated.

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

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

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.

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

Deprecated.

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

CARTRIDGE - Static variable in class chemaxon.license.LicenseManager

Identifier of product: JChem Cartridge

CATIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint

CCLENGTH - Static variable in class chemaxon.struc.MolBond

Default bond length.

Cd - Static variable in class chemaxon.core.ChemConst

CDParameters - Class in chemaxon.descriptors

Manages parameters the CustomDescriptor class.

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

Creates an empty object.

CDParameters(int) - Constructor for class chemaxon.descriptors.CDParameters

Creates an empty object of the given type.

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

Creates a new descriptor configured from the given file.

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

Creates a new object based on a given configuration string.

CDX - Static variable in class chemaxon.formats.MFileFormat

ChemDraw CDX file.

CDXML - Static variable in class chemaxon.formats.MFileFormat

ChemDraw CDXML file.

Ce - Static variable in class chemaxon.core.ChemConst

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

Identifier of parameter: "cell".

CELL_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene

CellOrComponentId - Class in chemaxon.marvin.space

Class to identify cells and components.

CellOrComponentId(int) - Constructor for class chemaxon.marvin.space.CellOrComponentId

Creates a cell id.

CellOrComponentId(int, int) - Constructor for class chemaxon.marvin.space.CellOrComponentId

Creates an id.

cellSize - Variable in class chemaxon.descriptors.MDParameters

size - number of bits - of one descriptor cell

CELLSIZE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

The default viewer cell size.

cellwiseWeights - Variable in class chemaxon.descriptors.MDParameters

is cell weights for parametrized metrics

center - Variable in class chemaxon.marvin.space.monitor.Control

center - Variable in class chemaxon.marvin.space.monitor.DihedralControl

centerx() - Method in class chemaxon.marvin.space.BoundingBox

Returns the x coordinate of the center of the box.

centery() - Method in class chemaxon.marvin.space.BoundingBox

Returns the y coordinate of the center of the box.

centerz() - Method in class chemaxon.marvin.space.BoundingBox

Returns the z coordinate of the center of the box.

centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane

Puts the molecule into the center of the display.

Cf - Static variable in class chemaxon.core.ChemConst

CFGenerator - Class in chemaxon.descriptors

The CFGenerator class generates topological fingerprints of molecular graphs.

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

Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.

CFGenerator(int) - Constructor for class chemaxon.descriptors.CFGenerator

Deprecated.

since 5.4

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

The context function names.

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

The context function names.

Cfp - Interface in com.chemaxon.descriptors.fingerprints.cfp

Folded fixed length bit string representation of the CFP descriptor.

CFParameters - Class in chemaxon.descriptors

Manages fingerprint parameters.

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

Creates an empty object.

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

Creates a new object based on a given configuration file.

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

Creates a new object based on a given configuration string.

CfpComparator - Interface in com.chemaxon.descriptors.fingerprints.cfp

Comparator for Cfp descriptor representation.

CfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp

Calculates CFP (fixed length folded binary vector representation) descriptors.

CfpParameters - Class in com.chemaxon.descriptors.fingerprints.cfp

CFP parameters class.

CfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters

Constructor using the default settings.

CfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.cfp

Builder class for the immutable parameter object.

CfpParameters.ConstructCfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp

Interface representing CFP generator constructor.

CfpTableReader - Class in com.chemaxon.descriptors.fingerprints.cfp

MDTable reader for CFP.

CfpTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader

CfpTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.cfp

Factory class.

CHAIN - chemaxon.marvin.io.image.ImageExporter.CarbonDisplay

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

Calculates the number of chain atoms in the molecule excluding hydrogens.

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

Deprecated.

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

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

Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.

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

Deprecated.

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

chainOf(StandardizerWrapper...) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers

Create a chained wrapper.

chainTransformers(Transformer...) - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns a chain transformer.

chainTransformers(List<Transformer>) - Static method in class com.chemaxon.search.transformation.TransformerFactory

Returns a chain transformer.

changeColorMapperColors(int) - Method in class chemaxon.marvin.space.SurfaceColoring

Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.

Changes - Class in chemaxon.standardizer

The change set of the standardization procedure.

Changes(Molecule) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

Changes(Molecule, StandardizerAction) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

Changes(Molecule, Molecule) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

CHANGING - com.chemaxon.mapper.Mapper.MappingStyle

Only reaction center will be mapped

CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).

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

Gets a character of the document.

CHARGE_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Sets the circled charge's font.

CHARGE_FONT_SIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Sets the circled charge's font.

CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).

CHARGE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).

CHARGE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants

Option value constant for ignore charge searching (charge information is ignored during searching).

CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup

Charge is located on atoms and displayed on atoms.

CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup

Charge is located on atoms but displayed on the whole group (bracket).

CHARGE_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager

Identifier of plugin: Charge Plugin Group

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

Identifier of parameter: "chargeWithCircle".

CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants

Show charge symbols in a circle.

CHARGE_WITH_CIRCLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

CHARGE_WITH_CIRCLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts

CHARGED_H - Static variable in class chemaxon.struc.MolAtom

Include charged Hydrogen atom(s).

chargeFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Font type in circled charge display.

chargeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder

chargeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder

Sets whether formal charges of atoms should be considered in search.

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

ChargePlugin - Class in chemaxon.marvin.calculations

Plugin class for partial charge calculation.

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

Constructor.

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

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

Invokes a background thread which will run all checkers on the given molecule

check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator

check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator

check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker

check(Molecule) - Method in class chemaxon.checkers.InvalidChecker

check(Molecule) - Method in interface chemaxon.checkers.StructureChecker

Detects a specific error in the molecule.

check(Molecule) - Method in interface chemaxon.jep.MolCondition

Deprecated.

Returns true if molecule should be processed, false otherwise.

check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AliasChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker

Detects atom of the molecule has atom map.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker

Detects if the current atom of the molecule has atom value.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker

Check the atom of the molecule with index i has no atom map.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker

Detects atom of the molecule is a query atom.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker

Detects if the current atom has free electrons.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.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 - chemaxon.checkers.StructureCheckOptions.Mode

Indicates, that the structurechecker does not automatically fixes.

check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker

Determines if a non chiral molecule contains a chiral flag.

check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker

Determines if all asymmetric centers have absolute stereo configuration

check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker

This method contains the current checking mechanism.

check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker

check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker

Detects attached data in the molecule

check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker

check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker

check1(Molecule) - Method in class chemaxon.checkers.BracketsChecker

check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker

check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker

Determines if a non chiral molecule contains a chiral flag.

check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker

check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker

Iterates through the components and checks every component.

check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker

check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker

check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Detects implicitizable hydrogen atoms.

check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker

check1(Molecule) - Method in class chemaxon.checkers.IncorrectTetrahedralStereoChecker

check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker

check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker

Detects if molecule has charge

check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker

check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker

check1(Molecule) - Method in class chemaxon.checkers.NonStandardWedgeSchemeChecker

check1(Molecule) - Method in class chemaxon.checkers.NonStereoWedgeBondChecker

check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker

check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker

check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker

check1(Molecule) - Method in class chemaxon.checkers.RatomChecker

check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker

check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker

check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.RgroupBridgeRatomChecker

check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.SolventChecker

check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker

check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker

check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker

check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker

check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker

check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker

Deprecated.

In version 15.8.3 the checker logic was replaced with the logic implemented in Molecule's stereoClean() method.

check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker

check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker

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

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

Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems

checkAtno(int) - Static method in class chemaxon.struc.MolAtom

Check if the given atomic number is positive and less then atomic type maximum value.

checkBitCounts(int, int, int, int) - Static method in class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util

Check that descriptor comparison parameters are consistent.

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

checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule

Empty implementation, bond consistency is not checked in case of selections.

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

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

Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.

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

Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.

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

Deprecated.

As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

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

Deprecated.

As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

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

Deprecated.

As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

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

Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.

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

Checks if the document is the right version

CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory

Deprecated.

Chemaxon's default checker configuration file name

CheckerInfo - Annotation Type in chemaxon.checkers

This annotation is responsible for adding GUI based meta data for StructureChecker implementations

CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark

checkError() - Method in class chemaxon.util.ErrorHandler

Throws the exception stored in the object.

CheckerRunner - Interface in chemaxon.checkers.runner

The descendant of CheckerRunner interface has to provide the functionality to run StructureChecker instances automatically
on the given molecule and fix the problems with the associated StructureFixer instances.

Example:

CheckerRunner can be used directly with the checkAndWait method.

CheckerSeverity - Enum in chemaxon.checkers

This enum defines the constants which represent the severity of the StructureChecker implementations

checkException() - Method in class chemaxon.util.ErrorHandler

Throws the exception stored in the object.

checkFilter(String) - Static method in class chemaxon.sss.search.MolSearch

Checks the syntax of the filtering expression.

checkFilter(String, File) - Static method in class chemaxon.sss.search.MolSearch

Checks the syntax of the filtering expression.

checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Checks the input molecule.

checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule

Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.

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

Checks the internal consisitency of S-groups.

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

Checks the consistency of S-groups.

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

Checks the consistency of S-groups.

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

Checks whether the parameter s-group contains the atoms of this s-group.

checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup.

checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Checks result types.

checkValence(MolAtom) - Method in enum chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

checkValence(MoleculeGraph) - Method in enum chemaxon.struc.MoleculeGraph.ValenceCheckState

Deprecated.

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject

Is it a valid object in the document?

CHEM_CURATOR_COMPOUND - Static variable in class chemaxon.license.LicenseManager

Identifier of product: ChemCurator Compound

CHEM_CURATOR_FULL - Static variable in class chemaxon.license.LicenseManager

Identifier of product: ChemCurator Full

chemaxon.calculations - package chemaxon.calculations

Contains chemical computation modules.

chemaxon.calculations.bbb - package chemaxon.calculations.bbb

BBB score calculator.

chemaxon.calculations.cip - package chemaxon.calculations.cip

chemaxon.calculations.clean - package chemaxon.calculations.clean

chemaxon.calculations.cnsmpo - package chemaxon.calculations.cnsmpo

CNS MPO score calculator.

chemaxon.calculations.dipole - package chemaxon.calculations.dipole

chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize

chemaxon.calculations.nmr - package chemaxon.calculations.nmr

chemaxon.calculations.nmr.io - package chemaxon.calculations.nmr.io

chemaxon.calculations.stereo - package chemaxon.calculations.stereo

chemaxon.calculator - package chemaxon.calculator

chemaxon.checkers - package chemaxon.checkers

Structure checkers can be used to filter drawing mistakes or special structural elements.

chemaxon.checkers.result - package chemaxon.checkers.result

This package is used to identify problems found in molecules.

chemaxon.checkers.runner - package chemaxon.checkers.runner

This package supports the automatic running of structure checkers.

chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader

Extension package of the automatic runner functionality.

chemaxon.common.util - package chemaxon.common.util

chemaxon.core - package chemaxon.core

chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo

chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck

chemaxon.core.util - package chemaxon.core.util

chemaxon.descriptors - package chemaxon.descriptors

chemaxon.descriptors.scalars - package chemaxon.descriptors.scalars

chemaxon.fixers - package chemaxon.fixers

Structure fixers can be used to fix problems identified by structure checker instances.

chemaxon.formats - package chemaxon.formats

Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.

chemaxon.formats.recognizer - package chemaxon.formats.recognizer

Provides classes to recognize files of various file formats.

chemaxon.jchem.db - package chemaxon.jchem.db

chemaxon.jep - package chemaxon.jep

Chemical Terms Evaluator classes.

chemaxon.jep.context - package chemaxon.jep.context

Specific chemical terms evaluation contexts.

chemaxon.license - package chemaxon.license

Classes related licenses, license handling, validating, GUI and documentation.

chemaxon.marvin - package chemaxon.marvin

Contains utility classes for rendering molecules.

chemaxon.marvin.alignment - package chemaxon.marvin.alignment

The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.

chemaxon.marvin.alignment.atrop - package chemaxon.marvin.alignment.atrop

Utilities for AtropIsomerDetector.

chemaxon.marvin.beans - package chemaxon.marvin.beans

Provides bean classes for creating Marvin based user interface.

chemaxon.marvin.calculations - package chemaxon.marvin.calculations

Provides specific plugin, plugin loader and table form output implementations.

chemaxon.marvin.common - package chemaxon.marvin.common

Contains a class for handling user settings.

chemaxon.marvin.io - package chemaxon.marvin.io

Provides classes for molecule import and export through data streams.

chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats

Core package of any import/export module.

chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl

Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.

chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles

chemaxon.marvin.io.formats.vectgraphics - package chemaxon.marvin.io.formats.vectgraphics

chemaxon.marvin.io.image - package chemaxon.marvin.io.image

chemaxon.marvin.io.image.exporter - package chemaxon.marvin.io.image.exporter

chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer

Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.

chemaxon.marvin.modules.reaction - package chemaxon.marvin.modules.reaction

chemaxon.marvin.paint - package chemaxon.marvin.paint

Defines display options constants.

chemaxon.marvin.paint.constants - package chemaxon.marvin.paint.constants

chemaxon.marvin.plugin - package chemaxon.marvin.plugin

Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.

chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent

Classes to achieve concurrent processing of calculator plugins.

chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui

Calculator plugin common GUI classes.

chemaxon.marvin.services - package chemaxon.marvin.services

Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.

chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice

chemaxon.marvin.services.json - package chemaxon.marvin.services.json

chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice

chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap

chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice

chemaxon.marvin.sketch - package chemaxon.marvin.sketch

Contains the sketcher's core classes and various sketching modes.

chemaxon.marvin.sketch.swing.modules.documentstyle - package chemaxon.marvin.sketch.swing.modules.documentstyle

chemaxon.marvin.space - package chemaxon.marvin.space

Contains the core classes of MarvinSpace including the graphic canvas and the basic visualizer classes.

chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor

Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.

chemaxon.marvin.uif.dialog - package chemaxon.marvin.uif.dialog

chemaxon.marvin.util - package chemaxon.marvin.util

Contains some utilities for example for molecule cleaning and Swing.

chemaxon.marvin.util.codeassist - package chemaxon.marvin.util.codeassist

chemaxon.marvin.view - package chemaxon.marvin.view

Control records in MarvinView.

chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing

Swing support for MarvinView tables.

chemaxon.naming - package chemaxon.naming

Name to Structure conversion.

chemaxon.naming.document - package chemaxon.naming.document

Document to Structure (D2S) conversion.

chemaxon.naming.document.annotate - package chemaxon.naming.document.annotate

chemaxon.pharmacophore - package chemaxon.pharmacophore

Classes for pharmacophore point perception, pharmacophore fingerprint generation and pharmacophore dissimilarity calculations.

chemaxon.reaction - package chemaxon.reaction

Classes for reaction processing related tasks.

chemaxon.sss - package chemaxon.sss

chemaxon.sss.screen - package chemaxon.sss.screen

chemaxon.sss.search - package chemaxon.sss.search

chemaxon.sss.search.options - package chemaxon.sss.search.options

chemaxon.standardizer - package chemaxon.standardizer

Contains packages for structure standardization.

chemaxon.standardizer.actions - package chemaxon.standardizer.actions

Contains basic standardizer actions.

chemaxon.standardizer.advancedactions - package chemaxon.standardizer.advancedactions

Contains advanced standardizer actions.

chemaxon.standardizer.concurrent - package chemaxon.standardizer.concurrent

Contains classes for concurrent execution of standardization.

chemaxon.standardizer.configuration - package chemaxon.standardizer.configuration

Contains classes for handling configurations of standardizer.

chemaxon.standardizer.configuration.reader - package chemaxon.standardizer.configuration.reader

Contains classes for handling configuration deserialization.

chemaxon.standardizer.runner - package chemaxon.standardizer.runner

Contains classes for executing standardization based on a configuration.

chemaxon.struc - package chemaxon.struc

Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.

chemaxon.struc.graphics - package chemaxon.struc.graphics

Contains graphics MDocument elements.

chemaxon.struc.prop - package chemaxon.struc.prop

Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.

chemaxon.struc.sgroup - package chemaxon.struc.sgroup

S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.

chemaxon.util - package chemaxon.util

Provides general utility classes.

chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin

chemaxon.util.iterator - package chemaxon.util.iterator

Provides iterator classes for molecules and their components.

ChemConst - Class in chemaxon.core

ChemConst() - Constructor for class chemaxon.core.ChemConst

ChemContext - Interface in chemaxon.jep

Interface of expression evaluation contexts.

CHEMICAL_ATOM_TYPES - com.chemaxon.descriptors.alignment.AtomTyping

ChemicalFingerprint - Class in chemaxon.descriptors

The ChemicalFingerprint class implements topological fingerprints as a type of MolecularDescriptors.

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

Creates a new, empty instance of ChemicalFingerprint without allocating internal storage.

ChemicalFingerprint(CFParameters) - Constructor for class chemaxon.descriptors.ChemicalFingerprint

Creates a new instance of ChemicalFingerprint according to the parameters given.

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

Copy constructor.

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

Creates a new instance of ChemicalFingerprint according to the parameters given.

ChemJEP - Class in chemaxon.jep

Expression parser and evaluator for chemical expressions.

ChemJEP() - Constructor for class chemaxon.jep.ChemJEP

Constructor.

ChemJEP(Class) - Constructor for class chemaxon.jep.ChemJEP

Constructor.

CHEMLOCATOR_PERSONAL - Static variable in class chemaxon.license.LicenseManager

Identifier of product: ChemLocator Personal

CHEMLOCATOR_SERVER - Static variable in class chemaxon.license.LicenseManager

Identifier of product: ChemLocator Server

chiral_all - chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues

CHIRAL_ALL - chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption

CHIRAL_ALL_POSSIBLE - chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption

chiral_allPossible - chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues

CHIRAL_FLAG - chemaxon.checkers.StructureCheckerErrorType

Error type represents molecules marked with "absolute stereo" flag.

chiral_off - chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues

CHIRAL_OFF - chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption

chiral_selected - chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues

CHIRAL_SELECTED - chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption

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

Calculates the number of chiral centers.

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

Deprecated.

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

chiralCenterCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin

Deprecated.

Calculates the number of tetrahedral stereogenic centers.

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

Determines the chiral center atoms.

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

Deprecated.

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

ChiralFlagChecker - Class in chemaxon.checkers

Implementation of AbstractStructureChecker detecting "absolute stereo flag" on molecule.

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

Constructs ChiralFlagChecker instance

ChiralFlagErrorChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).

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

Default constructor

CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants

Axially chiral atom with M configuration.

CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants

Chirality mask in flags.

CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants

Axially chiral atom with P configuration.

CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants

Pseudo-asymmetric chiral atom of r configuration.

CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of R configuration.

CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants

Pseudo-asymmetric chiral atom of s configuration.

CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of S configuration.

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

Identifier of parameter: "chiralitySupport".

chiralityDisplay(ImageExporter.ChiralityDisplayOption) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the chirality display option.

CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants

R/S shown always.

CHIRALITYSUPPORT_ALL_POSSIBLE - Static variable in interface chemaxon.struc.StereoConstants

R/S shown always and highlight possible chiral centers as well.

CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants

R/S not shown for any molecule.

CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants

R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.

CIPStereoCalculator - Class in chemaxon.calculations.cip

Stereo calculator with the Cahn, Ingold, Prelog priority rules.

CIPStereoDescriptorIface - Interface in chemaxon.struc

Cahn-Ingold-Prelog (CIP) stereodescriptor interface.

CIPStereoDescriptorIface.CIPType - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue - Interface in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AtropStereoValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.AxialStereoValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.CisTransStereoValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue - Enum in chemaxon.struc

CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue - Enum 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 - 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 - 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 - com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo

Deprecated.

If substituents located on the same side of the reference plane.

CIS - Static variable in interface chemaxon.struc.StereoConstants

Cis double bond.

CIS_TRANS - Static variable in interface chemaxon.struc.StereoConstants

Cis and trans double bond mask.

CisDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans

Filter for CIS double bonds.

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

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

Calculates the CIS double bonds.

CISTRANS - chemaxon.struc.CIPStereoDescriptorIface.CIPType

CISTRANS - com.chemaxon.calculations.stereoanal.StereoConstants.Type

Cis-trans stereo center.

CISTRANS - com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType

Double bond stereoisomers.

CisTransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans

Filter for cis-trans stereo centers.

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

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

Calculates the CIS-TRANS double bonds.

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

Calculates the CIS-TRANS double bonds with attached data.

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

Cis-trans stereo center implementation.

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

Constructs a new instance of cis-trans stereo center.

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

Constructs a new instance of cis-trans stereo center with attached data.

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

Deprecated.

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

Deprecated.

CisTransStereoDescriptor - Class in chemaxon.struc

CisTransStereoDescriptor(CIPStereoDescriptorIface.CIPValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.CisTransStereoDescriptor

Cl - Static variable in class chemaxon.core.ChemConst

CLASS - Static variable in class chemaxon.marvin.services.localservice.LocalServiceDescriptor

Property key for Service class name as String

CLASS_NOT_FOUND_ERROR - Static variable in class chemaxon.util.ErrorHandler

className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

clean(int) - Method in class chemaxon.formats.MolConverter.Builder

Enables cleaning.

clean(int) - Method in class chemaxon.formats.MolConverter.Options

Deprecated.

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

Enables cleaning.

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

Deprecated.

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

Deprecated.

As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).

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

Clean the specified cell.

clean(int, String, MProgressMonitor) - Method in class chemaxon.struc.MoleculeGraph

Deprecated.

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 in chemaxon.standardizer.advancedactions

Type of clean action (partial, full, template based or convert 3D to 2D)

clean3d(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

clean3d(Molecule, int) - Static method in class chemaxon.marvin.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

Clean3DAction - Class in chemaxon.standardizer.advancedactions

Clean molecule graph in 3D standardizer action

Clean3DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean3DAction

Initializes the action with parameters

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

Clean all cells.

Cleaner - Class in chemaxon.calculations.clean

Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.

Cleaner() - Constructor for class chemaxon.calculations.clean.Cleaner

CleanFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which cleans the molecule in 2d

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

CLEANING_2D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "clean2dOpts".

CLEANING_3D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "clean3dOpts".

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

Identifier of parameter: "cleanDim".

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

Identifier of parameter: "cleanOpts".

cleanup() - Method in class chemaxon.marvin.space.GraphicComponent

cleanup() - Method in class chemaxon.marvin.space.PharmacophoreArrow

cleanup() - Method in class chemaxon.marvin.space.PharmacophorePoint

cleanup(long) - Method in class chemaxon.reaction.ConcurrentReactorProcessor

Cancels work currently executed, awaits termination of associated worker threads and releases any resource this processor has reserved.

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

Clean-up after R-group removal.

CleanUtil - Class in chemaxon.marvin.util

Utility methods for cleaning.

CleanUtil() - Constructor for class chemaxon.marvin.util.CleanUtil

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

Clears the descriptor, all values are set to zero.

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

Clears the fingerprint: sets all bins to store zero value.

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

Clears the descriptor: sets all cells to store zero value.

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

Clears the fingerprint, all values are set to zero.

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

Clears the fingerprint: sets all bins to store zero value.

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

Clears the fingerprint: sets all bins to store zero value.

clear() - Method in class chemaxon.descriptors.ScalarDescriptor

Clears the descritor: sets its value to zero value.

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

Clears the fingerprint, all values are set to zero.

clear() - Method in class chemaxon.formats.MolConverter.Builder

Clears all settings.

clear() - Method in class chemaxon.formats.MolConverter.Options

Deprecated.

clear() - Method in interface chemaxon.jep.ChemContext

Clears the context.

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

Clears the context.

clear() - Method in class chemaxon.jep.context.MolContext

Clears the context.

clear() - Method in class chemaxon.jep.context.ReactionContext

Clears the context.

clear() - Method in class chemaxon.marvin.space.BoundingBox

Clears all previously set coordinate from the box.

clear() - Method in class chemaxon.marvin.space.monitor.Monitor

Deletes all items from selectedItems.

clear() - Method in class chemaxon.pharmacophore.PMap

Sets every feature for every atom to false

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

Clears the configuration of action

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

Clears the document.

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

Clear query properties, charge, and hcount.

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

Clears the molecule.

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

Clears the molecule.

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

Clears properties.

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

Clears the document.

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

Clears the display.

CLEAR - chemaxon.standardizer.actions.AbsoluteStereoAction.Type

Deprecated.

Remove absolute stereo

clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

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

Deletes the cached information depending on the given options.

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

Used in initializing searches.

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

Clears the checker marks

clearClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler

Clears the clipboard by creating an empty Transferable and placing it on the clipboard.

clearClipboardConditionally() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler

Clears the clipboard, if ClipboardHandler.isClearClipboardBeforeExport() is true.

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

Delete all comparator from the search object.

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

Clears the extra label.

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

Clears extra atom labels.

clearFeatures(int) - Method in class chemaxon.pharmacophore.PMap

Clears all features corresponding to the given atom index.

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

Initializes molecule for import.

clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph

Clears the bonds vector, the properties, the flags, and sets the origin coordinates to 0.

clearForImport(String) - Method in class chemaxon.struc.RgMolecule

Clear the edges vector and the properties.

clearForImport(String) - Method in class chemaxon.struc.RxnMolecule

Clear the edges vector and the properties.

clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane

Reset undo queue.

clearInactiveTasks(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil

Clears the inactive tasks list.

ClearIsotopesAction - Class in chemaxon.standardizer.actions

Clear isotopes standardizer action

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

Initializes the action

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

Clears all lines.

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

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

Clears the extra prerequisites of the structure search specified using addMatch calls.

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

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

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

Deletes the graphical objects from this.

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

Clears all MObject-s that belong to this S-groups.

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

Removes all properties from this atom.

clearProperties() - Method in class chemaxon.struc.MolBond

Removes all properties from this bond.

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

Clears RDfile/SDfile properties.

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

Clears query props.

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

clearSelection(int) - Method in class chemaxon.marvin.space.GraphicScene

Sets all components and parts of components to be unselected in the given cell.

clearSelections() - Method in class chemaxon.marvin.space.GraphicCell

Sets all components and parts of components to be unselected.

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

Clears the atomSets and the bondSets.

ClearStereoAction - Class in chemaxon.standardizer.actions

Clear stereo standardizer action

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

Initializes the action with parameters

ClearWedgeFixer - Class in chemaxon.fixers

Clears wedges.

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

CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Flag that indicates an import operation

CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Flag that indicates an export operation

CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Undefined clipboard operation state identifier

CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable

Temporary property name to mark the molecule if it comes from a file via the clipboard

ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer

Facade of the Clipboard handling in Marvin.

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

Clipboard operation type.

clipSurface(BoundingBox) - Method in class chemaxon.marvin.space.SurfaceComponent

The bounding box of the surface can be used to determine 6 clipping planes and clip (do not draw) parts lying outside of the box.

clone() - Method in class chemaxon.checkers.AbstractStructureChecker

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

clone() - Method in class chemaxon.checkers.SubstructureChecker

clone() - Method in class chemaxon.core.util.BondTable

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

Creates a new instance with identical internal state.

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

Creates a new instance with identical internal state.

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

Creates a new instance with identical internal state.

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

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.MolecularDescriptor

Creates a new instance with identical internal state.

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

Creates a new instance with identical internal state.

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

Creates a copy with identical internal state.

clone() - Method in class chemaxon.descriptors.ScalarDescriptor

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.HAcc

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.HDon

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.Heavy

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.LogD

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.LogP

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.Mass

Creates a new instance with identical internal state.

clone() - Method in class chemaxon.descriptors.scalars.TPSA

Creates a new instance with identical internal state.

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

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

clone() - Method in class chemaxon.formats.MolConverter.Builder

Clones the object.

clone() - Method in class chemaxon.formats.MolConverter.Options

Deprecated.

clone() - Method in class chemaxon.pharmacophore.PMap

Clones this PMap object.

clone() - Method in class chemaxon.sss.search.MolSearchOptions

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

Makes an identical copy of this SearchObject.

clone() - Method in class chemaxon.standardizer.AbstractStandardizerAction

clone() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction

Deprecated.

clone() - Method in class chemaxon.standardizer.actions.AliasToGroupAction

clone() - Method in class chemaxon.standardizer.actions.AromatizeAction

clone() - Method in class chemaxon.standardizer.actions.ClearStereoAction

clone() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

clone() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

clone() - Method in class chemaxon.standardizer.actions.ExpandAction

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

clone() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

clone() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

clone() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

clone() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

clone() - Method in class chemaxon.standardizer.actions.TautomerizeAction

clone() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction

clone() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction

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

clone() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction

clone() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction

clone() - Method in class chemaxon.standardizer.advancedactions.TransformAction

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

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

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

clone() - Method in class chemaxon.struc.CTransform3D

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

Make an identical copy.

clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint

clone() - Method in class chemaxon.struc.graphics.MBracket

clone() - Method in class chemaxon.struc.graphics.MChemicalStruct

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MEFlow

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

clone() - Method in class chemaxon.struc.graphics.MEllipse

clone() - Method in class chemaxon.struc.graphics.MFont

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MMidPoint

clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky

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

clone() - Method in class chemaxon.struc.graphics.MRectangle

clone() - Method in class chemaxon.struc.graphics.MRectanglePoint

clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky

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

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

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

Creates a clone.

clone() - Method in class chemaxon.struc.MObject

Creates a clone.

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

Clones the atom.

clone() - Method in class chemaxon.struc.MolBond

Make a copy of this object.

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

Makes an identical copy of the molecule.

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

Make an identical copy of the molecule.

clone() - Method in class chemaxon.struc.MPoint

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

Clones this object.

clone() - Method in class chemaxon.struc.prop.MBooleanProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MDoubleProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MHCoords3DProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MIntegerProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MMoleculeProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MObjectProp

Clones the object.

clone() - Method in class chemaxon.struc.prop.MStringProp

Clones the object.

clone() - Method in class chemaxon.struc.QueryBond

Make a copy of this object.

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

Clone the markush structure.

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

Make an identical copy of the reaction structure.

clone() - Method in class chemaxon.struc.SelectionMolecule

Create a clone of this SelectionMolecule.

clone() - Method in class chemaxon.struc.sgroup.SgroupAtom

Clones the S-group superatom and it's SuperatomSgroup as well.

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

Clones the SuperatomSgroup (and not the Molecule).

cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule

Copies the specified atoms.

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

Copies the specified atoms.

cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond

Clones this bond.

cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.QueryBond

Clones this bond.

cloneBondTable(BondTable) - Static method in class chemaxon.core.util.BondTable

Clones the bond table.

cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MHashProp

Clones the object.

cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MListProp

Clones the object.

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

Clones the configuration

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule

Copies the specified atoms and bonds of this molecule to another one.

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

Copies the specified atoms of this molecule graph to another one.

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Copies the specified atoms of this graph to another one.

clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Copies the specified nodes and edges of this graph to another one.

clonecopy(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions

Copies parameters to other.

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

Copies all search options to other.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule

Makes another molecule identical to this one.

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

Make another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Make another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Make another molecule identical to this one.

clonecopy(MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule

Copies the clones of atoms and bonds of this graph to another one.

clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Copies the specified atoms and bonds of this molecule graph to another one.

clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule

Copies the specified atoms and bonds of this graph to another one.

clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions

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

Copies all search options except search type to other.

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

Copies the all the contents except the S-groups into another molecule object.

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

Creates a clone.

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

Creates a clone.

cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom

Clones the S-group superatom partially.

cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker

cloneItem() - Method in class chemaxon.checkers.InvalidChecker

cloneItem() - Method in interface chemaxon.checkers.StructureChecker

Returns a clone of this StructureChecker instance

cloneItem() - Method in class chemaxon.standardizer.AbstractStandardizerAction

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

cloneItem() - Method in interface chemaxon.standardizer.StandardizerAction

Returns a clone of this StandardizerAction instance

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

Deprecated.

As of Marvin 6.2, no replacement.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

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

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

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

Creates a clone.

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

Creates a clone.

cloneMFont() - Method in class chemaxon.struc.graphics.MFont

Creates a clone.

cloneMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

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

Deprecated.

as of Marvin 2014.09.01.0 use Molecule.clone() instead

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

Makes an identical copy of the molecule and its document.

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

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

cloneProp() - Method in class chemaxon.struc.MDocument.Prop

Creates a clone.

cloneProp() - Method in class chemaxon.struc.MProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MObjectProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MStringProp

Clones the object.

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

Clones the atom/bond sets from doc.

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

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.Sgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.DataSgroup

Gets a new DataSgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Gets a new Sgroup instance.

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

Gets the clone of the structure stored.

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

close() - Method in class chemaxon.formats.MolConverter

Closes the exporter and the output stream.

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

Closes the MolExportModule and the underlying stream.

close() - Method in class chemaxon.formats.MolImporter

Close the underlying input stream.

close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Interrupts parsing.

close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter

close() - Method in class chemaxon.marvin.io.MDocSource

Closes the underlying input stream(s).

close() - Method in class chemaxon.marvin.io.MolExportModule

Close the stream.

close() - Method in class chemaxon.marvin.io.MRecordImporter

Closes the input stream.

close() - Method in interface chemaxon.marvin.io.MRecordReader

Closes the input stream.

close() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator

close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer

Closes the importers.

close() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Closes the output.

close() - Method in interface com.chemaxon.calculations.common.ProgressObserver

Equivalent to ProgressObserver.done().

close() - Method in interface com.chemaxon.calculations.io.CloseableIterator

close() - Method in class com.chemaxon.calculations.io.MemoizingIterator

close(int) - Method in class chemaxon.formats.MolConverter

Closes the exporter.

close(int) - Method in class chemaxon.formats.MolExporter

Closes the MolExportModule and, optionally, the underlying stream.

close(int) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput

Closes the output.

CloseableIterator<T> - Interface in com.chemaxon.calculations.io

Closeable iterator.

CloseableIterators - Class in com.chemaxon.calculations.io

Utility class.

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

Closed flag.

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

Closes the sketcher window that belongs the the specified cell.

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

Closes the detached viewer window of the specified cell.

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

Closes all windows opened by this MarvinPane.

cluster(double[][], LanceWilliamsMerge, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm

Invoke clustering.

cluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

A spec for a clusterId.

cluster(DissimilarityInput, LanceWilliamsMerge, ProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm

Invoke clustering.

Cluster<T> - Interface in com.chemaxon.clustering.common

Cluster represents a group of structures.

clusterLevel(T) - Method in interface com.chemaxon.clustering.common.LevelAssigner

Level associated to a hierarchic cluster.

clusterLevelFunction() - Method in interface com.chemaxon.clustering.common.LevelAssigner

CLuster level association.

clusterOf(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler

Look up immediate parent of a structure present in the clustering.

clusterOf(T) - Method in interface com.chemaxon.clustering.common.HierarchicClustering

Identify the lowest level cluster containing the given item.

clusterOf(T) - Method in interface com.chemaxon.clustering.common.SingleLevelClustering

Identify the cluster containing the given item.

clusters() - Method in interface com.chemaxon.clustering.common.HierarchicCluster

Access further grouping of the represented elements.

clusters() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster

clusters() - Method in interface com.chemaxon.clustering.common.SingleLevelClustering

Represented cluster.

Cm - Static variable in class chemaxon.core.ChemConst

CmdlineUtils - Class in com.chemaxon.calculations.util

Command line related utilities.

CML - Static variable in class chemaxon.formats.MFileFormat

Chemical Markup Language.

Cn - Static variable in class chemaxon.core.ChemConst

CnsMpo - Class in chemaxon.calculations.cnsmpo

CNS MPO score calculator.

CnsMpo.Property - Class in chemaxon.calculations.cnsmpo

Simple DTO that contains the predicted value and its CNS MPO score.

CnsMpoFunction - Enum in chemaxon.calculations.cnsmpo

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

Co - Static variable in class chemaxon.core.ChemConst

CodeAssistConfiguration() - Constructor for class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration

CodeAssistFactory - Class in chemaxon.marvin.util.codeassist

Manages the creation of Chemical Terms related components, such as the Code Assist text field, toolbars, favorite and macro handling components, and validation response component.

CodeAssistFactory.CodeAssistConfiguration - Class in chemaxon.marvin.util.codeassist

Helper class for CodeAssistFactory to set up CodeAssist

codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Add mass number information to the given code.

coeffQuery(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder

Set query coefficient.

coeffTarget(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder

Set target coefficient.

colDec - Variable in class chemaxon.descriptors.PFParameters

atom set colors

color - Variable in class chemaxon.marvin.space.GraphicComponent

color - Variable in class chemaxon.marvin.space.MoleculeComponent

color - Variable in class chemaxon.marvin.space.SurfaceComponent

COLOR_MAPPER_BLUE_TO_GREEN - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in blue-cyan-green palette will be used.

COLOR_MAPPER_BLUE_TO_RED - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in blue-lightgray-red palette will be used.

COLOR_MAPPER_FIRE - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in "fire" palette will be used.

COLOR_MAPPER_GREEN_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in green-cyan-blue palette will be used.

COLOR_MAPPER_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in rainbow palette will be used.

COLOR_MAPPER_RED_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in red-lightgray-blue palette will be used.

COLOR_MAPPER_REVERSE_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring

Built-in reverse rainbow palette will be used.

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

Identifier of parameter: "colorScheme".

COLOR_SCHEMES - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Array of color schemes strings.

color3 - Variable in class chemaxon.marvin.space.SurfaceComponent

ColorGenerator - Class in chemaxon.marvin.util

A final class which provides a static access to a color distant color creator class.

ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator

coloring(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent

coloring(ImageExporter.Coloring) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Sets the coloring scheme.

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

Constant for setting all coloring options, currently scaffold and R-groups.

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

Constant for no hit coloring.

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

Constant for R-group coloring.

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

Constant for scaffold coloring.

COLORS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Color scheme mask in display option flags.

COLORS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Color scheme offset in display option flags.

colorType - Variable in class chemaxon.marvin.space.MoleculeComponent

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

Identifier of parameter: "cols".

com.chemaxon.apidiscovery - package com.chemaxon.apidiscovery

API Discovery framework.

com.chemaxon.apidiscovery.annotations - package com.chemaxon.apidiscovery.annotations

Annotations used by the API Discovery framework.

com.chemaxon.apidiscovery.interfaces - package com.chemaxon.apidiscovery.interfaces

Interfaces introduced for the API Discovery framework.

com.chemaxon.apidiscovery.util - package com.chemaxon.apidiscovery.util

Various utilities.

com.chemaxon.calculations.cli - package com.chemaxon.calculations.cli

com.chemaxon.calculations.common - package com.chemaxon.calculations.common

Common components of Calculator APIs.

com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal

API of the elemental analysis functionality.

com.chemaxon.calculations.gui - package com.chemaxon.calculations.gui

com.chemaxon.calculations.io - package com.chemaxon.calculations.io

com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility

com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal

API of the Stereo Analysis Plugin.

com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters

Core filter classes.

com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop

Atrop stereo filter implementations.

com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial

Axial stereo filter implementations.

com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans

Cis-trans stereo filter implementations.

com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral

Tetrahedral stereo filter implementations.

com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters

Stereocenter implementations of Stereo Analysis API.

com.chemaxon.calculations.stereoisomers - package com.chemaxon.calculations.stereoisomers

com.chemaxon.calculations.util - package com.chemaxon.calculations.util

Various utilities used in calculations, descriptors, clustering and overlap analysis.

com.chemaxon.clustering.common - package com.chemaxon.clustering.common

Common components of clustering related APIs.

com.chemaxon.clustering.framework - package com.chemaxon.clustering.framework

Hierarchic structural framework based clustering.

com.chemaxon.clustering.singlelinkage - package com.chemaxon.clustering.singlelinkage

Single linkage clustering algorithm.

com.chemaxon.clustering.sphex - package com.chemaxon.clustering.sphex

Sphere exclusion clustering algorithm.

com.chemaxon.clustering.util - package com.chemaxon.clustering.util

Clustering related utilities.

com.chemaxon.clustering.wards - package com.chemaxon.clustering.wards

Ward's minimum variance implemented as a generic agglomerative hierarchical clustering algorithm.

com.chemaxon.common.annotations - package com.chemaxon.common.annotations

com.chemaxon.descriptors.alignment - package com.chemaxon.descriptors.alignment

3D flexible alignment based molecular shape similarity calculation.

com.chemaxon.descriptors.common - package com.chemaxon.descriptors.common

Unguarded descriptor handling.

com.chemaxon.descriptors.db - package com.chemaxon.descriptors.db

Interfaces for database import/export.

com.chemaxon.descriptors.fingerprints.cfp - package com.chemaxon.descriptors.fingerprints.cfp

API of the Chemaxon hashed fingerprint family molecular descriptors.

com.chemaxon.descriptors.fingerprints.ecfp - package com.chemaxon.descriptors.fingerprints.ecfp

API of the ECFP fingerprint family molecular descriptors.

com.chemaxon.descriptors.fingerprints.maccs - package com.chemaxon.descriptors.fingerprints.maccs

ChemAxon implementation of the MACCS 166 bit fingerprints.

com.chemaxon.descriptors.fingerprints.pf2d - package com.chemaxon.descriptors.fingerprints.pf2d

API of the 2D pharmacophore fingerprint family molecular descriptors.

com.chemaxon.descriptors.metrics - package com.chemaxon.descriptors.metrics

Common descriptor comparison metrics.

com.chemaxon.descriptors.vectors.binary - package com.chemaxon.descriptors.vectors.binary

Generic binary vector descriptors.

com.chemaxon.descriptors.vectors.floats - package com.chemaxon.descriptors.vectors.floats

Generic floating point vector descriptors.

com.chemaxon.mapper - package com.chemaxon.mapper

com.chemaxon.overlap.io - package com.chemaxon.overlap.io

com.chemaxon.search - package com.chemaxon.search

Tools for chemical search.

com.chemaxon.search.mcs - package com.chemaxon.search.mcs

Contains classes for finding the maximum common substructure (MCS) of molecular structures.

com.chemaxon.search.mcs.buildup - package com.chemaxon.search.mcs.buildup

Contains MCS algorithm implementation based on the "build up" method.

com.chemaxon.search.mcs.maxclique - package com.chemaxon.search.mcs.maxclique

Contains MCS algorithm implementation based on the "maximum clique" method.

com.chemaxon.search.mcs.upperbound - package com.chemaxon.search.mcs.upperbound

Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.

com.chemaxon.search.transformation - package com.chemaxon.search.transformation

com.chemaxon.search.transformation.transformers - package com.chemaxon.search.transformation.transformers

com.chemaxon.version - package com.chemaxon.version

combine(Collection<? extends CalculatorInputChecker>) - Static method in interface chemaxon.calculator.CalculatorInputChecker

Combines the given checkers into a single one that reports all errors reported by the given checkers.

compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator

compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator

compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator

Compare two descriptors in serialized form.

compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator

compare(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator

Compare two descriptors.

compare(T, T) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator

compareAtoms(int, int) - Method in class chemaxon.sss.search.MolComparator

Compares atoms of indices a1 and a2.

compareBonds(int, int) - Method in class chemaxon.sss.search.MolComparator

Compares bonds of indices b1 and b2.

compareHit(int[], int) - Method in class chemaxon.sss.search.MolComparator

Checks a partial hit during the search algorithm.

compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor

Comparison method which uses the priority field for ordering.

compareTo(AtomIdentifier) - Method in class chemaxon.reaction.AtomIdentifier

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

compareTo(Object) - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord

comparisonContextFactory() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator

Get an unguarded context factory.

comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator

comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator

comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator

comparisonLinenote() - Method in interface com.chemaxon.descriptors.metrics.MetricFactory

Gets the string based parameterization description.

ComparisonResult - Interface in com.chemaxon.descriptors.common

Result of a descriptor comparison.

compatible(Guarded, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat

Ensure the guard object based compatibility of two objects.

compatibleWithGuard(Object, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat

Ensure the guard object based compatibility of two objects.

compile(String) - Method in class chemaxon.jep.ChemJEP

Compiles the expression string to an inner structure.

compile(String) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, Class) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

compile(String, Class, SymbolTable) - Method in class chemaxon.jep.Evaluator

Compiles the expression, creates ChemJEP object.

COMPLETE - com.chemaxon.mapper.Mapper.MappingStyle

All atoms will be mapped

CompleteLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage

component - Variable in class chemaxon.marvin.space.monitor.Control

COMPONENT - chemaxon.struc.SgroupType

COMPONENT_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene

COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent

COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MoleculeComponent

COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent

COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent

COMPONENT_TYPE_ENTIRE - Static variable in class chemaxon.marvin.space.GraphicComponent

Indicates if the entire component is selected by picking.

COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent

COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MoleculeComponent

COMPONENT_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent

componentBecameSelected() - Method in class chemaxon.marvin.space.GraphicCell

Returns true if a component became selected previously.

componentBecameSelected(int) - Method in class chemaxon.marvin.space.GraphicScene

Returns true if a component became selected previously in the given cell.

componentBecameUnselected() - Method in class chemaxon.marvin.space.GraphicCell

Returns true if a component became unselected previously.

componentBecameUnselected(int) - Method in class chemaxon.marvin.space.GraphicScene

Returns true if a component became unselected previously in the given cell.

ComponentChecker<E> - Class in chemaxon.checkers

Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).

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

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

ComponentElement - Class in chemaxon.marvin.space

Class to identify parts of GraphicComponents mainly during selection.

ComponentElement(ComponentElement) - Constructor for class chemaxon.marvin.space.ComponentElement

Copies the given ComponentElement.

ComponentElement(GraphicComponent, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement

Creates a new instance of ComponentElement of a simple (not structured) GraphicComponent.

ComponentElement(GraphicComponent, int, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement

Creates a new instance of ComponentElement of a complex (structured) GraphicComponent.

ComponentElement(GraphicComponent, int, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement

Creates a new instance of ComponentElement.

ComponentElement(GraphicComponent, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement

Creates a new instance of ComponentElement.

componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Hides windows if the parent frame is hidden.

componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Does nothing.

componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Does nothing.

componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MViewPane

componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Shows windows if the parent frame is hidden.

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

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

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

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

COMPOSITION - chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType

Result type with the string id "composition".

COMPRESS - Static variable in class chemaxon.formats.MdlCompressor

Compression flag.

compressedData - Variable in class chemaxon.descriptors.PFParameters

Buffer for compressed data, used in MolecularDescriptor.toData( final int[] ).

computeFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Computes the scaling factor for the unscaled NMR spectrum function.

computeFunctionScale(double, double[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

computeNext() - Method in class com.chemaxon.calculations.io.MemoizingIterator

computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration

computeSurface(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MSpaceEasy

Activates the container cell of the MoleculeVisualizer, and computes its Connolly surface.

computeSurface(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Computes the given type of surface in the active cell of the viewer.

ConcurrentReactorProcessor - Class in chemaxon.reaction

Executes a chemical reaction: creates products from reactants with reaction center data.

ConcurrentReactorProcessor() - Constructor for class chemaxon.reaction.ConcurrentReactorProcessor

ConcurrentStandardizerProcessor - Class in chemaxon.standardizer

Performs standardization of molecules in concurrent mode.

ConcurrentStandardizerProcessor() - Constructor for class chemaxon.standardizer.ConcurrentStandardizerProcessor

ConcurrentStandardizerProcessor.MolTransformer - Interface in chemaxon.standardizer

Molecule transformer.

CONFIDENCE - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the confidence that the structure is correct.

config - Variable in class chemaxon.checkers.StructureCheckOptions

The configuration of the structure check.

CONFIG_DIR - Static variable in class chemaxon.jep.Evaluator

Default directory for storing configuration files.

CONFIG_PATH_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction

The key of configuration path parameter of the abstract action.

configFilePath - Variable in class chemaxon.descriptors.MDParameters

location of the configuration file

ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader

This interface is provided for classes which can read the configuration of CheckerRunner.

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

Identifier of parameter: "confirmTransfer".

CONFORMATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager

Identifier of plugin: Conformation Plugin Group

ConformerPlugin - Class in chemaxon.marvin.calculations

Plugin class for conformer calculation.

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

Constructor.

CONJUGATED - Static variable in class chemaxon.struc.MolBond

Conjugation state of the bond.

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

Sets whether the common substructures should be connected or they can consist of multiple fragments.

connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule

connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Sets the original connections to the new atom.

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject

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

field indicates constant argument

constructBvGenerator(BvParameters) - Method in interface com.chemaxon.descriptors.vectors.binary.BvParameters.ConstructBvGenerator

Construct new instance

constructCfpGenerator(CfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.ConstructCfpGenerator

Constructor invocation.

constructEcfpGenerator(EcfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.ConstructEcfpGenerator

Constructor invocation.

constructMaccsGenerator(MaccsParameters) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.ConstructMaccsGenerator

Constructor invocation.

constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.ConstructPfGenerator

Constructor invocation.

containerFrame - Variable in class chemaxon.marvin.space.MSpaceEasy

contains(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox

Tells whether the given location is inside the box.

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

Tests whether the document contains all objects of another document.

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

Searches an object in the document.

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

Checks if the molecule graph contains the specified atom.

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

Checks if the molecule graph contains the specified atom.

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

Checks if the root structure or an R-group contains the specified node.

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

Checks if a reactant, agent or product structure contains the specified node.

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

Is this atom contained by the s-group?

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

Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.

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

Checks if the root structure or an R-group contains the specified edge.

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

Checks if a reactant, agent or product structure contains the specified edge.

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

Does the molecule graph contain the specified fragment?

contains(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether the container contains the specified property object.

contains(MProp) - Method in class chemaxon.struc.prop.MCollectionProp

Tests whether the collection contains the specified property.

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

Checks if the S-group contains the atoms of another S-group.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.MObject

Checks if the object contains the specified atom reference.

containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell

Tells whether the component is in the cell.

containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

Returns true if the component exists in the scene.

containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Decides whether a molecule graph contains coordinate bonds.

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

Decides whether the structure of this sgroup contains a ladder-type repeating unit.

containsMulticenterSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Decides whether a molecule contains Multicenter S-groups.

containsOnlyOne(Class) - Method in class chemaxon.struc.MDocument

Tests whether the document contains only one object of the specified class.

containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle

containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject

containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom

Returns true if this atom has a mapping for the specified property key.

containsPropertyKey(String) - Method in class chemaxon.struc.MolBond

Returns true if this bond has a mapping for the specified property key.

containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if molecule contains pseudo atom.

containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Decides whether a molecule contains SRU S-groups.

CONTEXT - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the context of the structure recognized in the text.

CONTEXT_INDEX - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: index of the hit inside the context.

contract(int) - Method in class chemaxon.struc.Sgroup

Sets the state to Sgroup.XSTATE_C.

contract(int) - Method in interface chemaxon.struc.sgroup.Expandable

Contracts the S-group.

contract(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Contracts this S-group.

contract(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Contracts this S-group.

ContractGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule

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

contractOrExpandSgroups(int, String, boolean) - Method in class chemaxon.marvin.view.MDocStorage

Contract or expand S-groups in the specified cell.

contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.view.MDocStorage

Contract or expand S-groups in all molecules.

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

Contracts all S-groups.

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

Contracts all S-groups.

ContractSgroupsAction - Class in chemaxon.standardizer.actions

Standardizer action contracting s-groups of the target molecule

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

Initializes the action

control - Variable in class chemaxon.marvin.space.monitor.DihedralMonitor

control - Variable in class chemaxon.marvin.space.monitor.Monitor

control(int) - Method in class chemaxon.marvin.space.monitor.Control

Does control on z event.

control(int) - Method in class chemaxon.marvin.space.monitor.DihedralControl

One part of the molecule being in one of the end of the torsion bond will be rotated around the bond.

control(int) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor

Passes the control event to the control.

control(int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl

Changes the location say translates the component of the control in the global coordinate system.

control(int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl

Changes the orientation that is rotates the component of the control in the global coordinate system.

control(int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl

Changes the location say translates the component of the control in its local coordinate system.

control(int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl

Changes the orientation say rotates the component of the control in its local coordinate system.

control(int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor

Causes the monitor's controll to take action with 1 parameter.

control(int) - Method in class chemaxon.marvin.space.monitor.ResizeControl

Resizes the component in z direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.

control(int, int) - Method in class chemaxon.marvin.space.monitor.Control

Does control on x-y events.

control(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl

Does nothing.

control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl

Changes the location say translates the component of the control in the global coordinate system.

control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl

Changes the orientation say rotates the component of the control in the global coordinate system.

control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl

Changes the location say translates the component of the control in its local coordinate system.

control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl

Changes the orientation say rotates the component of the control in its local coordinate system.

control(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor

Causes the monitor's controll to take action with 2 parameters.

control(int, int) - Method in class chemaxon.marvin.space.monitor.ResizeControl

Resizes the component in x, y direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.

Control - Class in chemaxon.marvin.space.monitor

Transformation on a GraphicComponent that changes the coordinates, and not just the view.

Control() - Constructor for class chemaxon.marvin.space.monitor.Control

Creates a new instance of Control

convert() - Method in class chemaxon.formats.MdlCompressor

Compression/decompression

convert() - Method in class chemaxon.formats.MolConverter

Convert the next molecule.

convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor

(Un)compress the specified molfile or SDfile.

convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy

convert(TransferDataImporter) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler

Convert transfer data available on clipboard in one of the requested flavors.

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

Creates an MDL mol or compressed mol representation of the molecule.

convert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule

Convert a molecule to a string or byte array.

convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult

convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method converts the entities contained in this result according to the convertData.

convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.ModeConverter

convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.TypeConverter

convert(String, boolean) - Method in interface chemaxon.naming.NameConverter

Convert a name into the corresponding structure.

convert(String, int) - Static method in class chemaxon.formats.MdlCompressor

(Un)compress the specified molfile or SDfile.

ConvertAliasToGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the aliases to contracted abbreviated groups in the molecule

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

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 in chemaxon.standardizer.actions

Type of conversion

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

Convert explicit Hydrogen atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize

Convert explicit Hydrogen atoms of the molecule to implicit.

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

Convert explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.

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

Convert explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.

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

Converts explicit lone pairs from a molecule to implicit.

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

Convert implicit Hydrogen atoms of the molecule to explicit.

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

Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

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

Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

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

Convert implicit lone pairs of the atoms of a molecule to explicit.

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

Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX.

ConvertPiMetalBondsAction - Class in chemaxon.standardizer.actions

Convert Pi-Metal coordinate bond to coordinate bond action.

ConvertPiMetalBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertPiMetalBondsAction

Initializes a convert pi-metal bond action

ConvertPseudoToGroupFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the pseudo informations to contracted abbreviated groups in the molecule

ConvertPseudoToGroupFixer() - Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer

convertResult(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner

Deprecated.

This method converts the result by changing the atoms and bonds back to the original instead of the cloned ones

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker

Handles the mapping of a cloned and expanded molecule result to the original molecule.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker

This implementation does nothing.

convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker

This implementation does nothing.

ConvertToAtomFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information

ConvertToAtomFixer() - Constructor for class chemaxon.fixers.ConvertToAtomFixer

ConvertToCarbonFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms

ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer

ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond

ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer

ConvertToElementalFormFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms

ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer

ConvertToEnhancedStereoAction - Class in chemaxon.standardizer.actions

Convert to enhanced stereo standardizer action

ConvertToEnhancedStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Initializes the action with parameters

convertToFrags() - Method in class chemaxon.struc.Molecule

Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.

ConvertToIonicFormFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.

ConvertToIonicFormFixer() - Constructor for class chemaxon.fixers.ConvertToIonicFormFixer

ConvertToPlainDoubleBondFixer - Class in chemaxon.fixers

Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.

ConvertToPlainDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToPlainDoubleBondFixer

ConvertToSingleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the bond to single bond.

ConvertToSingleBondFixer() - Constructor for class chemaxon.fixers.ConvertToSingleBondFixer

convertToSmilingFormat(Molecule) - Static method in class chemaxon.formats.MFileFormatUtil

Tries to convert a molecule to a SMILES related format.

convertToSmilingFormat(MProp) - Static method in class chemaxon.formats.MFileFormatUtil

Try to convert a property to text with a SMILES related format argument.

convertToString(MDocument, String, int) - Static method in class chemaxon.formats.MolExporter

Converts the document to text format.

convertToString(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler

Convert key of MPropertyContainer to string.

convertToString(MProp, String) - Static method in class chemaxon.marvin.io.MPropHandler

Converts the property to text format.

convertToString(String) - Method in class chemaxon.struc.MProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop

Deprecated.

As of release 5.7, replaced by MolExporter.convertToString(MDocument, String, int)

convertToString(String, int) - Method in class chemaxon.struc.MProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).

convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).

convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).

convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp

Deprecated.

As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)

ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts crossed double bond to wiggly

ConvertToWigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToWigglyDoubleBondFixer

convertTransform(CTransform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle

coordBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Coordinate bond display style.

coordBondStyleAtMulticenter(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder

Coordinate bond display style when it connects to a multicenter atom.

COORDDEP - Static variable in class chemaxon.struc.MProp

Coordinate dependent property.

COORDINATE - Static variable in class chemaxon.struc.MolBond

Coordinate bond flag.

COORDINATE_BOND_ARROW_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_AT_MULTICENTER_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_AT_MULTICENTER_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_AT_MULTICENTER_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_HASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_STYLE - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "coordinateBondStyle".

COORDINATE_BOND_STYLE_AT_MULTICENTER - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "coordinateBondStyleAtMulticenter".

COORDINATE_BOND_STYLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_STYLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

COORDINATE_BOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Deprecated.

CoordinateBondOnMulticenterStyle - Enum in chemaxon.marvin.paint.constants

Holds the values for the possible rendering styles for Coordinate bonds connected to Multicenter atoms.

CoordinateBondStyle - Enum in chemaxon.marvin.paint.constants

Holds the values for the possible rendering styles for Coordinate bonds.

CoordinationSystemErrorChecker - Class in chemaxon.checkers

Detects errors of multicenter coordination systems.

CoordinationSystemErrorChecker() - Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker

Default constructor

COORDS_UPDATE - Static variable in interface chemaxon.struc.sgroup.Expandable

Deprecated.

As of Marvin 6.2, no replacement.
Not supported feature.

COPOLYMER - chemaxon.struc.SgroupType

COPOLYMER_ALT - chemaxon.struc.SgroupType

COPOLYMER_BLK - chemaxon.struc.SgroupType

COPOLYMER_RAN - chemaxon.struc.SgroupType

COPY_AS_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants

Default format to be selected on Copy as dialog.

COPY_AS_IMAGE_BITMAP - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated.

COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated.

COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated.

COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants

Deprecated.

COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants

Deprecated.

since 5.3.3 has no sense

CopyOptConstants - Interface in chemaxon.marvin.util

Deprecated.

since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this interface either non exists in the new implementation or its value has changed. See the constants own description for details.

copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket

Copies line properties to another line object.

copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow

copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline

Copies line properties to another line object.

correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

countAllAtoms() - Method in class chemaxon.struc.MolAtom

Counts all atoms represented by this atom.

countAllAtoms() - Method in class chemaxon.struc.Sgroup

Counts the total number of atoms recursively.

countAllAtoms() - Method in class chemaxon.struc.sgroup.SgroupAtom

Counts all atoms represented by this atom.

countEnumerations() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the number of all enumerated structures, no arithmetic overflow because counts in BigInteger.

countEnumerationsMagnitude() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin

Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures.

countExpandableContractableSgroups() - Method in class chemaxon.struc.Molecule

Counts the expandable and contractable S-groups.

countNumberOfClusters(HierarchicClustering<?, ? extends HierarchicCluster<?>>) - Static method in class com.chemaxon.clustering.util.Util

Count the number of clusters in a clustering.

countOrderedComponentSgroups() - Method in class chemaxon.struc.Molecule

Counts the ordered component S-groups.

countRecords(MProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.view.MDocStorage

Counts the total number of records and sets the size of the document storage.

countRecordsInFraction(double, int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage

Deprecated.

COVALENT_COUNTER_ION - chemaxon.checkers.StructureCheckerErrorType

Error type represents that incorrectly drawn covalent counter ion had found in the molecule

COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Covalent hydration error remark.

CovalentCounterionChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).

CovalentCounterionChecker() - Constructor for class chemaxon.checkers.CovalentCounterionChecker

Default constructor

covalentRadiusOf(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the covalent radius in C-C bond length units.

cpk - chemaxon.marvin.io.image.ImageExportParamConstants.coloringValues

CPK - chemaxon.marvin.io.image.ImageExporter.Coloring

CPK_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts

CPK color scheme in display option flags.

CPK_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

CPK color scheme.

Cr - Static variable in class chemaxon.core.ChemConst

crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule

create() - Method in class com.chemaxon.apidiscovery.CreatorWrapper

Invoke creator method.

create() - Static method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings

Constructs a new StereoisomerSettings object with default settings.

create(byte[]) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule

Deprecated.

create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D

create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory

create(Molecule, Molecule) - Method in interface com.chemaxon.search.CustomMatcherFactory

Creates a custom matcher for atom and bond pairs of the given query and target structures.

create(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

Creates a similarity calculator object according to the user defined parameters.

create(String) - Static method in class chemaxon.util.DotfileUtil

Opens a dotfile for writing.

create(String, int, int) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

Creates a similarity calculator object according to the user defined parameters.

create(String, PSymbols) - Static method in class chemaxon.pharmacophore.PMap

Creates a PMap object from a pharmacophore point list string.

create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Loads a plugin, first tries to load it from CLASSPATH, then from JAR.

createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas

Constructs an elemental analysis from molecular formula.

createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value

createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value

createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value and type

createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument

Returns a service argument based on value and type

createAromatizedSearcher(AromatizationMethod) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher that considers aromatization differences of the input molecule.

createAromatizedSearcher(AromatizationMethod, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher which considers aromatization according to the specified rules and initializes it with the specified search options.

createArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler

Creates an array property.

createArrayXSD(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler

Creates an array property from the XSD type.

createAtomIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.

createAtomNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an iterator to get the atom neighbours of the specified atom.

createBondIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.

createBondNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an iterator to get the bonds connecting to the specified atom.

createBondTable(int, int) - Static method in class chemaxon.core.util.BondTable

Creates a new bond table for a molecule graph with the specified number of atoms and bonds.

createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil

createChemicalTermsTextPane() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.

createChemicalTermsTextPane(boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.

createChemicalTermsTextPane(boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.

createChemicalTermsTextPane(CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.

createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Creates a JTextPane instance with code assist capabilities.

createChemicalTermsTextPane(String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.

createChemicalTermsTextPane(String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space

createChemicalTermsTextPane(String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(String, boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space

createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.

createChemicalTermsTextPane(String, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space

createChemicalTermsTextPane(String, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(String, String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.

createChemicalTermsTextPane(String, String, boolean, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.

createChemicalTermsTextPane(String, String, boolean, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.

createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.

createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Creates a JTextPane instance with code assist capabilities.

createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory

Deprecated.

use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.

createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes

createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument

Creates a ServiceArgument constant based on string value and argument type.
Supported types are String, Integer, Long, Double, Float and Boolean

createDefaultParameterPanel(Class, String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory

createDefaultParameterPanel(String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory

Creates default parameter panel based on XML config.

createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph

Creates a dehydrogenized version of the molecule.

createEMF(String, String) - Static method in class chemaxon.util.ImageExportUtil

Creates a .NET based EMF picture.

createErrorMessage(StandardizerConfiguration) - Static method in class chemaxon.standardizer.configuration.StandardizerConfiguration

Creates an error message based on an invalid configuration

createExportModule() - Method in class chemaxon.formats.MFileFormat

Creates the export module.

createExportModule(String) - Method in class chemaxon.formats.MFileFormat

Creates the export module.

createExportModule(String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates an export module for the specified format.

createExportModule(String, String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates an export module for the specified format with the specified encoding.

createFeatureMap(Molecule) - Method in class chemaxon.pharmacophore.PMapper

Creates the feature ID -> atom index BitSet HashMap for the given target molecule.

createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers

Deprecated.

Use ProgressObservers.nullProgressObserver() instead.

createGData() - Method in class chemaxon.marvin.space.SurfaceComponent

createGearch() - Method in class chemaxon.struc.Molecule

createGearch() - Method in class chemaxon.struc.MoleculeGraph

createGearch() - Method in class chemaxon.struc.RgMolecule

createGearch() - Method in class chemaxon.struc.RxnMolecule

createGearch() - Method in class chemaxon.struc.SelectionMolecule

createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

CreateGroupAction - Class in chemaxon.standardizer.advancedactions

Create Group standardizer action

CreateGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.CreateGroupAction

Initializes a create group standardizes action

createImage(Buffer, int, int) - Method in class chemaxon.marvin.space.GraphicScene

createImageExporterParameter(Properties, String, MDocument) - Static method in class chemaxon.util.ImageExportUtil

Creates the Image Exporter parameter String based on the values in the Properties object.

createImportMod(MolInputStream) - Static method in class chemaxon.marvin.io.MRecordImporter

Creates an importer for the specified molecule input stream.

createImportMod(String) - Static method in class chemaxon.marvin.io.MRecordImporter

Creates an importer for the specified molecule format.

createImportModule() - Method in class chemaxon.formats.MFileFormat

Creates the molecule import module.

createInDocumentAt(DPoint3, MDocument) - Static method in class chemaxon.struc.NoStructure

Creates a NoStructure at the given location.

createInDocumentFrom(Molecule, MDocument) - Static method in class chemaxon.struc.NoStructure

Creates a NoStructure from the given component.

createLicenseManagerPanel() - Static method in class chemaxon.license.LicenseManager

Creates the main panel which is used for end-user license managing.

createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane

Deprecated.

as of Marvin 3.3.1, replaced by SwingUtil.createMenu

createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil

Utility method to create a menu with a label specified as a resource.

createMenu(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu with a label specified as a resource.

createMenuItem(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu with a label specified as a resource.

createMenuItem(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu with a label specified as a resource.

createMenuItem(ResourceBundle, String, Class<?>, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a menu item with a label specified as a resource.

createMessagePane(String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a message pane with HTML text content.

createMMoleculeProp(String) - Static method in class chemaxon.marvin.io.MPropHandler

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Returns the molecule form with largest distribution.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin

Returns the canonical tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the modified input molecule (e.g.

createMol() - Method in class chemaxon.formats.MolImporter

Creates a target molecule object for import.

createMol() - Method in class chemaxon.marvin.io.formats.mdl.MolImport

Creates a new target molecule object.

createMol() - Method in class chemaxon.marvin.io.MolImportModule

Creates a new target molecule object for the import.

createMol() - Method in class chemaxon.marvin.io.MRecordImporter

Creates an empty target molecule for import.

createMolConverter(InputStream, OutputStream, String[], int[]) - Static method in class chemaxon.formats.MolConverter

Creates a MolConverter instance with the attributes specified in the parameters.

createMolecule() - Method in class chemaxon.struc.Sgroup

Creates a molecule object that contains only this group.

createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Creates a molecule object that contains only one SuperatomSgroup identical to this one.

createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup

Creates a cloned sgroup instance and a molecule object that contains only this sgroup.

createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable

Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.

createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory

Creates a MoleculeIterator object for iterating through a molecule array (Molecule[]).

createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory

Creates a MoleculeIterator object for iterating through collection of molecules (Molecule objects).

createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter

Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.

createNeighbourBonds(Molecule, MolBond, boolean) - Static method in class chemaxon.checkers.StructureCheckerHelper

This method returns a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond

createNew() - Static method in class chemaxon.marvin.calculations.HlbPlugin.Builder

Constructs a new HlbPlugin instance.

createNew(Molecule) - Static method in class chemaxon.marvin.alignment.MCSAlignment.Factory

Constructs a new instance of ConformationAlignment class.

createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters

Construct a builder for this parameter class, initialized to default.

createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters

Construct a builder for this parameter class, initialized to default.

createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters

Construct a builder for this parameter class, initialized to default.

createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.binary.BvParameters

Construct a builder for this parameter class, initialized to default.

createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.floats.FvParameters

Construct a builder for this parameter class, initialized to default.

createNewCell() - Method in class chemaxon.marvin.space.GraphicScene

Sets an empty cell to be the active cell.

createNewReader(String) - Static method in class com.chemaxon.descriptors.db.MDTableReader

Create an MDTableReader from the xml configuration string.

createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader

Create a PfTableReader from the xml configuration string.

createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader

Create a PfTableReader from the xml configuration string.

createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader

Create a PfTableReader from the xml configuration string.

createNext() - Method in class chemaxon.struc.graphics.MTextAttributes

Creates identical attributes for the next section.

createNoCancelObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers

Deprecated.

Use ProgressObservers.noCanceller()

createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers

Deprecated.

Use ProgressObservers.createStrictNullObserver().

createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates the parameter panel.

createPartialMappingMatcher() - Method in interface com.chemaxon.search.CustomMatcherFactory

createReaction(MoleculeGraph, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

createReader(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory

Generates reader object.

createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader.Factory

createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader.Factory

createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader.Factory

createRecognizer() - Method in class chemaxon.formats.MFileFormat

Creates a recognizer module.

createRecognizer(String) - Method in class chemaxon.formats.MFileFormat

Deprecated.

as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead

createRecordReader(MolInputStream, String) - Method in class chemaxon.formats.MFileFormat

Creates the record reader.

createRecordReader(InputStream, String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates a record reader for an input stream.

createRecordReader(InputStream, String, String, String) - Static method in class chemaxon.formats.MFileFormatUtil

Creates a record reader for an input stream.

createResult(Molecule, List<StructureCheckerResult>) - Method in class chemaxon.checkers.ReactionChecker

This method a merged StructureCheckerResult from the List of StructureCheckerResult which contains the problems of the components in the reaction

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AliasChecker

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomChecker

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.PseudoAtomChecker

createResult(Molecule, List<MolBond>) - Method in class chemaxon.checkers.BondChecker

createResult(Molecule, List<E>) - Method in class chemaxon.checkers.ComponentChecker

Creates a StructureCheckerResult from a List containing the components.

createResultView(String, MolPanel) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

createRgComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.

createRotationAboutBond(MolBond, double) - Static method in class chemaxon.marvin.util.CleanUtil

Creates a rotation transformation about a bond.

createRxnComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory

Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.

createSavedCoordsArray(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Creates an empty array for the atomic coordinates of a structure.

createScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler

Creates a scalar property.

createScalar(String, String, MProgressMonitor) - Static method in class chemaxon.marvin.io.MPropHandler

Creates a scalar property.

createScalarXSD(String, String) - Static method in class chemaxon.marvin.io.MPropHandler

Creates a scalar property from the XSD type.

createSearcher(Transformer, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Constructs a searcher with the specified parameters.

createSearcherWithoutAromatization() - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher that does not handle aromatization.

createSearcherWithoutAromatization(MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher that doesn't consider aromatization.

createSearcherWithoutAromatization(SimpleSearcher, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory

Creates a searcher with the specified search options, other parameters (query, target, etc.) are copied from the specified searcher if possible (in case of BaseMolSearch).

createSelectionPanel(int) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace selection panel to the container.

createSelectionPanelAndProgressBar() - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace selection panel to the container.

createSetColoringParameter(Properties, MDocument) - Static method in class chemaxon.util.ImageExportUtil

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.

Use ResonancePlugin.createStandardizedMolecule(Molecule) instead

createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin

Deprecated.

createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Deprecated.

Use CalculatorPlugin.createStandardizedMolecule(Molecule) instead

createStatistics - Variable in class chemaxon.descriptors.MDGenerator

indicates if statistical data has to be gathered during generation

createStrictNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers

Returns a SubProgressObserver which ignores observed data.

createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a sub-panel with a title.

createTopLeftConstraints() - Static method in class chemaxon.marvin.util.SwingUtil

Creates GridBagConstraints for the top left component.

createViewPanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates view panel with given molecules, places molecule properties in formatted texts.

createViewPanel(Molecule[], int, int, int, int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay

Creates view panel with given molecules, places molecule properties in formatted texts.

createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter

Constructs the specified visitor implementation.

createVisitor(ImmutableList.Builder<T>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter

Constructs the specified visitor implementation.

createWriter(OutputStream) - Method in class chemaxon.marvin.io.image.ImageExporter

Creator - Annotation Type in com.chemaxon.apidiscovery.annotations

Creator methods produce instances of specific classes.

CreatorWrapper<T> - Class in com.chemaxon.apidiscovery

CreatorWrapper acts as a type- and instance -dependent service loader.

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 - chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Crossed double bond type

CROSSED_DOUBLE_BOND - 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.

use ConvertToWigglyDoubleBondFixer

CrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.CrossedDoubleBondFixer

Deprecated.

CROSSLINK - 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 - chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes

CSSR - 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.

as of Marvin 2014.07.21.0 intended for internal use only

CubeRecognizer() - Constructor for class chemaxon.formats.recognizer.CubeRecognizer

Deprecated.

currentBond - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

Current bond pointer of the iterator.

currentMetricIndex - Variable in class chemaxon.descriptors.MDParameters

index of the parametrized metric currently in use

cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Move the cursor down.

cursorLeft(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorRight(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorToRowEnd(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorToRowStart(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorUp(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Moves the cursor up.

CUSTOM_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

custom name property

CustomDescriptor - Class in chemaxon.descriptors

The CustomDescriptor class implements a generic molecular descriptor class which supports third party or use defined descriptors.

CustomDescriptor() - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.

CustomDescriptor(int, int) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.

CustomDescriptor(CDParameters) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new instance of CustomDescriptor according to the parameters given.

CustomDescriptor(CustomDescriptor) - Constructor for class chemaxon.descriptors.CustomDescriptor

Copy constructor.

CustomDescriptor(String) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new instance of CustomDescriptor according to the parameters given.

CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants

Identifier of parameter: "customizationEnabled".

CustomMatcher - Interface in com.chemaxon.search

Interface for custom matching of atoms and bonds during search.

customMatcherFactory - Variable in class com.chemaxon.search.MatchingOptions.Builder

CustomMatcherFactory - Interface in com.chemaxon.search

Factory interface for creating CustomMatcher objects.

customMatching(CustomMatcherFactory) - Method in class com.chemaxon.search.MatchingOptions.Builder

Sets the factory to be used to create a custom matcher.

customMatching(CustomMatcherFactory) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder

customPaletteColors - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent

CUSTOMXML - com.chemaxon.descriptors.fingerprints.ecfp.EcfpAtomTypizers

Custom XML configurated ECFP atom typizer.

cv_inChain - chemaxon.marvin.io.image.ImageExportParamConstants.carbonLabelVisibilityValues

cv_off - chemaxon.marvin.io.image.ImageExportParamConstants.carbonLabelVisibilityValues

cv_on - chemaxon.marvin.io.image.ImageExportParamConstants.carbonLabelVisibilityValues

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, ...).

DASHED - chemaxon.marvin.io.image.ImageExporter.LineType

DASHED - chemaxon.marvin.paint.constants.AnyBondStyle

Dashed line is used when rendering Any bonds.

data - Variable in class chemaxon.descriptors.MDParameters

buffer for external data format generation, used in MolecularDescriptor.toData()

DATA - 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

DATABASE_SEARCH_ERROR - Static variable in class chemaxon.util.ErrorHandler

DatabaseSearchException - Exception in chemaxon.jchem.db

Error occurred during structural search in database.

DatabaseSearchException() - Constructor for exception chemaxon.jchem.db.DatabaseSearchException

Constructs a new exception with null as its detail message.

DatabaseSearchException(String) - Constructor for exception chemaxon.jchem.db.DatabaseSearchException

Constructs a new exception with the specified detail message.

DatabaseSearchException(String, Throwable) - Constructor for exception chemaxon.jchem.db.DatabaseSearchException

Constructs a new exception with the specified detail message and cause.

DatabaseSearchException(Throwable) - Constructor for exception chemaxon.jchem.db.DatabaseSearchException

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).

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.

date() - Method in annotation type com.chemaxon.common.annotations.SubjectToRemoval

DAYLIGHT_DOWNWEDGE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Daylight style down wedge orientation flag.

DAYLIGHT_DOWNWEDGE_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Daylight style down wedge orientation.

Db - Static variable in class chemaxon.core.ChemConst

DBS_ALL - Static variable in interface chemaxon.struc.StereoConstants

Double bond stereo checking for all double bonds.

DBS_MARKED - Static variable in interface chemaxon.struc.StereoConstants

Double bond stereo checking for marked double bonds only.

DBS_NONE - Static variable in interface chemaxon.struc.StereoConstants

No double bond stereo checking.

deactivateActiveCell() - Method in class chemaxon.marvin.space.GraphicScene

Sets the active cell to be no longer active.

DEAROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph

General dearomatization.

DEAROM_HUCKELCHECK - Static variable in class chemaxon.struc.MoleculeGraph

Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.

DEAROM_HUCKELCHECK_EX - Static variable in class chemaxon.struc.MoleculeGraph

Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.

dearomatize() - Method in class chemaxon.struc.Molecule

Dearomatize molecule.

dearomatize() - Method in class chemaxon.struc.MoleculeGraph

Dearomatize molecule.

dearomatize(int) - Method in class chemaxon.struc.MoleculeGraph

Dearomatize molecule.

DearomatizeAction - Class in chemaxon.standardizer.actions

Dearomatization standardizer action

DearomatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DearomatizeAction

Initializes the action

DearomatizeFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts the aromatic rings in the molecule into Kekule representation.

DearomatizeFixer() - Constructor for class chemaxon.fixers.DearomatizeFixer

DEBUG - Static variable in class chemaxon.marvin.common.ParameterConstants

Identifier of parameter: "debug".

Debye - chemaxon.calculations.dipole.DipoleResult.Unit

Debye unit.

DEBYE_TO_EA - Static variable in class chemaxon.calculations.dipole.DipoleResult

Debye to eA conversion upon multiplication.

decForm - Variable in class chemaxon.descriptors.MDParameters

to format floating point output

decode(String, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes

Reads attributes of the next section from a string.

decode(String, MFont, MTextAttributes.MFontCreator, double) - Method in class chemaxon.struc.graphics.MTextAttributes

Reads attributes of the next section from a string.

decodeHIsotopeMass(int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil

Extract H isotope information from the given Chemaxon compressed mol format code of the atom.

decompress(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Uncompresses input byte array and stores the uncompressed array in params.data.

DECOMPRESS - Static variable in class chemaxon.formats.MdlCompressor

Decompression.

decorateSubPanel(JPanel, String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates border and title for a panel.

decQProp(String) - Method in class chemaxon.struc.MolAtom

Decrements the value of a query property.

DECREASE_LINEAR - Static variable in class chemaxon.marvin.space.SurfaceColoring

The property values will decrease when getting farther from the atom center.

DECREASE_RECIPROCAL_SQUARE - Static variable in class chemaxon.marvin.space.SurfaceColoring

The property values will decrease when getting farther from the atom center.

DECREASE_SQUARE - Static variable in class chemaxon.marvin.space.SurfaceColoring

The property values will decrease when getting farther from the atom center.

decValenceProp() - Method in class chemaxon.struc.MolAtom

Decrements the value of the valence property.

DEF_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.