Index (Marvin Desktop Suite API documentation (c) 1998-2026 Chemaxon)

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A_ALL - Static variable in class chemaxon.struc.graphics.MTextAttributes: All identifiers.
A_BOLD - Static variable in class chemaxon.struc.graphics.MTextAttributes: Identifier of the font's bold subattribute.
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_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_ITALIC - Static variable in class chemaxon.struc.graphics.MTextAttributes: Identifier of the font's italic subattribute.
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.
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.chemterms.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.
ABBREVIATED_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that abbreviated groups have been found in the molecule
ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that only contracted abbreviated groups have been found in the molecule
ABBREVIATED_GROUP_WITH_ONLY_EXPANDED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that only expanded abbreviated groups have been found in the molecule
ABBREVIATED_GROUPS - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "abbrevgroups".
ABBREVIATED_GROUPS_ALLOWED - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "abbrevgroupsAllowed".
AbbreviatedGroupChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
AbbreviatedGroupChecker() - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker: Default constructor.
AbbreviatedGroupChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker: Parameterized constructor.
ABS - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.EnhancedStereoType: Stereogenic centers belonging to ABS represent absolute stereochemistry, i.e.
ABS_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Absolute stereoconfiguration label visibility flag.
ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.search.api.SearchConstants: Option for absolute stereo matching.
ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.search.api.SearchConstants: Option for absolute stereo matching.
ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.search.api.SearchConstants: Option for absolute stereo matching.
ABSENT_CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the 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
ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "absLabelVisible" or "absLabel".
ABSOLUTE_STEREO_CONFIGURATION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that all asymmetric centers in the molecule have absolute stereo configuration
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
AbstractAtropStereoDescriptor<T> - Class in chemaxon.core.calculations.stereo: Abstract base class of atrop stereo descriptors.
AbstractAtropStereoDescriptor(T, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor
AbstractAxialStereoDescriptor<T> - Class in chemaxon.core.calculations.stereo: Abstract base class of axial stereo descriptors.
AbstractAxialStereoDescriptor(T, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor
AbstractCisTransStereoDescriptor<T> - Class in chemaxon.core.calculations.stereo: Abstract base class of double-bond stereo descriptors.
AbstractCisTransStereoDescriptor(T, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor
AbstractSearch - Class in chemaxon.search: Abstract base class of all structural search classes.
AbstractSearch() - Constructor for class chemaxon.search.AbstractSearch
AbstractSgroupAction - Class in chemaxon.standardizer: Abstract class for standardizer actions modifying S-groups.
AbstractSgroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.AbstractSgroupAction: Initializes an abstract s-group action with the exclude list
AbstractStandardizerAction - Class in chemaxon.standardizer: Abstract implementation of the StandardizerAction.
AbstractStandardizerAction(Map<String, String>) - Constructor for class chemaxon.standardizer.AbstractStandardizerAction: Initializes the functionality of the abstract implementation.
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
AbstractTetrahedralStereoDescriptor<T> - Class in chemaxon.core.calculations.stereo: Abstract base class of tetrahedral stereo descriptors.
Ac - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ac.
accept(StereoCenterVisitor) - Method in class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter
accept(StereoCenterVisitor) - Method in class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter
accept(StereoCenterVisitor) - Method in class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter
accept(StereoCenterVisitor) - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenter: Accepts visitors.
accept(StereoCenterVisitor) - Method in class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter
accept(Molecule) - Method in interface chemaxon.core.util.MolFilter: Returns true if molecule is accepted by the filter.
accept(Molecule) - Method in class chemaxon.core.util.ValenceFilter: Returns true if molecule has no valence error.
accept(String...) - Static method in record class chemaxon.formats.Recognizer.RecognizerResult: Creates a Recognizer.RecognizerResult object accepting the given formats.
accept(List<String>) - Static method in record class chemaxon.formats.Recognizer.RecognizerResult: Creates a Recognizer.RecognizerResult object accepting the given formats.
ACCEPT_ONLY_SAME - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColorNotSpecifiedCase
acceptedFormats() - Method in record class chemaxon.formats.Recognizer.RecognizerResult: Returns the value of the acceptedFormats record component.
ACCEPTOR_SIGN - Static variable in class chemaxon.calculations.HBDAPlugin: Acceptor sign displayed in GUI.
ACCORD - Static variable in class chemaxon.formats.MFileFormat: ACCORD file format
ACCP - Static variable in class chemaxon.alignment.Pharmacophore3D
ACCURATE - Enum constant in enum class chemaxon.alignment.AlignmentAccuracyMode: Atomic contribution with correction terms.
ACCURATE - Enum constant in enum class chemaxon.alignment.AtropIsomerDetector.Accuracy
ACIDIC - Static variable in class chemaxon.calculations.PkaPlugin: Constant denoting acidic pKa.
actionPerformed(ActionEvent) - Method in class chemaxon.marvin.common.MAction: Sets the action state, performs a custom action, then propagates the event.
ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: action string token of the checker
ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor: action string tokens of the fixer
ACTIONSTRING_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: action string token of the action
actionStringToken() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the action string token of the checker
actionStringToken() - Element in annotation interface chemaxon.fixers.FixerInfo: Returns the action string token of the fixer.
actionStringToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the action string tokens of the action as a string, divided by comma characters
activeParts - Variable in class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor
activeParts - Variable in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor
activeParts - Variable in class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor
activeParts - Variable in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
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(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Adds an atom to the molecule.
add(MolAtom) - Method in class chemaxon.struc.RgMolecule: Adds an atom to the root structure.
add(MolAtom) - Method in class chemaxon.struc.RxnMolecule: Adds an atom to a reactant, product or agent structure.
add(MolAtom) - Method in class chemaxon.struc.SelectionMolecule: Adds an atom to the molecule.
add(MolAtom) - Method in class chemaxon.struc.Sgroup: Adds a new atom to the S-group.
add(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Adds a new atom to the S-group.
add(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Adds a new atom to the S-group.
add(MolAtom, boolean) - Method in class chemaxon.struc.SelectionMolecule: Adds an atom to the molecule.
add(MolBond) - Method in class chemaxon.struc.MolAtom: Add a bond if it had not been already added.
add(MolBond) - Method in class chemaxon.struc.Molecule
add(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Adds a bond to the molecule.
add(MolBond) - Method in class chemaxon.struc.RgMolecule: Adds a bond to the root structure.
add(MolBond) - Method in class chemaxon.struc.RxnMolecule: Adds a bond to a reactant, product, agent.
add(MolBond) - Method in class chemaxon.struc.SelectionMolecule: Adds a bond to the graph.
add(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom: Add an edge if it had not been already added.
add(MolBond, boolean) - Method in class chemaxon.struc.MoleculeGraph: Add a bond to the molecule.
add(MolBond, boolean) - Method in class chemaxon.struc.SelectionMolecule: Add a bond to the molecule.
add(MolBond, MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom: Add an edge to the given atom of the sgroup, if it had not been already added.
add(MProp) - Method in class chemaxon.struc.prop.MListProp: Adds an element.
add(Point3D) - Method in class chemaxon.struc.Point3D: Add the given point to this one.
add(Point3D, Point3D) - Static method in class chemaxon.struc.Point3D: Calculates the sum of the two vectors
add(CheckerFixerFactory.CheckerClassDescriptor) - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Adds a checker class descriptor to the factory
add(CheckerFixerFactory.FixerClassDescriptor) - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Adds a fixer class descriptor to the factory
add(InputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder: Adds an input stream containing standardizer specifications to be stored by the output factory
add(InputStream) - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Adds an input stream containing checker and fixer specifications to be stored by the output factory
add(String) - Method in class chemaxon.checkers.AtomLabels: Adds an atom label to the atom labels
add(String, double) - Method in class chemaxon.chemterms.ConstantTableBuilder: Adds a double constant to this builder.
add(String, Molecule) - Method in class chemaxon.chemterms.ConstantTableBuilder: Adds a molecule constant to this builder.
add(String, Molecule[]) - Method in class chemaxon.chemterms.ConstantTableBuilder: Adds a molecule array constant to this builder.
add(String, String) - Method in class chemaxon.chemterms.ConstantTableBuilder: Adds a string constant to this builder.
add(URL) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder: Adds an input stream containing standardizer specifications to be stored by the output factory
add(URL) - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Adds an input stream containing checker and fixer specifications to be stored by the output factory
add(Properties) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder: Adds a property map containing properties of standardizer actions to be stored by the output factory
add(Properties) - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Adds a property map containing properties of checkers and fixers to be stored by the output factory
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.common.TableOptions: Adds an action listener.
addActions(List<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Adds actions to the configuration
addActionToGroup(String, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Adds an action to the group
addActionToGroups(Collection<String>, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Adds an action to a list of groups
addAll(ConstantTable) - Method in class chemaxon.chemterms.ConstantTableBuilder: Adds all constants in the given table to this builder.
addAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes: Adds atoms to the "added atom" list.
addAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes: Adds atoms to the "added atom" list.
addArgument(ServiceArgument<?>) - Method in class chemaxon.calculations.services.ServiceDescriptor: Adds a new argument to the end of the argument list
addAtom(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Adds a new atom to this multiplet.
addAtom(MolAtom) - Method in class chemaxon.standardizer.Changes: Adds an atom to the "added atom" list.
addAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes: Adds an atom to the "added atom" list.
addAtom0(MolAtom) - Method in class chemaxon.struc.Molecule: Adds an atom.
addAtom0(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Adds an atom.
addAtom0(MolAtom) - Method in class chemaxon.struc.SelectionMolecule: Adds an atom.
addAtomPair(int, int) - Method in class chemaxon.alignment.AlignOnPairedAtoms: Adds an alignment constraint between the reference and aligned molecule.
addAtomPair(int, int, double) - Method in class chemaxon.alignment.AlignOnPairedAtoms: Adds an alignment constraint between the reference and aligned molecule.
addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Adds all atoms and bonds to the specified molecule.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.Molecule: Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RgMolecule
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule
addAtomWithBonds(MolAtom) - Method in class chemaxon.struc.SelectionMolecule: Adds an atom to the molecule.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Adds an atom without setting its parentGraph and index fields.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.SelectionMolecule: Adds an atom without setting its parentGraph and index fields.
addAttachmentPoint(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Adds a new free attachment point for an atom.
addAttachmentPoint(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Adds a new free attachment point of the given attachment atom and order.
addAttachmentPoint(MolAtom, int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Adds a new free attachment point.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MBracket: Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MEFlow
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectron
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectronContainer
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MNameTextBox: Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MPolyline: Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRectangle: Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRoundedRectangle: Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox: Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject: Adds the attribute names to the specified list.
addBond0(MolBond) - Method in class chemaxon.struc.Molecule: Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.SelectionMolecule: Adds a bond.
addBondWithoutChangingIt(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Adds a bond without setting its parentGraph and index fields.
addBracket(MBracket) - Method in class chemaxon.struc.Sgroup: Adds a bracket to this S-group.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox: Adds attribute names to the specified list.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject: Adds attribute names to the specified list.
addCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup: Adds a central atom to this sgroup.
addChar(char) - Method in class chemaxon.struc.graphics.MReactionSign
addChar(char) - Method in class chemaxon.struc.graphics.MTextBox: Adds a character to the text.
addCheckerMark(MDocument.CheckerMark) - Method in class chemaxon.struc.MDocument: Adds a checker mark to the document.
addChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup: Adds a child S-group.
AddChiralFlagFixer - Class in chemaxon.fixers: Absent chiral flag fixer.
AddChiralFlagFixer() - Constructor for class chemaxon.fixers.AddChiralFlagFixer
addCleanedRgroupAttachmentPoint(MolAtom, int, int) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Attaches a new R-group attachment point to the given atom by a bond of a specified type, and calculates appropriate atom coordinates for the attachment point using some sort of partial clean.
addComparator(MolComparator) - Method in class chemaxon.search.MolSearch: Add a comparator to the search object.
addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule: Adds a reactant, product or agent.
addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule: Adds a reactant, product or agent.
addConstraintsFromUserMappedAtoms() - Method in class chemaxon.alignment.Alignment: An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.
addCouplingConstants(double[]) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Adds a new coupling constant array.
addCrossingBonds(List<MolBond>, List<MolBond>) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Sets the crossing bonds (head and tail) of a ladder-type polymer.
addData(Molecule, MolAtom, String, String) - Method in class chemaxon.formats.MolExportModule: Adds a data sgroup to the given atom in the given molecule with fieldName and value.
addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup: Adds a line to the data stored in the field.
addDihedralStep(DihedralScanResult.ScanStep) - Method in class chemaxon.alignment.DihedralScanResult: Add a new step.
AddExplicitHydrogensAction - Class in chemaxon.standardizer.actions: Standardizer action that adds explicit hydrogens to the molecule.
AddExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AddExplicitHydrogensAction: Initializes the action
addGroup(GroupDefinition) - Method in class chemaxon.standardizer.actions.CreateGroupAction: Adds a group definition to the group list of the action
addGroup(String) - Method in class chemaxon.standardizer.actions.CreateGroupAction: Adds a group to the list defined by its abbreviation
addHeavyAtomLimitChecker(int) - Method in class chemaxon.calculations.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.converter.MolConverter.Builder: Adds an input file.
addInput(InputStream, String) - Method in class chemaxon.formats.converter.MolConverter.Builder: Adds an input stream.
addInput(String, String) - Method in class chemaxon.formats.converter.MolConverter.Builder: Adds an input file.
addInputChecker(TaggedCalculatorInputChecker) - Method in class chemaxon.calculations.CalculatorPlugin: Adds the specified input checker to this plugin.
addItemListener(ItemListener) - Method in class chemaxon.calculations.gui.MChart
addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams: Defines a label component inside the MarvinView table.
addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams: Defines a label component inside the MarvinView table.
addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MReactionSign
addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MTextBox
addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.common.MDocStorage: Adds a listener if it is not yet added.
addMatch(int[], int[], int) - Method in class chemaxon.search.AbstractSearch: 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[], int) - Method in class chemaxon.search.MolSearch
addMatch(int, int) - Method in class chemaxon.search.MolSearch: Adds a fixed matching between the given query and target atoms.
addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane: Adds a menubar change listener.
addMolecule(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams: Defines a molecule viewer component inside the MarvinView table.
addMolecule(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams: Defines a molecule viewer component inside the MarvinView table.
addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.alignment.Alignment: Add molecule to align
addNodeColorWeight(int, int, double) - Method in class chemaxon.alignment.Alignment: User may define extra weights between colors defined at setColoringScheme.
addNodeColorWeight(int, int, double) - Method in class chemaxon.alignment.PairwiseAlignment
addNodeColorWeight(int, int, double) - Method in interface chemaxon.alignment.PairwiseComparison
addNodeColorWeight(int, int, double) - Method in class chemaxon.alignment.PairwiseSimilarity3D
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MElectronContainer
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint: Point added to a document.
addNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint: Point added to a document.
addNotify(MDocument) - Method in class chemaxon.struc.MObject: Called when the object is added to a document.
addNumbering - Variable in class chemaxon.formats.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.
addParameter(PkaTrainingResult.PkaType, int, String, double) - Method in class chemaxon.calculations.PkaTrainingResult: Add parameter to the result
addParameters(File) - Method in class chemaxon.descriptors.MDParameters: Sets parameters from an XML config file keeping all previous settings.
addParameters(String) - Method in class chemaxon.descriptors.MDParameters: Sets parameters from an XML string representation keeping all previous settings.
addParametrizedMetric(String, String, String) - Method in class chemaxon.descriptors.MDParameters: Expands the set of parametrized metrics with a new item.
addParametrizedMetricNode(String, String, String) - Method in class chemaxon.descriptors.MDParameters: Adds a ParametrizedMetric node to the DOM tree.
addParametrizedMetricsNode() - Method in class chemaxon.descriptors.MDParameters: Adds the ParametrizedMetrics node to the DOM tree.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.calculations.api.ProgressableCalculator: Adds a PropertyChangeListener to listen for property changes
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
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 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(PropertyChangeListener) - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.structurechecker.CheckerRunner: Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.calculations.api.ProgressableCalculator: Adds a PropertyChangeListener to listen for specified property changes
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.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 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.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.structurechecker.CheckerRunner: Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed
addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Adds an atom to the list of paradigmatic repeating unit atoms.
addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule: Adds an R-group member.
addRgroupAttachmentPoint(int, int) - Method in class chemaxon.struc.MolAtom: Attaches a new R-group attachment point to this atom by a bond of a specified type.
addRgroupBridgeMember(RgroupBridgeId, Molecule) - Method in class chemaxon.struc.RgMolecule: Adds a definition member to an R-group bridge.
addRGroupsInPlaceOfImplHs(Molecule) - Static method in class chemaxon.search.RgroupDecomposition: Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s.
addRGroupsInPlaceOfImplHs(Molecule, int) - Static method in class chemaxon.search.RgroupDecomposition: Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s.
addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule: Creates an RgMolecule containing R-groups of this object from the 'simplified molecule' object made of 'm'.
addSalt(String, Molecule) - Method in class chemaxon.standardizer.actions.StripSaltsAction: Adds a salt to the salt list of the action
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.Molecule: Adds an S-group to this object.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule: Adds an S-group to this object.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule: Adds an S-group to this object.
addSgroupClones(Molecule, Molecule, Molecule) - Method in class chemaxon.struc.Molecule: Adds the S-groups of a child molecule clone to the new parent molecule clone.
addSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule: Adds S-groups to this object and its parent.
addSimpleAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Adds a non-SgroupAtom atom without setting its parentGraph and index fields.
addSolvent(String, Molecule) - Method in class chemaxon.standardizer.actions.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.MReactionSign
addString(String) - Method in class chemaxon.struc.graphics.MTextBox: Adds a string to the text.
addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters: Add a thread-local name to structure converter.
addTo(Container) - Method in class chemaxon.marvin.common.MAction: Add menu item to the specified menu.
addTo(Container, int) - Method in class chemaxon.marvin.common.MAction: Add menu item to the specified menu.
addTo(Container, int, Object) - Method in class chemaxon.marvin.common.MAction: Add menu item to the specified menu.
addToSelection(MDocument, MSelectionDocument) - Static method in class chemaxon.struc.NoStructure: Adds the selected NoStrutures from the document to the selectionDocument
addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings: Add an element to marvinsketch's recent file list
addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings: Add an element to marvinview's recent file list
addUserComparator(MolComparator) - Method in class chemaxon.search.api.options.SearchOptions: Adds the given user-defined comparator to the search.
addUserConstraint(int, int, int, int) - Method in class chemaxon.alignment.Alignment: Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
addWeight(int, int, double) - Method in class chemaxon.alignment.NodeColor: Adds a user-defined weight for the alignment of two types.
adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph: Checks whether the molecule has multiple chiral centers
AdvancedCheckerRunner - Class in chemaxon.structurechecker: CheckerRunner implementation with advanced fixing capabilities.
AdvancedCheckerRunner(StructureCheckerConfigurationReader) - Constructor for class chemaxon.structurechecker.AdvancedCheckerRunner: Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(StructureCheckerConfigurationReader, CheckerFixerFactory) - Constructor for class chemaxon.structurechecker.AdvancedCheckerRunner: Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.structurechecker.AdvancedCheckerRunner: Constructs CheckerRunner with more advanced fixing capabilities.
affectsPerformance() - Method in enum class chemaxon.calculations.api.CalculatorTag: Returns whether the presence of this tag affects the performance of the calculator.
Ag - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ag.
AGENT - Static variable in class chemaxon.chemterms.ReactionContext
AGENTS - Static variable in class chemaxon.struc.RxnMolecule: "Agent" structure type.
Al - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Al.
alias - Variable in class chemaxon.calculations.services.ServiceArgument: the alias of the argument
alias() - Element in annotation interface chemaxon.checkers.PersistentProperty: Returns the alias name of the annotated property
alias() - Element in annotation interface chemaxon.standardizer.PersistentProperty: Returns the alias name of the annotated property
ALIAS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that alias values have been found in the molecule
ALIAS - Static variable in class chemaxon.calculations.services.ServiceDescriptor: Property key for Service alias as String
ALIAS_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that alias values that could be converted to elements have been found in the molecule
ALIAS_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that alias values that could be converted to abbreviated groups have been found in the molecule
ALIAS_NONE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that alias values have been found in the molecule, but they cannot be converted to elements or abbreviated groups
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: Standardizer action that converts atom aliases to actual atoms.
AliasToAtomAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToAtomAction: Initializes the action
AliasToGroupAction - Class in chemaxon.standardizer.actions: Standardizer action that converts atom aliases to abbreviated groups.
AliasToGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToGroupAction: Initializes the action with parameters
align() - Method in class chemaxon.alignment.Alignment: 3D alignment on two or more molecules.
align() - Method in class chemaxon.alignment.AlignOnPairedAtoms
align() - Method in class chemaxon.alignment.AlignRigidEasy: does a simple one-to-one atom mappin and aligns.
align() - Method in class chemaxon.alignment.MolAligner: Executes the best alignment based on hit map provided earlier
align(int[]) - Method in class chemaxon.alignment.MolAligner: Calculates and performs the best alignment possible specified by the hit map array.
align(int[][]) - Method in class chemaxon.alignment.AlignRigidEasy: Rigid alignment on the user defined atom index
align(Molecule) - Method in interface chemaxon.alignment.MCSAlignment: Align the given molecule to the reference.
align(Molecule, Molecule, int[]) - Static method in class chemaxon.alignment.MolAligner: Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
align(Molecule, Molecule, int[][]) - Static method in class chemaxon.alignment.MolAligner: Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
ALIGN_AS_IS - Enum constant in enum class chemaxon.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.alignment: 3D Alignment aligns two or more 3D molecules onto each other.
Alignment() - Constructor for class chemaxon.alignment.Alignment
Alignment(AlignmentProperties) - Constructor for class chemaxon.alignment.Alignment
ALIGNMENT_OFF - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: The structure is displayed with the original coordinates.
ALIGNMENT_PARTIAL_CLEAN - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: The substructure part of the target will get the exact coordinates of the query, and new coordinates will be generated for the remainder of the structure.
ALIGNMENT_ROTATE - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: The structure is rotated according to the substructure.
AlignmentAccuracyMode - Enum Class in chemaxon.alignment: Settings for the representation of a molecular shape.
AlignmentBase - Class in chemaxon.alignment: Base class for the alignment algorithms.
AlignmentException - Exception Class in chemaxon.alignment: Exception thrown when an error occurs during molecular alignment operations.
AlignmentException() - Constructor for exception class chemaxon.alignment.AlignmentException
AlignmentException(String) - Constructor for exception class chemaxon.alignment.AlignmentException
AlignmentException(Throwable) - Constructor for exception class chemaxon.alignment.AlignmentException
AlignmentMolecule - Class in chemaxon.alignment: Represents a molecule in the context of 3D molecular alignment with its coordinates and transformation state.
AlignmentMoleculeFactory - Class in chemaxon.alignment: Creates an AlignmentMolecule form a Molecule based on the settings.
AlignmentMoleculeFactory() - Constructor for class chemaxon.alignment.AlignmentMoleculeFactory
AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.alignment: Interface for providing progress feedback during alignment operations.
AlignmentPlugin - Class in chemaxon.calculations: Calculator plugin for aligning molecule onto each other in 2D and 3D.
AlignmentPlugin() - Constructor for class chemaxon.calculations.AlignmentPlugin
AlignmentProperties - Enum Class in chemaxon.alignment: Predefined configurations for 3D molecular alignment.
AlignmentProperties.ColoringScheme - Enum Class in chemaxon.alignment
AlignmentProperties.ColorNotSpecifiedCase - Enum Class in chemaxon.alignment
AlignmentProperties.DegreeOfFreedomType - Enum Class in chemaxon.alignment: Enumeration of degree of freedom types defining how molecules can move and flex during alignment operations.
AlignmentProperties.FlexibilityMode - Enum Class in chemaxon.alignment: Conformational flexibility treatment during the alignment for a pair of a molecule.
AlignmentProperties.NodeType - Enum Class in chemaxon.alignment
AlignmentProperties.OrientationType - Enum Class in chemaxon.alignment
AlignmentProperties.ProximityPotentialType - Enum Class in chemaxon.alignment
AlignmentResult - Interface in chemaxon.alignment: Represents the result of a molecular alignment operation.
AlignOnPairedAtoms - Class in chemaxon.alignment: Overlays two molecules using the user defined atom pairs.
AlignOnPairedAtoms() - Constructor for class chemaxon.alignment.AlignOnPairedAtoms
AlignRigidEasy - Class in chemaxon.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.alignment.AlignRigidEasy
ALIPHATIC - Static variable in class chemaxon.struc.MolAtom: Aliphatic query atom.
ALIPHATIC_RINGCENTER - Static variable in class chemaxon.alignment.Pharmacophore3D
aliphaticAtomCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.
aliphaticBondCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.
aliphaticRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of aliphatic ring systems of the molecule.
aliphaticRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
aliphaticRings() - Method in class chemaxon.core.calculations.Ring: Identifies the aliphatic rings in the molecule.
aliphaticRings(int) - Method in class chemaxon.core.calculations.Ring: Identifies aliphatic rings in the molecule having a given size (number of atoms).
ALL - Enum constant in enum class chemaxon.search.api.options.HomologyTranslationOption: All atoms can have translation.
ALL - Enum constant in enum class chemaxon.search.api.options.TargetHomologyMatchingMode
ALL_H - Static variable in class chemaxon.struc.MolAtom: Include any Hydrogen atom.
ALL_MATCH_AMBIG - Enum constant in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption: Ambiguous aromatic parts of the target Markush structure can be matched by aliphatic and aromatic forms as well.
ALL_PERM - Enum constant in enum class chemaxon.alignment.AlignmentProperties.OrientationType
allringsystems - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
allStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: All stereo centers of molecule.
allStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: All stereo centers with attached data.
Am - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Am.
AMINOACID - Enum constant in enum class chemaxon.struc.SgroupType
AMINOACID_BOND_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "aminoAcidBondColoringEnabled".
AminoAcidSgroup - Class in chemaxon.struc.sgroup: Amino acid S-groups.
AminoAcidSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.AminoAcidSgroup: Constructs an AminoAcidSgroup in expanded state.
AminoAcidSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.AminoAcidSgroup: Constructs an aminoAcidSgroup.
AminoAcidSgroup(Molecule, String, String) - Constructor for class chemaxon.struc.sgroup.AminoAcidSgroup: Creates an expanded amino acid s-group with the given one and three letter names.
AminoAcidSgroup(AminoAcidSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.AminoAcidSgroup: Copy constructor.
AminoAcidSgroup(SuperatomSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.AminoAcidSgroup: Copy constructor.
ANCHOR - Static variable in class chemaxon.alignment.NodeColor
ANCHOR - Static variable in class chemaxon.alignment.Pharmacophore3D
AND - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.EnhancedStereoType: Stereogenic centers belonging to an ANDn group (e.g.
AND - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
angle2D(double, double) - Method in class chemaxon.struc.Point3D: Calculates the absolute angle in the XY plane of the vector pointing from this point to the other point.
angle3D(Point3D) - Method in class chemaxon.struc.Point3D: Calculate the angle of two vectors (this and p) in the range 0.0 through pi.
ANIMATE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "animate".
ANIMATION_DELAY - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "animDelay".
ANIMATION_FPS - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "animFPS".
ANIMATION_SYNCHRONIZATION - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "animSync".
ANTI - Static variable in interface chemaxon.struc.StereoConstants: Non-CIP stereodescriptor, anti (relative configuration).
ANY - Enum constant in enum class chemaxon.struc.BondType: Any bond type.
ANY - Enum constant in enum class chemaxon.struc.SgroupType
ANY - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the any atom A.
ANY - Static variable in class chemaxon.struc.MolBond: Any bond type.
ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
AnyBondStyle - Enum Class in chemaxon.rendering.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
API usage examples - Search tag in class chemaxon.reaction.mapper.AutoMapper: Section
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.formats.MolExportModule: Append a character n times to the string buffer.
appendLeft(String, int) - Method in class chemaxon.formats.MolExportModule: Append a string to the buffer in %-ns format.
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 chemaxon.calculations.gui.CalculatorPluginDisplay: Appends the pH text.
appendRight(int, int, char) - Method in class chemaxon.formats.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.formats.MolExportModule: Append a string to the buffer in the right hand side of an n-characters wide field.
apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculations.api.CalculatorInputChecker
apply(TaggedCalculator, Molecule) - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker
apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculations.api.TaggedCalculatorInputChecker: Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.
apply(Molecule) - Method in interface chemaxon.calculations.api.CalculatorInputChecker: Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.
applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane: Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.
applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane: Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.
Ar - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ar.
ARC_BRACES - Static variable in class chemaxon.struc.graphics.MBracket: The default arc angle of the Braces Rectangle in degrees.
ARC_ROUND - Static variable in class chemaxon.struc.graphics.MBracket: The default arc angle of the Rounded Rectangle in degrees.
areAttachmentPointsVisible() - Method in class chemaxon.marvin.beans.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.search.api.options.SearchOptions: Obtain monomer transformation information.
arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane: Are popup menus enabled?
ARGUMENTS - Static variable in class chemaxon.calculations.services.ServiceDescriptor: Property key for Arguments as an Unmodifiable List
ARO_R - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction: Number of aromatic rings.
AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph: Aromatization type for ambiguous 5-membered rings.
AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph: Basic aromatization.
AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph: Huckel aromatization.
AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph: General (Daylight conform) aromatization.
AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph: Loose aromatization.
AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph: Substructure aromatization.
AROMATIC - Enum constant in enum class chemaxon.struc.BondType: Aromatic bond type.
AROMATIC - Static variable in class chemaxon.struc.MolAtom: Aromatic query atom.
AROMATIC - Static variable in class chemaxon.struc.MolBond: Aromatic bond type.
AROMATIC_ATOM - Static variable in class chemaxon.alignment.Pharmacophore3D
AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom: Aromatic or aliphatic query atom.
AROMATIC_RINGCENTER - Static variable in class chemaxon.alignment.Pharmacophore3D
aromaticAtomCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of all aromatic atoms in the molecule.
aromaticBondCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of all aromatic bonds in the molecule.
AROMATICITY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that aromaticity problems have been 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.core.calculations.Ring: Calculates the number of all aromatic ring systems in the molecule (SSSR).
aromaticRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
aromaticRings() - Method in class chemaxon.core.calculations.Ring: Identifies the aromatic rings in the molecule.
aromaticRings(int) - Method in class chemaxon.core.calculations.Ring: Indentifies aromatic rings in the molecule having a given size (number of rings).
aromatize - Variable in class chemaxon.formats.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.common.MDocStorage: Aromatize or dearomatize molecule in the specified cell.
AromatizeAction - Class in chemaxon.standardizer.actions: Standardizer action that aromatizes the molecule.
AromatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AromatizeAction: Initializes the action with parameters
AromatizeAction.Type - Enum Class in chemaxon.standardizer.actions: Type of aromatization
aromatizeAll(boolean, int, String[]) - Method in class chemaxon.marvin.common.MDocStorage: Aromatize or dearomatize molecules in all cells.
arrangeComponents(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Arranges molecule components (reactants, agents, products, R-group definitions) nicely.
arrangeComponents(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
arrangeComponents(MoleculeGraph, boolean, boolean) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
arrangeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Arrange data attached to DataSgroup.
arrangeHydrogenIncerments(Molecule, int, String, double) - Method in class chemaxon.calculations.CalculatorPlugin
arrangeMolecules(MoleculeGraph[], int, int) - Static method in class chemaxon.core.calculations.clean.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.core.calculations.clean.CleanUtil: Arranges reaction components nicely
arrangeRelativeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Arrange data attached to DataSgroup.
arrangeSgBrackets(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Arrange sgroup brackets in the molecule.
ARROW - Enum constant in enum class chemaxon.rendering.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.struc.PeriodicTable: Atomic number of the element As.
ASK - Enum constant in enum class chemaxon.checkers.FixMode: on problem requests user interaction
asProperties(String) - Method in class chemaxon.marvin.common.UserSettings
asSet() - Method in enum class chemaxon.calculations.api.CalculatorTag: Returns a cached set that contains this element only.
asymmetricAtomCount() - Method in class chemaxon.core.calculations.stereo.Stereochemistry: Calculates the number of atoms having four different ligands.
asymmetricAtoms() - Method in class chemaxon.core.calculations.stereo.Stereochemistry: Retrieves the indexes of atom having four different ligands.
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.calculations.services: Callback interface for asynchronous service calls
At - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element At.
ATMAP_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Show atom mapping flag.
ATNUM_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Show atom numbers flag.
atom - Variable in class chemaxon.struc.IteratorFactory.NeighbourIterator: Deprecated.

The atom whose the neighbours are processed.
ATOM - Static variable in class chemaxon.calculations.CalculatorPlugin: Calculation domain type: calculation refers to atoms.
ATOM - Static variable in class chemaxon.chemterms.AtomContext
ATOM_ATOM_MAP - Static variable in class chemaxon.checkers.result.ConversionConstants: The key of the map from cloned atoms to original atoms.
ATOM_COUNT - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "atomcount".
ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "atomFont".
ATOM_FONT_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "atomFontSize".
ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atom maps have been found in the molecule
ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "atomMappingVisible".
ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "atomNumberingType".
ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Deprecated.
in 6.2.0 use atomNumberingType parameter instead.
ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "atomPropertiesVisible".
ATOM_QUERY_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atoms having query properties have been found in the molecule
ATOM_SET - Static variable in class chemaxon.marvin.common.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.common.SketchParameterConstants: Identifier of parameter: "atomStrings".
ATOM_SYMBOL_VISIBLE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
ATOM_SYMBOLS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "atomSymbolsVisible".
ATOM_TYPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atoms with the specified symbol have been found in the molecule
ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom: Number of atom types in the elements array
ATOM_TYPE_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum atom number.
ATOM_TYPES - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColoringScheme
ATOM_VALUE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atom values have been found in the molecule
atomChanged(MolAtom) - Method in interface chemaxon.core.calculations.clean.Cleaner.AtomChangeEventListener
AtomChecker - Class in chemaxon.checkers: Descendants of the abstract ComponentChecker 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.chemterms: Expression evaluation context containing an input molecule and an input atom.
AtomContext() - Constructor for class chemaxon.chemterms.AtomContext: Constructor.
atomCount - Variable in class chemaxon.struc.MoleculeGraph: The number of atoms.
atomCount() - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the number of atoms in the molecule.
atomCount() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the number of atoms in the molecule.
atomCount() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the number of atoms in the molecule including implicit hydrogens.
atomCount(int) - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int) - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int, int) - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the number of atoms of a given element in the molecule.
atomCount(int, int) - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the number of atoms of a given element in the molecule.
ATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement: Atom count of the molecule
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.struc.IteratorFactory.AtomIterator: Deprecated.

Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
AtomLabels - Class in chemaxon.checkers: Stores a list of atom labels to be used for certain structure checkers.
AtomLabels() - Constructor for class chemaxon.checkers.AtomLabels: Initializes the atom labels
AtomMapChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting atoms with atom map numbers.
AtomMapChecker() - Constructor for class chemaxon.checkers.AtomMapChecker: Default constructor
atomMapMatching(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether atom map numbers should be considered in search.
atomMapping() - Method in interface chemaxon.alignment.MCSAlignmentResult: Array of atom - atom mapping.
AtomNeighbourIterator(MolAtom) - Constructor for class chemaxon.struc.IteratorFactory.AtomNeighbourIterator: Deprecated.

Constructs an iterator to process the atoms connecting to the specified atom according to the atom and bond related behavior of this factory.
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 an unmodifiable list view of the atoms in the molecule.
AtomSelection - Class in chemaxon.calculations.stereo.stereocenters: Selection which contains atom indexes.
AtomSelection(List<Integer>, List<Integer>) - Constructor for class chemaxon.calculations.stereo.stereocenters.AtomSelection: Constructs an AtomSelection from lists.
atomSet - Variable in class chemaxon.struc.Sgroup: Set for storing the atoms of the S-group's graph.
ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants: Either stereo atom type.
ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants: Stereo atom type mask.
ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants: No stereo atom type specified.
ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants: Specific stereo atom type.
AtomTypeChecker - Class in chemaxon.checkers: A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.
AtomTypeChecker() - Constructor for class chemaxon.checkers.AtomTypeChecker: Default constructor.
AtomTypeChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomTypeChecker: Parameterized constructor providing the possibility for descendants to initialize with their own error type.
AtomTypeChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomTypeChecker: Parameterized constructor.
atomTypeMatching(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether atom types should be considered in search.
AtomValueChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting atoms with atom values (labels).
AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker: Default constructor.
ATPROP_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Show atom properties flag.
ATROP - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.StereoType: Atrop stereo center.
ATROP - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoType
ATROPISOMER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atropisomers have been found in the molecule
AtropisomerChecker - Class in chemaxon.checkers: Deprecated.
This checker is no longer supported.
AtropisomerChecker() - Constructor for class chemaxon.checkers.AtropisomerChecker: Deprecated.

Initializes the atropisomer structure checker
AtropIsomerDetector - Class in chemaxon.alignment: Molecular mechanics based atropisomer detection.
AtropIsomerDetector() - Constructor for class chemaxon.alignment.AtropIsomerDetector
AtropIsomerDetector.Accuracy - Enum Class in chemaxon.alignment: Sampling accuracy levels used in atrop bond detection, controlling the number of dihedral rotation steps.
AtropStereoCenter - Class in chemaxon.calculations.stereo.stereocenters: Atrop stereo center implementation.
AtropStereoCenter(AtomSelection, CIPStereoValue.AtropStereoIUPACValue) - Constructor for class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter: Constructs a new instance of axial stereo center.
AtropStereoCenter(AtomSelection, CIPStereoValue.AtropStereoIUPACValue, List<AttachedData>) - Constructor for class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter: Constructs a new instance of axial stereo center with attached data.
atropStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the atrop stereocenters.
atropStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the atrop stereocenters with attached data.
AtropStereoDescriptor - Class in chemaxon.core.calculations.stereo: Descriptor representing atrop stereo information.
AtropStereoDescriptor(CIPStereoValue.AtropStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AtropStereoDescriptor
AtropStereoIUPACDescriptor - Class in chemaxon.core.calculations.stereo: Descriptor representing atrop stereo information.
AtropStereoIUPACDescriptor(CIPStereoValue.AtropStereoIUPACValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AtropStereoIUPACDescriptor
ATSYM_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Show atom symbols in 3D flag.
ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom: S-group attachment point on first and second site.
ATTACH_NONE - Static variable in class chemaxon.struc.MolAtom: There is no S-group attachment point setting on this atom.
ATTACH_UNKNOWN - Static variable in class chemaxon.struc.MolAtom: S-group attachment point information
ATTACH1 - Static variable in class chemaxon.struc.MolAtom: S-group attachment point on first site.
ATTACH2 - Static variable in class chemaxon.struc.MolAtom: S-group attachment point on second site.
ATTACHED_DATA - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that attached data have been found in the molecule
ATTACHED_DATA_MATCH_EXACT - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for exact match of attached data.
ATTACHED_DATA_MATCH_GENERAL - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for general match of attached data.
ATTACHED_DATA_MATCH_IGNORE - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for ignoring attached data.
AttachedData - Class in chemaxon.calculations.stereo.stereocenters: Data object which contains a name and a data (String).
AttachedData(String, String) - Constructor for class chemaxon.calculations.stereo.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.
AttachedDataChecker.DataExclusionList - Class in chemaxon.checkers: A list of Strings to be excluded by AttachedDataChecker.
ATTACHMENT_ATOM - Static variable in interface chemaxon.search.api.SearchConstants: Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.
ATTACHMENT_LABEL - Static variable in interface chemaxon.search.api.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.search.api.SearchConstants: Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int).
ATTACHMENT_NONE - Static variable in interface chemaxon.search.api.SearchConstants: Constant for attachment point representation in ligands: none (no attachment point data).
ATTACHMENT_POINT - Static variable in interface chemaxon.search.api.SearchConstants: Constant for attachment point representation in ligands: R-group attachment.
ATTACHMENT_RLABEL - Static variable in interface chemaxon.search.api.SearchConstants: Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String).
AttachmentPoint - Class in chemaxon.struc.sgroup: Attachment Point class for the Superatom S-group.
AttachmentPoint(MolAtom, int, MolBond) - Constructor for class chemaxon.struc.sgroup.AttachmentPoint: Constructs an AttachmentPoint object
Au - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Au.
AUTO - Enum constant in enum class chemaxon.rendering.constants.AnyBondStyle: Automatically decide whether Dashed or Solid rendering is used.
AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Automatic check for structures.
AUTO_SCALE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "autoscale".
AUTO_TAB_SCALE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "autoTabScale".
AutoMapper - Class in chemaxon.reaction.mapper: AutoMapper is a tool that performs automated chemical reaction mapping.
AutoMapper() - Constructor for class chemaxon.reaction.mapper.AutoMapper: Initializes an AutoMapper object
AutoMapper.Options - Class in chemaxon.reaction.mapper: Configuration options for automated reaction mapping when using static mapping methods.
AutoMapper.ResultIterator - Interface in chemaxon.reaction.mapper: Auto-closeable result iterator for AutoMapper.
AUTOMATIC_FOG_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "automaticFogEnabled".
AUTOMATIC_REACTION_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "automaticReactionEnabled".
AUTORM - Static variable in class chemaxon.marvin.common.MAction: Remove menu items automatically when the menu becomes invisible.
AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat: Image object (java.awt.Image).
AXIAL - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.StereoType: Axial stereo center (eg.
AXIAL - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoType
AxialStereoCenter - Class in chemaxon.calculations.stereo.stereocenters: Axial stereo center implementation.
AxialStereoCenter(AtomSelection, CIPStereoValue.AxialStereoIUPACValue) - Constructor for class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter: Constructs a new instance of axial stereo center.
AxialStereoCenter(AtomSelection, CIPStereoValue.AxialStereoIUPACValue, List<AttachedData>) - Constructor for class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter: Constructs a new instance of axial stereo center with attached data.
axialStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the axial stereocenters.
axialStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the axial stereocenters with attached data.
AxialStereoDescriptor - Class in chemaxon.core.calculations.stereo: Axial type stereo descriptor.
AxialStereoDescriptor(CIPStereoValue.AxialStereoValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AxialStereoDescriptor
AxialStereoIUPACDescriptor - Class in chemaxon.core.calculations.stereo: Axial type stereo descriptor.
AxialStereoIUPACDescriptor(CIPStereoValue.AxialStereoIUPACValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.AxialStereoIUPACDescriptor

B

B - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element B.
Ba - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ba.
BACKGROUND - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "background".
BACKGROUNDLOAD_ENABLED - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "bgloadEnabled".
BACKGROUNDLOAD_PRIORITY - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "bgload".
backgroundThread - Variable in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Background thread.
balabanIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "ballRadius".
BALLSTICK - Enum constant in enum class chemaxon.rendering.constants.RenderingStyle: Stick rendering style with balls at atoms
BASE64 - Static variable in class chemaxon.formats.MFileFormat: BASE64 encoded file.
BASIC - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type: Basic aromatization
BASIC - Static variable in class chemaxon.calculations.PkaPlugin: Constant denoting basic pKa.
BasicCheckerRunner - Class in chemaxon.structurechecker: Deprecated.
Don't use this class directly, use AdvancedCheckerRunner instead.
BasicCheckerRunner(StructureCheckerConfigurationReader) - Constructor for class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Initiate a BasicCheckerRunner instance which can execute StructureChecker instances read from configurationReader
BasicCheckerRunner(StructureCheckerConfigurationReader, CheckerFixerFactory) - Constructor for class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Initiate a BasicCheckerRunner instance which can execute StructureChecker instances read from configurationReader
BasicCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Initiate a BasicCheckerRunner instance with specified StructureChecker list.
BasicCheckerRunner(List<StructureChecker>, boolean) - Constructor for class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Initiate a BasicCheckerRunner instance with specified StructureChecker list.
BBB - Class in chemaxon.calculations.bbb: BBB score calculator.
BBB.Property - Class in chemaxon.calculations.bbb: Simple result class that contains the predicted value, its BBB score, and the BBB score multiplied by the corresponding BBB multiplier.
BBBFunction - Enum Class in chemaxon.calculations.bbb: Base phys-chem property calculators and its score functions for BBB score calculation.
BCUT - Class in chemaxon.descriptors: Implements BCUT descriptors.
BCUT() - Constructor for class chemaxon.descriptors.BCUT: Creates a new, empty BCUT descriptor.
BCUT(BCUT) - Constructor for class chemaxon.descriptors.BCUT: Copy constructor.
BCUT(BCUTParameters) - Constructor for class chemaxon.descriptors.BCUT: Creates a new instance according to the parameters.
BCUT(String) - Constructor for class chemaxon.descriptors.BCUT: Creates a new instance according to the parameters.
BCUTGenerator - Class in chemaxon.descriptors: Descriptor generator class for the BCUT descriptor.
BCUTGenerator() - Constructor for class chemaxon.descriptors.BCUTGenerator: Creates and initializes a BCUT descriptor generator object.
BCUTParameters - Class in chemaxon.descriptors: Manages parameters for the BCUT descriptor class.
BCUTParameters() - Constructor for class chemaxon.descriptors.BCUTParameters: Creates an empty object.
BCUTParameters(File) - Constructor for class chemaxon.descriptors.BCUTParameters: Creates a new object based on a given configuration file.
BCUTParameters(String) - Constructor for class chemaxon.descriptors.BCUTParameters: Creates a new object based on a given configuration string.
Be - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Be.
beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane: Changes the cursor to hourglass at the beginning of a long operation.
bemismurcko - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
bemismurckoloose - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
Beta - Annotation Interface in chemaxon.common.annotations: Indicates that a public API entity (public class, method, or field) is subject to incompatible changes, or even removal, in a future release.
Bh - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Bh.
Bi - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Bi.
BicycloStereoDescriptor - Class in chemaxon.struc: This class is the atom index based representation which can be assigned to 'endo', 'exo', 'syn', 'anti' ligands of bicyclo[x.y.z]alkanes in case of 0 dimension molecules.
BicycloStereoDescriptor(MolAtom, int, MolAtom[], MolAtom[]) - Constructor for class chemaxon.struc.BicycloStereoDescriptor: Creates a new stereo descriptor for bicyclo stereo.
BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters: descriptor type constants
binaryAsymmetricEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the asymmetric Euclidean distance of binary descriptors.
binaryAsymmetricNormalizedEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the asymmetric normalized Euclidean distance of binary descriptors.
binaryAsymmetricNormalizedEuclidean(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics: Calculates the asymmetric normalized Euclidean distance of binary descriptors.
binaryAsymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates asymmetric Tanimoto dissimilarity for binary descriptors.
binaryAsymmetricTanimoto(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics: Calculates asymmetricTanimoto dissimilarity for binary descriptors.
binaryEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the Euclidean distance of two binary descriptors.
binaryNormalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the normalized Euclidean distance of two binary descriptors.
binaryNormalizedEuclidean(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics: Calculates the normalized Euclidean distance of two binary descriptors.
binaryTanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates Tanimoto dissimilarity for binary descriptors.
binaryTanimoto(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics: Calculates Tanimoto dissimilarity for binary descriptors.
binaryTversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates Tversky dissimilarity for binary descriptors.
binaryWeightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric Euclidean distance of binary descriptors.
binaryWeightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.
binaryWeightedAsymmetricNormalizedEuclidean(int[], int, int[], int, float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.
binaryWeightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted Euclidean distance of binary descriptors.
binaryWeightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted normalized Euclidean distance of binary descriptors.
binaryWeightedNormalizedEuclidean(int[], int, int[], int, int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted normalized Euclidean distance of binary descriptors.
Bk - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Bk.
BLUE - Static variable in class chemaxon.calculations.CalculatorPlugin: Constant storing the blue rgb value (the basic pKa result color).
BOLD - Static variable in class chemaxon.struc.graphics.MFont: Bold font style.
BOLD - Static variable in class chemaxon.struc.MolBond: "Bold" attribute of the bond.
BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "boldBondWidth".
BOND_ANGLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that bond angle problems have been found in the molecule
BOND_BOND_MAP - Static variable in class chemaxon.checkers.result.ConversionConstants: The key of the map from cloned bonds to original bonds.
BOND_DRAGGED_ALONG - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "bondDraggedAlong".
BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "bondHashSpacing".
BOND_LENGTH - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that bond length problems have been found in the molecule
BOND_LENGTH - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "bondLength".
BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "bondLengthVisible".
BOND_SET - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "bondSet".
BOND_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "bondSetColor".
BOND_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "bondSpacing".
BOND_TOPOLOGY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains bond(s) with topology
BondAngleChecker - Class in chemaxon.checkers: Bond Angle Checker detects non-preferred 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, Molecule, List<MolBond>, 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.core.calculations.TopologyAnalyzer: Calculates the number of bonds in the molecule including bonds of implicit hydrogens.
BondInfo(int, int, int) - Constructor for class chemaxon.alignment.DihedralScanResult.BondInfo: Construct.
BondIterator() - Constructor for class chemaxon.struc.IteratorFactory.BondIterator: Deprecated.

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.rendering.constants.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, Molecule, List<MolBond>, 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
BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.struc.IteratorFactory.BondNeighbourIterator: Deprecated.

Constructs an iterator to process the bonds connecting to the specified atom.
bonds() - Method in class chemaxon.struc.MolAtom: Provides an unmodifiable list view of the connected bonds of the atom.
bonds() - Method in class chemaxon.struc.MoleculeGraph: Provides an unmodifiable list view of the bonds in the molecule.
BondTable - Class in chemaxon.struc: Provides easy lookup of bonds between pairs of atoms in a molecule graph.
BondTopologyChecker - Class in chemaxon.checkers: Checker detects bonds with reacting center bond marks.
BondTopologyChecker() - Constructor for class chemaxon.checkers.BondTopologyChecker: Default constructor
bondType(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer: Determines the type of a bond (aromatic bonds are automatically recognized)
BondType - Enum Class in chemaxon.struc: General chemical bond types.
bondTypeMatching(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether bond types should be considered in search.
bondweights(double[], Transform3D) - Method in class chemaxon.struc.MolAtom: Calculates the average of the bond unit vectors pointing out of this atom.
BOOL - Static variable in class chemaxon.formats.OptionDescriptor: Boolean option.
booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp: Gets the boolean value.
BORDER - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "border".
BOTH - Static variable in class chemaxon.calculations.StereoisomerPlugin: Deprecated.
Br - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Br.
brackets - Variable in class chemaxon.struc.Sgroup
BRACKETS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Representing that the molecule contains brackets
BracketsChecker - Class in chemaxon.checkers: Detects brackets (generic 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.formats.PositionedInputStream: Reads a character and writes into the buffer.
build() - Method in interface chemaxon.calculations.api.CalculatorBuilder: Returns the calculator object.
build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
build() - Method in class chemaxon.chemterms.ConstantTableBuilder: Creates a new constant table based on this builder.
build() - Method in class chemaxon.formats.converter.MolConverter.Builder: Builds the MolConverter.
build() - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
build() - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Creates a search options object with the settings specified by this builder instance.
build() - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder: Builds a StandardizerActionFactory based on the previously added InputStream instances
build() - Method in class chemaxon.struc.ValenceCheckOptions.Builder: Builds a ValenceCheckOptions object.
build() - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Builds a CheckerFixerFactory based no the previously added InputStream and Properties instances
builder() - Static method in class chemaxon.chemterms.ConstantTable: Creates a new builder for a constant table.
builder() - Static method in class chemaxon.struc.ValenceCheckOptions: Creates a new builder.
Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder
Builder() - Constructor for class chemaxon.calculations.HLBPlugin.Builder: Deprecated.
Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder
Builder() - Constructor for class chemaxon.formats.converter.MolConverter.Builder: Constructs an empty Builder object.
Builder() - Constructor for class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
Builder() - Constructor for class chemaxon.search.mcs.McsSearchOptions.Builder: Creates a Builder object with the default settings.
Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder
Builder() - Constructor for class chemaxon.struc.ValenceCheckOptions.Builder
Builder() - Constructor for class chemaxon.structurechecker.CheckerFixerFactory.Builder
Builder(McsSearchOptions) - Constructor for class chemaxon.search.mcs.McsSearchOptions.Builder: Creates a Builder object containing the settings of the given search options object.
BuildupMcs - Class in chemaxon.search.mcs: Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
BuildupMcs(McsSearchOptions) - Constructor for class chemaxon.search.mcs.BuildupMcs: Creates a new BuildupMcs object with the given search options.
BUTTON_MENUBAR - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "buttonmenubar".
BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure: For internal usage only.

C

C - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element C.

C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter

Close the underlying stream.

C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter

Flush the output stream and force any buffered output bytes to be written out.

C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator

Name of the 13C chemical shift atom property.

C13 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus

13C NMR

Ca - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Ca.

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.core.calculations.clean.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(Point3D[], Point3D, double) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Deprecated.

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

Calculates the geometrical center.

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

Calculates the geometrical center.

calcCenter(Point3D) - Method in class chemaxon.struc.MoleculeGraph

Calculates the geometrical center.

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct

Calculates the geometrical center.

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MElectronContainer

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Calculates the geometrical center.

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MPolyline

Calculates the geometrical center.

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MRectangle

Calculates the geometrical center.

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.MObject

Calculates the geometrical center.

calcCenter(Point3D, Transform3D) - Method in class chemaxon.struc.MPoint

Calculates the geometrical center.

calcCenter(Transform3D) - Method in class chemaxon.struc.MDocument

Calculates the geometrical center.

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

Calculates the graph invariants with the assumption that hydrogens are removed.

calcDividingPoint(Point3D, Point3D, double) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Deprecated.

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 the hybridization state for each atom.

calclogD(double) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.calcLogD(double) instead. This method will be removed in a future version.

calcLogD(double) - Method in class chemaxon.calculations.LogDPlugin

Returns the logD value at fixed pH.

calcMaxDist() - Method in class chemaxon.alignment.MinMaxDistance

calcMinDist() - Method in class chemaxon.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(Point3D) - 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(Point3D) - Method in class chemaxon.struc.MoleculeGraph

Calculates the center of the outer rectangle.

CALCRGB_OFF - Static variable in class chemaxon.calculations.CalculatorPlugin

Calculator rgb offset.

calcSimplePolymerBracket(Point3D, Point3D, double) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Deprecated.

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.alignment.MMPAlignment

Runs the MCS alignment calculation on the two structures of the constructor.

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

Calculate best alignment based on the hit map

calculate(Molecule) - Method in class chemaxon.alignment.AtropIsomerDetector

Run the atropisomer calculation.

calculate(Molecule) - Static method in class chemaxon.calculations.bbb.BBB

Calculates the BBB properties and scores of the given Molecule.

calculate(Molecule) - Method in enum class chemaxon.calculations.bbb.BBBFunction

Calculates the BBB property, its score and its multiplied score.

calculate(Molecule) - Static method in class chemaxon.calculations.cnsmpo.CnsMpo

Calculates the CNS MPO properties and scores of the given molecule.

calculate(Molecule) - Method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction

Calculates the CNS MPO property and its score.

calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator

calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator

Calculates NMR spectrum for the given input molecule.

calculate(MoleculeGraph, EnumSet<CIPStereoType>, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoCalculator

Calculates the stereo descriptors of the given molecule with timeout information.

calculate(T) - Method in interface chemaxon.calculations.api.Calculator

Calculates with the given data

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

Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.

calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoCalculator

Calculates the stereo descriptors of the given molecule.

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.core.calculations.stereo.CIPStereoCalculator

Calculates the stereo descriptors of the given molecule.

calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer

Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.

calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoType>, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoCalculator

Calculates the stereo descriptors of the given molecule.

calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.AminoAcidSgroup

calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Calculates the coordinates during expand and contract.

calculateIntrinsicSolubility(Molecule) - Method in class chemaxon.calculations.solubility.SolubilityCalculator

Calculates intrinsic solubility.

calculatePhDependentSolubility(Molecule, double) - Method in class chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubility.

calculatePhDependentSolubility(Molecule, double[]) - Method in class chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubilities.

calculatePhDependentSolubility(Molecule, double, double, double) - Method in class chemaxon.calculations.solubility.SolubilityCalculator

Calculates pH-dependent solubilities.

calculateSimilarityUpperBound() - Method in class 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 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.

Calculator<T,R> - Interface in chemaxon.calculations.api

Generic calculator interface

CalculatorBuilder<T> - Interface in chemaxon.calculations.api

Builder interface for Calculator.

CalculatorError - Interface in chemaxon.calculations.api

An error that might occur when a calculator is initialized.

CalculatorInputChecker - Interface in chemaxon.calculations.api

Simple interface of classes that are used by calculators to check if they can process an input molecule.

CalculatorLogger - Class in chemaxon.calculations.api

Logger for calculators.

CalculatorLogger() - Constructor for class chemaxon.calculations.api.CalculatorLogger

CalculatorLogger(OutputStream, String) - Constructor for class chemaxon.calculations.api.CalculatorLogger

CalculatorLogger(String) - Constructor for class chemaxon.calculations.api.CalculatorLogger

CalculatorLogger(String, String) - Constructor for class chemaxon.calculations.api.CalculatorLogger

CalculatorLogger.Level - Enum Class in chemaxon.calculations.api

Logging levels controlling the verbosity of calculator log output.

CalculatorPlugin - Class in chemaxon.calculations

Common base class for calculator plugins.

CalculatorPlugin() - Constructor for class chemaxon.calculations.CalculatorPlugin

Constructor.

CalculatorPlugin(Consumer<Molecule>, Consumer<Molecule>) - Constructor for class chemaxon.calculations.CalculatorPlugin

Constructor.

CalculatorPlugin.HydrogenData - Class in chemaxon.calculations

Data structure holding information about hydrogen atoms in molecules.

CalculatorPluginDisplay<P> - Class in chemaxon.calculations.gui

Common base class for calculator plugin displays.

CalculatorPluginDisplay() - Constructor for class chemaxon.calculations.gui.CalculatorPluginDisplay

CalculatorPluginException - Exception Class in chemaxon.calculations

Exception thrown in case of plugin processing or calculation errors.

CalculatorPluginException() - Constructor for exception class chemaxon.calculations.CalculatorPluginException

Default constructor.

CalculatorPluginException(String) - Constructor for exception class chemaxon.calculations.CalculatorPluginException

Constructor with message.

CalculatorPluginException(String, Throwable) - Constructor for exception class chemaxon.calculations.CalculatorPluginException

Constructor with wrapped exception.

CalculatorPluginException(Throwable) - Constructor for exception class chemaxon.calculations.CalculatorPluginException

Constructor with wrapped exception.

CalculatorPluginInputException - Exception Class in chemaxon.calculations

Exception that is thrown when an input molecule of CalculatorPlugin is rejected.

CalculatorPluginInputException(CalculatorError) - Constructor for exception class chemaxon.calculations.CalculatorPluginInputException

CalculatorPluginMDocSource - Class in chemaxon.calculations

Multimolecular result source object based on result MDocument Iterator.

CalculatorPluginMDocSource(Iterator, int) - Constructor for class chemaxon.calculations.CalculatorPluginMDocSource

Constructor.

CalculatorPluginOutput<P> - Class in chemaxon.calculations.output

Class providing plugin output in table form.

CalculatorPluginOutput() - Constructor for class chemaxon.calculations.output.CalculatorPluginOutput

Default constructor.

CalculatorPluginOutput(CalculatorPlugin) - Constructor for class chemaxon.calculations.output.CalculatorPluginOutput

Constructor that sets plugin.

CalculatorPluginOutputAccess - Interface in chemaxon.calculations.output

Interface providing plugin output access.

CalculatorPluginService<P> - Class in chemaxon.calculations

Base class for types that implement a functionality related to a specific CalculatorPlugin.

CalculatorPluginService() - Constructor for class chemaxon.calculations.CalculatorPluginService

CalculatorTag - Enum Class in chemaxon.calculations.api

List of optional tags that can be reported by a TaggedCalculator.

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

Calculates the molecule width.

calcWidth(Graphics2D) - Method in class chemaxon.struc.graphics.MNameTextBox

Calculates the width of the string in the name text box.

callContextFunction(String, List<Object>) - Method in class chemaxon.chemterms.AtomContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in interface chemaxon.chemterms.ChemTermsContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in class chemaxon.chemterms.MolContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in class chemaxon.chemterms.ReactionContext

Executes the specified context function with the given parameters.

callContextFunction(String, List<Object>) - Method in class chemaxon.chemterms.SearchContext

Executes the specified context function with the given parameters.

callService(HttpServiceDescriptor, Object...) - Method in class chemaxon.calculations.services.HttpServiceHandler

callService(JsonServiceDescriptor, Object...) - Method in class chemaxon.calculations.services.JsonServiceHandler

callService(LocalServiceDescriptor, Object...) - Method in class chemaxon.calculations.services.LocalServiceHandler

callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.calculations.services.ServiceHandler

Performs thread-safe asynchronous service call.

callService(DT, Object...) - Method in class chemaxon.calculations.services.ServiceHandler

Performs a service call.

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.

cancel() - Method in class chemaxon.alignment.MMPAlignment

Cancel the ongoing calculation

cancel() - Method in class chemaxon.calculations.api.ProgressableCalculator

cancel() - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

cancel() - Method in interface chemaxon.structurechecker.CheckerRunner

Stops the background thread

cancelCalculation() - Method in class chemaxon.calculations.api.ProgressableCalculator

cancelled - Variable in class chemaxon.calculations.api.ProgressableCalculator

CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm

canonicalName(String) - Static method in class chemaxon.formats.Encoding

Standardize a Java encoding.

canRepeat() - Method in class chemaxon.calculations.CalculatorPlugin

Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.

canRepeat() - Method in class chemaxon.calculations.ChemicalNamePlugin

canRepeat() - Method in class chemaxon.calculations.StructuralFrameworksPlugin

carboaliphaticRingCount() - Method in class chemaxon.core.calculations.Ring

Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).

carboaromaticRingCount() - Method in class chemaxon.core.calculations.Ring

Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).

CARBON_VIS_INCHAIN - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Carbon-visibility is switched on in chain.

CARBON_VIS_INCHAIN_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

String constant for switching on carbon-visibility in chain.

CARBON_VIS_MASK - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Carbon-visibility mask.

CARBON_VIS_OFF - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Carbon-visibility is switched off.

CARBON_VIS_OFF_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

String constant for switching off carbon-visibility.

CARBON_VIS_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Carbon-visibility offset.

CARBON_VIS_ON - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Carbon-visibility is switched on.

CARBON_VIS_ON_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

String constant for switching on carbon-visibility.

CARBON_VIS_STYLES - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Array of carbon-visibility styles.

carboRingCount() - Method in class chemaxon.core.calculations.Ring

Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).

carboRingCount(int) - Method in class chemaxon.core.calculations.Ring

Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).

carboRings() - Method in class chemaxon.core.calculations.Ring

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).

carboRings(int) - Method in class chemaxon.core.calculations.Ring

Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.

CBasic - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType

CCLENGTH - Static variable in class chemaxon.struc.MolBond

Default bond length.

Cd - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cd.

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.struc.PeriodicTable

Atomic number of the element Ce.

CELL - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "cell".

CELL_SIZE - Static variable in class chemaxon.calculations.gui.CalculatorPluginDisplay

The default viewer cell size.

cellSize - Variable in class chemaxon.descriptors.MDParameters

size - number of bits - of one descriptor cell

CellType - Enum Class in chemaxon.marvin.common

Cell types in molecule tables.

cellwiseWeights - Variable in class chemaxon.descriptors.MDParameters

is cell weights for parametrized metrics

centralAtomIndex - Variable in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor

centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane

Puts the molecule into the center of the display.

Cf - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cf.

CFGenerator - Class in chemaxon.descriptors

The CFGenerator class generates topological fingerprints of molecular graphs.

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

Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.

CFNS - Static variable in class chemaxon.chemterms.AtomContext

The context function names.

CFNS - Static variable in class chemaxon.chemterms.ReactionContext

The context function names.

CFParameters - Class in chemaxon.descriptors

Manages fingerprint parameters.

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

Creates an empty object.

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

Creates a new object based on a given configuration file.

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

Creates a new object based on a given configuration string.

CHAc - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType

chainAtomCount() - Method in class chemaxon.core.calculations.Ring

Calculates the number of chain atoms in the molecule excluding hydrogens.

chainBondCount() - Method in class chemaxon.core.calculations.Ring

Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.

changes - Variable in class chemaxon.standardizer.AbstractSgroupAction

Changes - Class in chemaxon.standardizer

The change set of the standardization procedure.

Changes(Molecule) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

Changes(Molecule, StandardizerAction) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

Changes(Molecule, Molecule) - Constructor for class chemaxon.standardizer.Changes

Initializes the changes object.

CHANGING - Enum constant in enum class chemaxon.reaction.mapper.ReactionMapper.MappingStyle

Map only the atoms of the reaction center.

CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).

characters(char[], int, int) - Method in class chemaxon.naming.document.XmlToHtmlConverter

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

Gets a character of the document.

charge() - Method in record class chemaxon.calculations.elemental.FormulaAtom

Returns the value of the charge record component.

CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.search.api.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.search.api.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.search.api.SearchConstants

Option value constant for ignore charge searching (charge information is ignored during searching).

CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup

Charge is located on atoms and displayed on atoms.

CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup

Charge is located on atoms but displayed on the whole group (bracket).

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

Identifier of parameter: "chargeWithCircle".

CHARGE_WITH_CIRCLE_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts

CHARGE_WITH_CIRCLE_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts

CHARGED_H - Static variable in class chemaxon.struc.MolAtom

Include charged Hydrogen atom(s).

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

Sets whether formal charges of atoms should be considered in search.

ChargePlugin - Class in chemaxon.calculations

Plugin class for partial charge calculation.

ChargePlugin() - Constructor for class chemaxon.calculations.ChargePlugin

Constructor.

check() - Method in class chemaxon.structurechecker.AdvancedCheckerRunner

check() - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

check() - Method in interface chemaxon.structurechecker.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.calculations.solubility.SolubilityCalculator

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, MolAtom) - Method in class chemaxon.checkers.AliasChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker

Detects atom of the molecule has atom map.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker

Detects if the current atom of the molecule has atom value.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker

Check the atom of the molecule with index i has no atom map.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker

Detects atom of the molecule is a query atom.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker

Detects if the current atom has free electrons.

check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker

check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.BondTopologyChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker

Examines if the bond is a crossed double bond.

check(Molecule, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker

Detects bond of the molecule is crossing another bond or closer than the limit distance.

check(Molecule, MolBond) - Method in class chemaxon.checkers.QueryBondChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker

check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker

check(Molecule, E) - Method in class chemaxon.checkers.ComponentChecker

Checks if the component with index i has problem

check(T) - Method in interface chemaxon.calculations.api.Calculator

Checks if the given data is usable for the calculator or not

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

Deprecated.

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.DoubleBondStereoErrorChecker

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.WigglyBondChecker

check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker

checkAndWait() - Method in class chemaxon.structurechecker.AdvancedCheckerRunner

checkAndWait() - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

checkAndWait() - Method in interface chemaxon.structurechecker.CheckerRunner

Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems

checkAtno(int) - Static method in class chemaxon.struc.MolAtom

Check if the given atomic number is positive and less then atomic type maximum value.

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

checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule

Empty implementation, bond consistency is not checked in case of selections.

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

Add the bonds of the given atom to the S-group if the given atom and the other atom of the selected bond are both in the S-group.

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

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

Add the bonds of the given atom to the S-group if the given atom and the other atom of the selected bond are both in the S-group.

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

For internal use only.

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

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

replaced by Sgroup.checkConsistency()

checkData(T, String, CalculatorLogger) - Method in class chemaxon.calculations.api.ProgressableCalculator

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

Checks if the document is the right version

CheckerClassDescriptor() - Constructor for class chemaxon.structurechecker.CheckerFixerFactory.CheckerClassDescriptor

Initializes an empty checker class descriptor

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

Initializes a checker class descriptor

CheckerFixerFactory - Class in chemaxon.structurechecker

Factory for structure checkers and structure fixers.

CheckerFixerFactory.Builder - Class in chemaxon.structurechecker

Builder class for CheckerFixerFactory.

CheckerFixerFactory.CheckerClassDescriptor - Class in chemaxon.structurechecker

Descriptor of a checker class

CheckerFixerFactory.ClassDescriptor - Class in chemaxon.structurechecker

Descriptor of a class

CheckerFixerFactory.FixerClassDescriptor - Class in chemaxon.structurechecker

Descriptor of a fixer class

CheckerInfo - Annotation Interface in chemaxon.checkers

This annotation is responsible for adding GUI-related metadata for StructureChecker implementations.

CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark

CheckerRunner - Interface in chemaxon.structurechecker

Interface for structure checker runner implementations.

CheckerSeverity - Enum Class in chemaxon.checkers

This enum defines the constants which represent the severity of the StructureChecker implementations

checkFilter(String) - Static method in class chemaxon.search.MolSearch

Checks the syntax of the filtering expression.

checkFilter(String, File) - Static method in class chemaxon.search.MolSearch

Checks the syntax of the filtering expression.

checkLicense() - Method in class chemaxon.calculations.api.ProgressableCalculator

checkLicense() - Method in class chemaxon.calculations.CalculatorPlugin

checkMolecule(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.ChemicalNamePlugin

checkMolecule(Molecule) - Method in class chemaxon.calculations.ConformerPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.GeometryPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.HBDAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.IonChargePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.LogDPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.LogPPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.MSAPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.PkaPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.PolarizabilityPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.RefractivityPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.ResonancePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.TautomerPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.calculations.TPSAPlugin

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 consistency 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.calculations.CalculatorPlugin

Checks result types.

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MElectronContainer

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline

Is it a valid object in the document?

checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject

Is it a valid object in the document?

CHEMAXON - Enum constant in enum class chemaxon.calculations.LogPMethod

Chemaxon logP calculation method.

chemaxon.alignment - package chemaxon.alignment

Provides algorithms and tools to align molecules onto each other in 2D and 3D.

chemaxon.calculations - package chemaxon.calculations

Provides various chemical calculations and property predictions.

chemaxon.calculations.admet - package chemaxon.calculations.admet

Provides ADMET property predictions including hERG activity and classification predictors.

chemaxon.calculations.api - package chemaxon.calculations.api

Provides general API for chemical property calculators.

chemaxon.calculations.bbb - package chemaxon.calculations.bbb

Provides BBB score calculator.

chemaxon.calculations.cnsmpo - package chemaxon.calculations.cnsmpo

Provides CNS MPO score calculator.

chemaxon.calculations.dipole - package chemaxon.calculations.dipole

Provides molecular dipole moment calculation functionality.

chemaxon.calculations.elemental - package chemaxon.calculations.elemental

Provides classes for elemental analysis of molecules.

chemaxon.calculations.gui - package chemaxon.calculations.gui

Provides GUI components for displaying and configuring calculator plugins in MarvinSketch.

chemaxon.calculations.nmr - package chemaxon.calculations.nmr

Provides NMR (Nuclear Magnetic Resonance) chemical shift prediction calculations.

chemaxon.calculations.output - package chemaxon.calculations.output

Provides classes for formatting the output of chemical calculations for CLI usage.

chemaxon.calculations.services - package chemaxon.calculations.services

Provides API and support for accessing remote services.

chemaxon.calculations.solubility - package chemaxon.calculations.solubility

Provides aqueous solubility prediction and categorization for molecules.

chemaxon.calculations.stereo - package chemaxon.calculations.stereo

Provides calculators for stereo analysis and stereoisomer enumeration.

chemaxon.calculations.stereo.stereocenters - package chemaxon.calculations.stereo.stereocenters

Provides stereocenter implementations of Stereo Analysis API.

chemaxon.checkers - package chemaxon.checkers

Provides structure checkers, which can be used to identify drawing mistakes or special structural elements in chemical structures.

chemaxon.checkers.result - package chemaxon.checkers.result

Provides classes that represent the results of various structure checkers.

chemaxon.chemterms - package chemaxon.chemterms

Provides Chemical Terms Evaluator classes.

chemaxon.common.annotations - package chemaxon.common.annotations

Provides annotations for Chemaxon classes.

chemaxon.common.version - package chemaxon.common.version

Provides version information of Chemaxon products.

chemaxon.core.calculations - package chemaxon.core.calculations

Provides essential calculations for molecular structures.

chemaxon.core.calculations.clean - package chemaxon.core.calculations.clean

Provides 2D and 3D structure cleaning algorithms for coordinate generation and optimization.

chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo

Provides common descriptor and calculator classes for stereochemistry.

chemaxon.core.util - package chemaxon.core.util

Provides utility classes related to core chemistry.

chemaxon.descriptors - package chemaxon.descriptors

Provides molecular descriptor generators and QSAR modeling.

chemaxon.descriptors.pharmacophore - package chemaxon.descriptors.pharmacophore

Provides classes for pharmacophore point perception, pharmacophore fingerprint generation and dissimilarity calculation.

chemaxon.descriptors.scalars - package chemaxon.descriptors.scalars

Provides scalar molecular descriptors (e.g., hydrogen bond donor and acceptor counts).

chemaxon.fixers - package chemaxon.fixers

Provides structure fixers, which can be used to fix problems identified by structure checkers.

chemaxon.formats - package chemaxon.formats

Provides utility classes for importing and exporting molecular structures, and for converting between various molecule file formats.

chemaxon.formats.converter - package chemaxon.formats.converter

Provides the command-line molecule format conversion utility.

chemaxon.license.api - package chemaxon.license.api

Provides the API for the built-in license checking of Chemaxon products and tools.

chemaxon.marvin.beans - package chemaxon.marvin.beans

Provides bean classes for creating Marvin Classic user interface.

chemaxon.marvin.common - package chemaxon.marvin.common

Provides common classes for Marvin Classic tools.

chemaxon.marvin.datatransfer - package chemaxon.marvin.datatransfer

Provides the clipboard handler infrastructure in Marvin.

chemaxon.marvin.util - package chemaxon.marvin.util

Provides utility classes for Marvin GUI.

chemaxon.naming - package chemaxon.naming

Provides classes for Name to Structure (N2S) and Structure to Name (S2N) conversion.

chemaxon.naming.document - package chemaxon.naming.document

Provides Document to Structure (D2S) conversion and document annotation.

chemaxon.reaction - package chemaxon.reaction

Provides classes for reaction processing and enumeration.

chemaxon.reaction.mapper - package chemaxon.reaction.mapper

Provides reaction mapping algorithms for automatic atom-atom mapping of reactants to products.

chemaxon.rendering.constants - package chemaxon.rendering.constants

Provides constants for molecule rendering styles and options.

chemaxon.search - package chemaxon.search

Provides chemical structure searching.

chemaxon.search.api - package chemaxon.search.api

Provides the public API for chemical structure searching.

chemaxon.search.api.options - package chemaxon.search.api.options

Provides configuration options for structure search behavior.

chemaxon.search.hitdisplay - package chemaxon.search.hitdisplay

Provides utilities for displaying and highlighting search hits in molecular structures.

chemaxon.search.mcs - package chemaxon.search.mcs

Provides classes for finding the maximum common substructure (MCS) of molecular structures.

chemaxon.search.util - package chemaxon.search.util

Provides utility classes for structure search.

chemaxon.standardizer - package chemaxon.standardizer

Provides the main classes of the Standardizer tool.

chemaxon.standardizer.actions - package chemaxon.standardizer.actions

Provides Standardizer actions.

chemaxon.standardizer.configuration - package chemaxon.standardizer.configuration

Provides classes for handling configurations of Standardizer.

chemaxon.struc - package chemaxon.struc

Provides classes for implementing and manipulating chemical structures.

chemaxon.struc.graphics - package chemaxon.struc.graphics

Provides classes representing graphics MDocument elements.

chemaxon.struc.prop - package chemaxon.struc.prop

Provides utility classes that represent molecular properties and handle data conversion.

chemaxon.struc.sgroup - package chemaxon.struc.sgroup

Provides classes and interfaces related to structural groups (S-groups) of molecules.

chemaxon.structurechecker - package chemaxon.structurechecker

Provides the main classes of the Structure Checker tool.

chemaxon.structurechecker.configuration - package chemaxon.structurechecker.configuration

Provides classes for handling configurations of Structure Checker.

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.

ChemicalNamePlugin - Class in chemaxon.calculations

Plugin for generating chemical names and identifiers.

ChemicalNamePlugin() - Constructor for class chemaxon.calculations.ChemicalNamePlugin

ChemTermsContext - Interface in chemaxon.chemterms

Interface of expression evaluation contexts.

ChemTermsContext.ProvidesFunction - Annotation Interface in chemaxon.chemterms

Repeatable annotation used on ChemTermsContext implementations to declare the context functions supported by the ChemTermsContext.callContextFunction(String, List) method.

ChemTermsContext.ProvidesFunctionContainer - Annotation Interface in chemaxon.chemterms

Container for the repeatable ChemTermsContext.ProvidesFunction annotation.

ChemTermsEvaluator - Class in chemaxon.chemterms

Evaluates Chemical Terms expressions.

ChemTermsEvaluator() - Constructor for class chemaxon.chemterms.ChemTermsEvaluator

Default constructor.

ChemTermsEvaluator(File) - Constructor for class chemaxon.chemterms.ChemTermsEvaluator

Constructor.

ChemTermsEvaluator(String) - Constructor for class chemaxon.chemterms.ChemTermsEvaluator

Constructor.

ChemTermsException - Exception Class in chemaxon.chemterms

Exception thrown during the compilation or evaluation of Chemical Terms expressions.

ChemTermsException() - Constructor for exception class chemaxon.chemterms.ChemTermsException

ChemTermsException(String) - Constructor for exception class chemaxon.chemterms.ChemTermsException

ChemTermsException(String, Throwable) - Constructor for exception class chemaxon.chemterms.ChemTermsException

ChemTermsException(Throwable) - Constructor for exception class chemaxon.chemterms.ChemTermsException

ChemTermsExpression<C> - Class in chemaxon.chemterms

Expression parser and evaluator for chemical expressions.

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

Represents that the molecule is marked with "absolute stereo" flag

chiralCenterCount() - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Calculates the number of chiral centers.

chiralCenters() - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Determines the chiral center atoms.

ChiralFlagChecker - Class in chemaxon.checkers

Implementation of AbstractStructureChecker detecting "absolute stereo flag" on molecule.

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

Constructs ChiralFlagChecker instance

ChiralFlagErrorChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).

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

Default constructor

CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants

Axially chiral atom with M configuration.

CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants

Chirality mask in flags.

CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants

Axially chiral atom with P configuration.

CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants

Pseudo-asymmetric chiral atom of r configuration.

CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of R configuration.

CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants

Pseudo-asymmetric chiral atom of s configuration.

CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants

Chiral atom of S configuration.

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

Identifier of parameter: "chiralitySupport".

CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants

R/S shown always.

CHIRALITYSUPPORT_ALL_POSSIBLE - Static variable in interface chemaxon.struc.StereoConstants

R/S shown always and highlight possible chiral centers as well.

CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants

R/S not shown for any molecule.

CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants

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

No longer supported, use StereoConstants.CHIRALITYSUPPORT_ALL option instead.

CIPStereoCalculator - Class in chemaxon.core.calculations.stereo

Stereo calculator with the Cahn, Ingold, Prelog (CIP) priority rules.

CIPStereoCalculator() - Constructor for class chemaxon.core.calculations.stereo.CIPStereoCalculator

CIPStereoCalculator.CIPStereoCalculatorResult - Record Class in chemaxon.core.calculations.stereo

Wrapper for the calculated descriptor with timeout information.

CIPStereoCalculatorResult(CIPStereoDescriptor, boolean) - Constructor for record class chemaxon.core.calculations.stereo.CIPStereoCalculator.CIPStereoCalculatorResult

Creates an instance of a CIPStereoCalculatorResult record class.

CIPStereoDescriptor - Interface in chemaxon.core.calculations.stereo

Cahn-Ingold-Prelog (CIP) stereodescriptor interface.

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

CIPStereoType - Enum Class in chemaxon.core.calculations.stereo

CIP stereo type.

CIPStereoValue - Interface in chemaxon.core.calculations.stereo

CIP stereo value.

CIPStereoValue.AtropStereoIUPACValue - Enum Class in chemaxon.core.calculations.stereo

Atrop stereo value, conforms to IUPAC.

CIPStereoValue.AtropStereoValue - Enum Class in chemaxon.core.calculations.stereo

Atrop stereo value.

CIPStereoValue.AxialStereoIUPACValue - Enum Class in chemaxon.core.calculations.stereo

Axial stereo value, conforms to IUPAC.

CIPStereoValue.AxialStereoValue - Enum Class in chemaxon.core.calculations.stereo

Axial stereo value.

CIPStereoValue.CisTransStereoIUPACValue - Enum Class in chemaxon.core.calculations.stereo

Double-bond stereo value, conforms to IUPAC.

CIPStereoValue.CisTransStereoValue - Enum Class in chemaxon.core.calculations.stereo

Double-bond stereo value.

CIPStereoValue.TetrahedralStereoIUPACValue - Enum Class in chemaxon.core.calculations.stereo

Tetrahedral stereo value, conforms to IUPAC.

CIPStereoValue.TetrahedralStereoValue - Enum Class in chemaxon.core.calculations.stereo

Tetrahedral stereo value.

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

Represents that the molecule contains circular R-group references

CircularRGroupReferenceChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting circular R-group references.

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

Initializes the checker

CIS - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoValue

Cis stereo value.

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.

cisDoubleBonds() - Method in class chemaxon.calculations.stereo.StereoAnalysis

Calculates the CIS double bonds.

CISTRANS - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.StereoType

Cis-trans stereo center.

CISTRANS - Enum constant in enum class chemaxon.calculations.stereo.StereoisomerSettings.StereoisomerType

Double bond stereoisomers.

CISTRANS - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoType

cisTransDoubleBonds() - Method in class chemaxon.calculations.stereo.StereoAnalysis

Calculates the CIS-TRANS double bonds.

cisTransDoubleBondsWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis

Calculates the CIS-TRANS double bonds with attached data.

CisTransStereoCenter - Class in chemaxon.calculations.stereo.stereocenters

Cis-trans stereo center implementation.

CisTransStereoCenter(AtomSelection, CIPStereoValue.CisTransStereoIUPACValue) - Constructor for class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter

Constructs a new instance of cis-trans stereo center.

CisTransStereoCenter(AtomSelection, CIPStereoValue.CisTransStereoIUPACValue, List<AttachedData>) - Constructor for class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter

Constructs a new instance of cis-trans stereo center with attached data.

CisTransStereoDescriptor - Class in chemaxon.core.calculations.stereo

Double-bond stereo descriptor.

CisTransStereoDescriptor(CIPStereoValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.CisTransStereoDescriptor

CisTransStereoIUPACDescriptor - Class in chemaxon.core.calculations.stereo

Double-bond stereo descriptor.

CisTransStereoIUPACDescriptor(CIPStereoValue.CisTransStereoIUPACValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.CisTransStereoIUPACDescriptor

Cl - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cl.

CLASS - Static variable in class chemaxon.calculations.services.LocalServiceDescriptor

Property key for Service class name as String

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

className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

className - Variable in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor

clean(int) - Method in class chemaxon.formats.converter.MolConverter.Builder

Enables cleaning.

clean(int, String) - Method in class chemaxon.formats.converter.MolConverter.Builder

Enables cleaning.

clean(int, String, int, String, ProgressMonitor, String[]) - Method in class chemaxon.marvin.common.MDocStorage

Clean the specified cell.

clean(MoleculeGraph, int) - Static method in class chemaxon.core.calculations.clean.Cleaner

Calculates atom coordinates.

clean(MoleculeGraph, int, String) - Static method in class chemaxon.core.calculations.clean.Cleaner

Calculates atom coordinates.

clean(MoleculeGraph, int, String, ProgressMonitor) - Static method in class chemaxon.core.calculations.clean.Cleaner

Calculates atom coordinates.

Clean2DAction - Class in chemaxon.standardizer.actions

Standardizer action that cleans the molecule graph in 2D.

Clean2DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.Clean2DAction

Initializes the action with parameters

Clean2DAction.Type - Enum Class in chemaxon.standardizer.actions

Type of clean action (partial, full, template based or convert 3D to 2D)

clean3d(Molecule) - Static method in class chemaxon.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

clean3d(Molecule, int) - Static method in class chemaxon.alignment.MMPAlignment

Utility for preprocessing structure for alignment.

Clean3DAction - Class in chemaxon.standardizer.actions

Standardizer action that cleans the molecule graph in 3D.

Clean3DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.Clean3DAction

Initializes the action with parameters

cleanAll(int, String, ProgressMonitor, String[]) - Method in class chemaxon.marvin.common.MDocStorage

Clean all cells.

Cleaner - Class in chemaxon.core.calculations.clean

Class to clean MoleculeGraphs, Molecules, SelectionMolecules and S-groups.

Cleaner() - Constructor for class chemaxon.core.calculations.clean.Cleaner

Cleaner.AtomChangeEventListener - Interface in chemaxon.core.calculations.clean

Listener interface to be notified on atom changes during partial clean.

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(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.

cleanupRemovedRgroupMember(MoleculeGraph, int) - Method in interface chemaxon.struc.RgMoleculeGraph

Clean-up after R-group removal.

CleanUtil - Class in chemaxon.core.calculations.clean

Utility methods for cleaning.

CleanUtil() - Constructor for class chemaxon.core.calculations.clean.CleanUtil

clear() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Clears the display.

clear() - Method in class chemaxon.chemterms.AtomContext

Clears the context.

clear() - Method in interface chemaxon.chemterms.ChemTermsContext

Clears the context.

clear() - Method in class chemaxon.chemterms.MolContext

Clears the context.

clear() - Method in class chemaxon.chemterms.ReactionContext

Clears the context.

clear() - Method in class chemaxon.chemterms.SearchContext

Clears the context.

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.pharmacophore.PMap

Sets every feature for every atom to false

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.converter.MolConverter.Builder

Clears all settings.

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.

clearAssigned() - Method in class chemaxon.alignment.AlignmentMolecule

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

Deletes the cached information depending on the given options.

clearChangesInUserComparators() - Method in class chemaxon.search.api.options.SearchOptions

Used in initializing searches.

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

Clears the checker marks

clearComparators() - Method in class chemaxon.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.descriptors.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

Standardizer action that clears isotope information (mass numbers) from atoms.

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

Initializes the action

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

Clears all lines.

clearMark() - Method in class chemaxon.formats.PositionedInputStream

Disables the mark (if any) on this stream.

clearMatch() - Method in class chemaxon.search.AbstractSearch

Clears the extra prerequisites of the structure search specified using addMatch calls.

clearMatch() - Method in class chemaxon.search.MolSearch

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

Removes all MObjects that belong to this 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.MObject

Removes all properties from this MObject.

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

Removes all properties from this atom.

clearProperties() - Method in class chemaxon.struc.MolBond

Removes all properties from this bond.

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

Clears RDfile/SDfile properties.

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

Clears query props.

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

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

Clears the atomSets and the bondSets.

ClearStereoAction - Class in chemaxon.standardizer.actions

Standardizer action that clears stereo information from the molecule.

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.datatransfer.MTransferable

Flag that indicates an import operation

CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.datatransfer.MTransferable

Flag that indicates an export operation

CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.datatransfer.MTransferable

Undefined clipboard operation state identifier

CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.datatransfer.MTransferable

Temporary property name to mark the molecule if it comes from a file via the clipboard

clipboardOperation - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable

Clipboard operation type.

clone() - Method in class chemaxon.checkers.AbstractStructureChecker

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

clone() - Method in class chemaxon.checkers.SubstructureChecker

clone() - Method in class chemaxon.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.pharmacophore.PMap

Clones this PMap object.

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.search.api.options.MolSearchOptions

clone() - Method in class chemaxon.search.api.options.SearchOptions

Makes an identical copy of this SearchObject.

clone() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Makes an identical copy of the Options

clone() - Method in class chemaxon.standardizer.AbstractSgroupAction

clone() - Method in class chemaxon.standardizer.AbstractStandardizerAction

clone() - Method in class chemaxon.standardizer.actions.AliasToGroupAction

clone() - Method in class chemaxon.standardizer.actions.AromatizeAction

clone() - Method in class chemaxon.standardizer.actions.Clean2DAction

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.CreateGroupAction

clone() - Method in class chemaxon.standardizer.actions.ExpandAction

clone() - Method in class chemaxon.standardizer.actions.GroupDefinition

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.RemoveSolventsAction

clone() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

clone() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

clone() - Method in class chemaxon.standardizer.actions.StripSaltsAction

clone() - Method in class chemaxon.standardizer.actions.TautomerizeAction

clone() - Method in class chemaxon.standardizer.actions.TransformAction

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

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

clone() - Method in class chemaxon.struc.BondTable

clone() - Method in class chemaxon.struc.graphics.MAnalysisBox

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

clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint

clone() - Method in class chemaxon.struc.graphics.MBracket

clone() - Method in class chemaxon.struc.graphics.MChemicalStruct

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MEFlow

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

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

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

clone() - Method in class chemaxon.struc.graphics.MEllipse

clone() - Method in class chemaxon.struc.graphics.MFont

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MMidPoint

clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky

clone() - Method in class chemaxon.struc.graphics.MMoleculeMovie

Creates a clone.

clone() - Method in class chemaxon.struc.graphics.MNameTextBox

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

clone() - Method in class chemaxon.struc.graphics.MRArrow

clone() - Method in class chemaxon.struc.graphics.MRectangle

clone() - Method in class chemaxon.struc.graphics.MRectanglePoint

clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky

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

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

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

Creates a clone.

clone() - Method in class chemaxon.struc.MObject

Creates a clone.

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

Clones the atom.

clone() - Method in class chemaxon.struc.MolBond

Make a copy of this object.

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

Makes an identical copy of the molecule.

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

Make an identical copy of the molecule.

clone() - Method in class chemaxon.struc.MPoint

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

Clones this object.

clone() - Method in class chemaxon.struc.PageSettings

Clones this object.

clone() - Method in class chemaxon.struc.Point3D

Make an identical copy.

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

Clones the object.

clone() - Method in class chemaxon.struc.prop.MByteArrayProp

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.AminoAcidSgroup

Clones the AminoAcidSgroup (and not the Molecule).

clone() - Method in class chemaxon.struc.sgroup.SgroupAtom

Clones the S-group superatom and it's SuperatomSgroup as well.

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

Clones the SuperatomSgroup (and not the Molecule).

clone() - Method in class chemaxon.struc.Transform3D

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.struc.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.search.api.options.MolSearchOptions

Copies all search options to other.

clonecopy(SearchOptions) - Method in class chemaxon.search.api.options.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.search.api.options.MolSearchOptions

Copies all search options except search type to other.

clonecopyOptions(SearchOptions) - Method in class chemaxon.search.api.options.SearchOptions

Copies all search options except search type to other.

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

Copies the all the contents except the S-groups into another molecule object.

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

Creates a clone.

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

Creates a clone.

cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom

Clones the S-group superatom partially.

cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker

cloneItem() - Method in class chemaxon.checkers.InvalidChecker

cloneItem() - Method in interface chemaxon.checkers.StructureChecker

Returns a clone of this StructureChecker instance

cloneItem() - Method in class chemaxon.standardizer.AbstractStandardizerAction

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

cloneItem() - Method in interface chemaxon.standardizer.StandardizerAction

Returns a clone of this StandardizerAction instance

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

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

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

as of Marvin 6.3.
Not supported feature.

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

Creates a clone.

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

Creates a clone.

cloneMFont() - Method in class chemaxon.struc.graphics.MFont

Creates a clone.

cloneMolecule() - Method in class chemaxon.alignment.AlignmentMolecule

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.MByteArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MFontProp

cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MMoleculeStringProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MObjectProp

Clones the object.

cloneProp() - Method in class chemaxon.struc.prop.MStringProp

Clones the object.

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

Clones the atom/bond sets from doc.

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

Gets a new Sgroup instance.

cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.AminoAcidSgroup

Gets a new amino acid s-group 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 S-group 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.calculations.api.CalculatorLogger

close() - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Closes the output.

close() - Method in class chemaxon.formats.converter.MolConverter

Closes the exporter and the output stream.

close() - Method in class chemaxon.formats.MDocSource

Closes the underlying input stream(s).

close() - Method in class chemaxon.formats.MoleculeImporter

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

Closes the MolExportModule and the underlying stream.

close() - Method in class chemaxon.formats.MolExportModule

Close the stream.

close() - Method in class chemaxon.formats.MolImporter

Closes the underlying input stream.

close() - Method in interface chemaxon.formats.MolImporterInterface

Closes the underlying input stream.

close() - Method in class chemaxon.naming.document.DocumentAnnotator

close() - Method in interface chemaxon.reaction.mapper.AutoMapper.ResultIterator

close(int) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Closes the output.

close(int) - Method in class chemaxon.formats.converter.MolConverter

Closes the exporter.

close(int) - Method in class chemaxon.formats.MolExporter

Closes the MolExportModule and, optionally, the underlying stream.

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 specified cell.

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

Closes the detached viewer window of the specified cell.

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

Closes all windows opened by this MarvinPane.

Cm - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cm.

cmdParameters - Variable in class chemaxon.calculations.api.CalculatorLogger

CML - Static variable in class chemaxon.formats.MFileFormat

Chemical Markup Language.

Cn - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cn.

CnsMpo - Class in chemaxon.calculations.cnsmpo

CNS MPO score calculator.

CnsMpo.Property - Class in chemaxon.calculations.cnsmpo

Simple result class that contains the predicted value and its CNS MPO score.

CnsMpoFunction - Enum Class in chemaxon.calculations.cnsmpo

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

Co - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Co.

COL_MOLECULE - Static variable in class chemaxon.search.RgroupDecomposition

Constant for adding query-target column to ligand table.

COL_SCAFFOLD - Static variable in class chemaxon.search.RgroupDecomposition

Constant for adding scaffold column to ligand table.

collectLonePairContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

collectLonePairsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

collectMElectronContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

Collects all MElectronContainers of an atom, if the atom is part of a Molecule, which has an MDocument.

collectRadicalContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

collectRadicalsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer

color() - Method in class chemaxon.search.Decomposition

Colors ligands, scaffold, query and target by setting color data in atoms by calling MolAtom.setSetSeq(int).

color(Molecule) - Static method in class chemaxon.search.Decomposition

Colors a molecule by setting color data in atoms by calling MolAtom.setSetSeq(int).

color(Molecule, Molecule, int[], HitDisplayOptions) - Static method in class chemaxon.search.hitdisplay.HitDisplayUtil

Performs hit coloring directly on the specified target structure.

color(Molecule, Molecule, SearchHit, HitDisplayOptions) - Static method in class chemaxon.search.hitdisplay.HitDisplayUtil

Performs hit coloring directly on the specified target structure.

color(Molecule, String) - Static method in class chemaxon.search.Decomposition

Colors a molecule by setting color data in the specified molecule property (SDF tag).

color(String) - Method in class chemaxon.search.Decomposition

Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag).

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

Identifier of parameter: "colorScheme".

COLOR_SCHEMES - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Array of color schemes strings.

ColorGenerator - Class in chemaxon.marvin.util

A final class which provides a static access to a color distant color creator class.

ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator

colorHit(Molecule, Molecule, int[], HitDisplayOptions) - Static method in class chemaxon.search.hitdisplay.HitDisplayUtil

Returns the colored copy of the specified target structure, the original target is kept unchanged.

colorHit(Molecule, Molecule, SearchHit, HitDisplayOptions) - Static method in class chemaxon.search.hitdisplay.HitDisplayUtil

Returns the colored copy of the specified target structure, the original target is kept unchanged.

COLORING_ALL - Static variable in class chemaxon.calculations.MarkushEnumerationPlugin

Constant for setting all coloring options, currently scaffold and R-groups.

COLORING_NONE - Static variable in class chemaxon.calculations.MarkushEnumerationPlugin

Constant for no hit coloring.

COLORING_RGROUPS - Static variable in class chemaxon.calculations.MarkushEnumerationPlugin

Constant for R-group coloring.

COLORING_SCAFFOLD - Static variable in class chemaxon.calculations.MarkushEnumerationPlugin

Constant for scaffold coloring.

COLORS_MASK - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Color scheme mask in display option flags.

COLORS_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Color scheme offset in display option flags.

COLS - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "cols".

combine(Collection<? extends CalculatorInputChecker>) - Static method in interface chemaxon.calculations.api.CalculatorInputChecker

Combines the given checkers into a single one that reports all errors reported by the given checkers.

compareAtoms(int, int) - Method in class chemaxon.search.api.MolComparator

Compares atoms of indices a1 and a2.

compareBonds(int, int) - Method in class chemaxon.search.api.MolComparator

Compares bonds of indices b1 and b2.

compareHit(int[], int) - Method in class chemaxon.search.api.MolComparator

Checks a partial hit during the search algorithm.

compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.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.actions.GroupDefinition

compareTo(BicycloStereoDescriptor) - Method in class chemaxon.struc.BicycloStereoDescriptor

Compares two bicyclostereo descriptors.

compareTo(RgroupBridgeId) - Method in class chemaxon.struc.RgroupBridgeId

compareTo(AttachmentPoint) - Method in class chemaxon.struc.sgroup.AttachmentPoint

Compares two attachment points by their order.

compareTo(Object) - Method in class chemaxon.calculations.gui.PluginFactory.PluginRecord

compile(String) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Compiles the expression, creates ChemTermsExpression object.

compile(String) - Method in class chemaxon.chemterms.ChemTermsExpression

Updates this object to represent the given expression.

compile(String, C) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Compiles the expression, creates ChemTermsExpression object.

compile(String, C, ConstantTable) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Compiles the expression, creates ChemTermsExpression object.

compile(String, Class<? extends C>) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Compiles the expression, creates ChemTermsExpression object.

compile(String, Class<? extends C>, ConstantTable) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Compiles the expression, creates ChemTermsExpression object.

COMPILE_ERROR - Static variable in class chemaxon.chemterms.ChemTermsExpression

The compilation error message.

COMPLETE - Enum constant in enum class chemaxon.reaction.mapper.ReactionMapper.MappingStyle

Map all atoms.

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

ComponentChecker<E> - Class in chemaxon.checkers

Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).

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

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

componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Hides windows if the parent frame is hidden.

componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

Does nothing.

componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane

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 class chemaxon.calculations.elemental.ElementalAnalysis

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

composition(int) - Method in class chemaxon.core.calculations.ElementalAnalyzer

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

COMPOSITION - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType

Result type with the string id "composition".

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

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_DIR - Static variable in class chemaxon.chemterms.ChemTermsEvaluator

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

ConfigurationUtility - Class in chemaxon.standardizer.configuration

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

Use StandardizerConfiguration.filterGroups(String...) instead

ConfigurationUtility() - Constructor for class chemaxon.standardizer.configuration.ConfigurationUtility

Deprecated.

CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "confirmTransfer".

CONFORMATION - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

CONFORMER_CONFORMERS - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

CONFORMER_HASVALIDCONFORMER - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

CONFORMER_LECONFORMER - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

ConformerPlugin - Class in chemaxon.calculations

Plugin class for conformer calculation.

ConformerPlugin() - Constructor for class chemaxon.calculations.ConformerPlugin

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

Conjugation state of the bond.

CONJUGATED - Static variable in class chemaxon.struc.MolBond

Conjugation state of the bond.

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

Sets whether the common substructures should be connected or they can consist of multiple fragments.

connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule

connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Sets the original connections to the new atom.

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject

CONSENSUS - Enum constant in enum class chemaxon.calculations.LogPMethod

Consensus model using Chemaxon and Klopman's models and the PhysProp database.

constant - Variable in class chemaxon.calculations.services.ServiceArgument

field indicates constant argument

constants() - Method in class chemaxon.chemterms.ConstantTable

Returns an immutable set containing the names of the constants in this table.

constantTable() - Method in class chemaxon.chemterms.ChemTermsEvaluator

Returns the table of predefined constants (molecules, molecule sets and other constants defined in the built-in and the user-defined jep.script).

constantTable() - Method in class chemaxon.chemterms.ChemTermsExpression

Returns the constant table used by this parser.

ConstantTable - Class in chemaxon.chemterms

Immutable table of constants used in a Chemical Terms evaluator.

ConstantTableBuilder - Class in chemaxon.chemterms

A builder for a ConstantTable.

contains(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

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

Tests whether the document contains all objects of another document.

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

Searches an object in the document.

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

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

Checks if the molecule graph contains the specified atom.

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

Checks if the molecule graph contains the specified atom.

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

Checks if the root structure or an R-group contains the specified node.

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

Checks if a reactant, agent or product structure contains the specified node.

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

Is this atom contained by the S-group?

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

Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.

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

Checks if the root structure or an R-group contains the specified edge.

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

Checks if a reactant, agent or product structure contains the specified edge.

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

Does the molecule graph contain the specified fragment?

contains(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether the container contains the specified property object.

contains(MProp) - Method in class chemaxon.struc.prop.MCollectionProp

Tests whether the collection contains the specified property.

contains(String) - Method in class chemaxon.checkers.AtomLabels

Gets whether the atom labels contain the specified atom label

contains(String) - Method in class chemaxon.checkers.AttachedDataChecker.DataExclusionList

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

Checks if the S-group contains the atoms of another S-group.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MElectronContainer

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline

Checks if the atom set contains the specified atom object.

containsAtom(MolAtom) - Method in class chemaxon.struc.MObject

Checks if the object contains the specified atom reference.

containsConstant(String) - Method in class chemaxon.chemterms.ConstantTable

Returns true if this table contains the given constant.

containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.calculations.CalculatorPlugin

Decides whether a molecule graph contains coordinate bonds.

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

Decides whether the structure of this S-group contains a ladder-type polymer.

containsMulticenterSgroup(Molecule) - Static method in class chemaxon.calculations.CalculatorPlugin

Decides whether a molecule contains Multicenter S-groups.

containsPoint(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle

containsPoint(Point3D, Transform3D) - Method in class chemaxon.struc.MObject

containsPropertyKey(String) - Method in class chemaxon.struc.MObject

Returns true if this MObject has a mapping for the specified property key.

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.calculations.CalculatorPlugin

Returns true if molecule contains pseudo atom.

containsSRUSgroup(Molecule) - Static method in class chemaxon.calculations.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.common.MDocStorage

Contract or expand S-groups in the specified cell.

contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.common.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 that contracts S-groups of the molecule.

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

Initializes the action

ConversionConstants - Class in chemaxon.checkers.result

This class contains constants for converting atoms, bonds and S-groups in checker results.

ConversionConstants() - Constructor for class chemaxon.checkers.result.ConversionConstants

convert() - Method in class chemaxon.formats.converter.MolConverter

Convert the next molecule.

convert(byte[], int, int) - Method in class chemaxon.formats.Encoding

Converts a byte array to a string.

convert(double[][]) - Static method in class chemaxon.alignment.AlignRigidEasy

convert(double, double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Multiplies the parameters of this multiplet (unit conversion).

convert(Molecule) - Method in class chemaxon.formats.MolExportModule

Convert a molecule to a string or byte array.

convert(Molecule[], String, MPropertyContainer) - Method in class chemaxon.formats.MolExportModule

Convert a molecule array to a string or byte array.

convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult

convert(Molecule, Map<String, Map<?, ?>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method converts the entities contained in this result according to the convertData.

convert(String, boolean) - Method in interface chemaxon.naming.NameConverter

Convert a name into the corresponding structure.

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

ConvertDoubleBondsAction - Class in chemaxon.standardizer.actions

Standardizer action that converts double bonds to wiggly bonds.

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

Initializes the action with parameters

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

Type of conversion

convertExplicitHToImplicit(MoleculeGraph) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts explicit Hydrogen atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts explicit Hydrogen atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.

convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.

convertExplicitLonePairsToImplicit(MoleculeGraph) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts explicit lone pairs from a molecule to implicit.

convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts implicit Hydrogen atoms of the molecule to explicit.

convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.core.calculations.Hydrogenizer

Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.

convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.core.calculations.Hydrogenizer

Convert implicit lone pairs of the atoms of a molecule to explicit.

ConvertPiMetalBondsAction - Class in chemaxon.standardizer.actions

Standardizer action that converts Pi-metal single bonds to standard coordinate bonds.

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.structurechecker.BasicCheckerRunner

Deprecated.

This method provides the possibility to convert back the affected properties of the result if there was any convert in the molecule structure before check.

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 atoms with atom numbers originally contained in the alias information.

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

convertToBondType(int) - Static method in enum class chemaxon.struc.BondType

Creates BondType from the given number.

ConvertToCarbonFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts pseudo and query 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

Standardizer action that converts stereo information to enhanced stereo representation.

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.formats.MPropHandler

Converts the value associated with the given key in the given MPropertyContainer to string.

convertToString(MProp, String) - Static method in class chemaxon.formats.MPropHandler

Converts the property to text format.

ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers

A descendant of AbstractStructureFixer which converts crossed double bond to wiggly

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

convertTransform(Transform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle

COORDDEP - Static variable in class chemaxon.struc.MProp

Coordinate dependent property.

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

Coordinate bond.

COORDINATE - Static variable in class chemaxon.struc.MolBond

Coordinate bond flag.

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

Identifier of parameter: "coordinateBondStyle".

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

Identifier of parameter: "coordinateBondStyleAtMulticenter".

CoordinateBondOnMulticenterStyle - Enum Class in chemaxon.rendering.constants

Holds the values for the possible rendering styles for Coordinate bonds connected to Multicenter atoms.

CoordinateBondStyle - Enum Class in chemaxon.rendering.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

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

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

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

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

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

Default format to be selected on Copy as dialog.

copyOf(ShapeData) - Static method in class chemaxon.alignment.ShapeData

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

Copies the assigner properties to another assigner object.

copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket

Copies line properties to another line object.

copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow

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

Copies line properties to another line object.

copyProperties(MRArrow) - Method in class chemaxon.struc.graphics.MRArrow

Copies arrow properties to another arrow object.

correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

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

Counts all atoms represented by this atom.

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

Counts the total number of atoms recursively.

countAllAtoms() - Method in class chemaxon.struc.sgroup.SgroupAtom

Counts all atoms represented by this atom.

countEnumerations() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Returns the number of all enumerated structures, no arithmetic overflow because counts in BigInteger.

countEnumerationsMagnitude() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures.

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

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

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

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

countRecords(ProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.common.MDocStorage

Counts the total number of records and sets the size of the document storage.

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

Represents that incorrectly drawn covalent counter ions have been found in the molecule

COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.calculations.CalculatorPlugin

Covalent hydration error remark.

CovalentCounterionChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates and 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_SCHEME - Static variable in interface chemaxon.rendering.constants.DispOptConsts

CPK color scheme in display option flags.

CPK_SCHEME_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

CPK color scheme.

Cr - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cr.

crdMolRefresh() - Method in class chemaxon.alignment.AlignmentMolecule

crdSafeRefresh() - Method in class chemaxon.alignment.AlignmentMolecule

create() - Static method in class chemaxon.calculations.stereo.StereoisomerSettings

Constructs a new StereoisomerSettings object with default settings.

create(byte[], AlignmentProperties.DegreeOfFreedomType) - Static method in class chemaxon.alignment.AlignmentMolecule

Deserializes an AlignmentMolecule from a byte array.

create(AlignmentProperties.ColoringScheme) - Static method in class chemaxon.alignment.NodeColor

Factory method to create a NodeColor based on the given ColoringScheme.

create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

create(Molecule) - Static method in class chemaxon.alignment.Pharmacophore3D

create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

create(Molecule, Molecule) - Method in interface chemaxon.search.mcs.McsCustomMatcherFactory

Creates a custom matcher for atom and bond pairs of the given query and target structures.

create(String) - Static method in class chemaxon.calculations.CalculatorPlugin

Loads a plugin from the classpath based on its fully qualified name.

create(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory

Creates a similarity calculator object according to the user defined parameters.

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.descriptors.pharmacophore.PMap

Creates a PMap object from a pharmacophore point list string.

createAnalysis(Molecule) - Static method in class chemaxon.calculations.elemental.ElementalAnalysisFactory

Creates elemental analysis for the specified molecule.

createAnalysis(Molecule, boolean) - Static method in class chemaxon.calculations.elemental.ElementalAnalysisFactory

Creates elemental analysis for the specified molecule with the given options.

createAnalysis(Molecule, Set<Integer>, boolean) - Static method in class chemaxon.calculations.elemental.ElementalAnalysisFactory

Creates an elemental analysis from the specified molecule with the given options.

createAnalysis(String) - Static method in class chemaxon.calculations.elemental.ElementalAnalysisFactory

Constructs an elemental analysis from molecular formula.

createArgument(String, T) - Static method in class chemaxon.calculations.services.ServiceArgument

Returns a service argument based on value

createArgument(T) - Static method in class chemaxon.calculations.services.ServiceArgument

Returns a service argument based on value

createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.calculations.services.ServiceArgument

Returns a service argument based on value and type

createArgumentAs(T, Class<T>) - Static method in class chemaxon.calculations.services.ServiceArgument

Returns a service argument based on value and type

createArray(String, String, int, int) - Static method in class chemaxon.formats.MPropHandler

Creates an array property.

createArrayXSD(String, String, int, int) - Static method in class chemaxon.formats.MPropHandler

Creates an array property from the XSD type.

createAtomIterator() - Method in class chemaxon.struc.IteratorFactory

Deprecated.

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.struc.IteratorFactory

Deprecated.

Constructs an iterator to get the atom neighbours of the specified atom.

createBondIterator() - Method in class chemaxon.struc.IteratorFactory

Deprecated.

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.struc.IteratorFactory

Deprecated.

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

createBondTable(int, int) - Static method in class chemaxon.struc.BondTable

Creates a new bond table for a molecule graph with the specified number of atoms and bonds.

createBracket(Sgroup, Point3D[], int) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Deprecated.

createChecker(String, Map<String, String>) - Method in class chemaxon.structurechecker.CheckerFixerFactory

This method creates a requested (type represented in checkerId) StructureChecker instance with the give parameters

createConstantFromString(String, Class<?>) - Static method in class chemaxon.calculations.services.ServiceArgument

Creates a ServiceArgument constant based on string value and argument type.
Supported types are String, Integer, Long, Double, Float and Boolean

createDefaultParameterPanel(String, Component) - Static method in class 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.marvin.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.descriptors.pharmacophore.PMapper

Creates the feature ID -> atom index BitSet HashMap for the given target molecule.

createFixer(String) - Method in class chemaxon.structurechecker.CheckerFixerFactory

This method creates a StructureFixer instance identified by fixerId parameters

createGroup() - Method in class chemaxon.struc.sgroup.AminoAcidSgroup

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

CreateGroupAction - Class in chemaxon.standardizer.actions

Standardizer action that searches for groups in the molecule and contracts them.

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

Initializes a create group standardizes action

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

Creates the molecule import module.

createInDocumentAt(Point3D, MDocument) - Static method in class chemaxon.struc.NoStructure

Creates a NoStructure at the given location.

createInDocumentFrom(Molecule, MDocument) - Static method in class chemaxon.struc.NoStructure

Creates a NoStructure from the given component.

createMElectronContainer(Point3D[], MolAtom, boolean) - Static method in class chemaxon.struc.graphics.MElectronContainer

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.formats.MPropHandler

createModifiedInputMolecule(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin

Returns the modified input molecule (e.g.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.calculations.LogPPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

Returns the molecule form with largest distribution.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Returns the major tautomeric form of the molecule.

createModifiedInputMolecule(Molecule) - Method in class chemaxon.calculations.PkaPlugin

Returns the canonical tautomeric form of the molecule.

createMol() - Method in class chemaxon.formats.MolImportModule

Creates a new target molecule object for the import.

createMolConverter(InputStream, OutputStream, String[], int[]) - Static method in class chemaxon.formats.converter.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 S-group instance and a molecule object that contains only this S-group.

createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable

Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.

createMoleculeIterator(Molecule[]) - Static method in class chemaxon.formats.MoleculeIteratorFactory

Creates a MoleculeIterator object for iterating through the given array of Molecule objects.

createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.formats.MoleculeIteratorFactory

Creates a MoleculeIterator object for iterating through the given collection of Molecule objects.

createNew() - Static method in class chemaxon.calculations.HLBPlugin.Builder

Deprecated.

Constructs a new HLBPlugin instance.

createNew(Molecule) - Static method in class chemaxon.alignment.MCSAlignment.Factory

Constructs a new instance of ConformationAlignment class.

createNext() - Method in class chemaxon.struc.graphics.MTextAttributes

Creates identical attributes for the next section.

createParameterPanel() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Creates the parameter panel.

createPreConcatenatedAffineTransform(Graphics2D) - Method in class chemaxon.struc.graphics.MTextBoxTransformation

createReaction(MoleculeGraph, Point3D[]) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

createReaction(Molecule, Point3D[], int) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

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

Creates a recognizer module.

createRecordReader(MolInputStream, String) - Method in class chemaxon.formats.MFileFormat

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

Visibility will be restricted, no replacement method will be provided.

createRecordReader(InputStream, String) - Static method in class chemaxon.formats.MFileFormatUtil

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

For in-house use only. Will be moved.

createRecordReader(InputStream, String, String, String) - Static method in class chemaxon.formats.MFileFormatUtil

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

For in-house use only. Will be moved.

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 chemaxon.calculations.gui.CalculatorPluginDisplay

createRgComponentIterator() - Method in class chemaxon.struc.IteratorFactory

Deprecated.

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.core.calculations.clean.CleanUtil

Creates a rotation transformation about a bond.

createRxnComponentIterator() - Method in class chemaxon.struc.IteratorFactory

Deprecated.

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.core.calculations.clean.CleanUtil

Creates an empty array for the atomic coordinates of a structure.

createScalar(String, String) - Static method in class chemaxon.formats.MPropHandler

Creates a scalar property.

createScalar(String, String, ProgressMonitor) - Static method in class chemaxon.formats.MPropHandler

Creates a scalar property.

createScalarXSD(String, String) - Static method in class chemaxon.formats.MPropHandler

Creates a scalar property from the XSD type.

createServiceHandler() - Method in class chemaxon.calculations.services.HttpServiceDescriptor

createServiceHandler() - Method in class chemaxon.calculations.services.JsonServiceDescriptor

createServiceHandler() - Method in class chemaxon.calculations.services.LocalServiceDescriptor

createServiceHandler() - Method in class chemaxon.calculations.services.ServiceDescriptor

Creates a new service handler for this descriptor.

createSgroup(Molecule, SgroupType) - Static method in class chemaxon.struc.SgroupFactory

Creates an Sgroup with consistent sgroup type and dynamic object type.

createSgroupIterator() - Method in class chemaxon.struc.IteratorFactory

Deprecated.

Constructs an s-group iterator for the specified molecule of the factory.

createSpacePanel(Molecule[]) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Creates space panel with given molecules, creates colored surface to each molecule.

createStandardizedMolecule(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin

Creates standardized molecule, the original input molecule is cloned.

createStandardizedMolecule(Molecule) - Method in class chemaxon.calculations.ResonancePlugin

Creates standardized molecule, the original input molecule is cloned.

createStandardizedMolecule(Molecule) - Method in class chemaxon.calculations.TautomerPlugin

Creates standardized molecule, the original input molecule is cloned.

createStatistics - Variable in class chemaxon.descriptors.MDGenerator

indicates if statistical data has to be gathered during generation

createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil

Creates a sub-panel with a title.

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

Creates GridBagConstraints for the top left component.

createUserDefined(String, String, String, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, String, long) - Static method in class chemaxon.formats.MFileFormat

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

The support of user-defined formats will be removed.

createUserDefined(String, List<String>, List<String>, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, Map<String, Integer>, long) - Static method in class chemaxon.formats.MFileFormat

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

The support of user-defined formats will be removed.

createViewPanel(Molecule[]) - Method in class 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 chemaxon.calculations.gui.CalculatorPluginDisplay

Creates view panel with given molecules, places molecule properties in formatted texts.

CRITICAL_ERROR_MSG - Static variable in class chemaxon.calculations.CalculatorPlugin

Critical error message.

cross(Point3D, Point3D) - Static method in class chemaxon.struc.Point3D

Calculates the cross product of the two vectors

CROSSED - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type

Crossed double bond type

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

Represents that crossed double bonds have been 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

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

Cs - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Cs.

CSMDL_IN - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.

CSMOL_OUT - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed Molfiles and Rgfiles.

CSRDF - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed RDfiles.

CSRXN_OUT - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed Rxnfiles.

CSSDF_OUT - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Compressed SDfiles.

cssr - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes

CSSR - Enum constant in enum class chemaxon.search.api.options.SetOfSmallestRingsOption

Complete set of smallest rings.

CSV - Static variable in class chemaxon.formats.MFileFormat

ctab - Variable in class chemaxon.struc.MoleculeGraph

Connection table.

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.struc.PeriodicTable

Atomic number of the element Cu.

currentBond - Variable in class chemaxon.struc.IteratorFactory.NeighbourIterator

Deprecated.

Current bond pointer of the iterator.

currentMetricIndex - Variable in class chemaxon.descriptors.MDParameters

index of the parametrized metric currently in use

cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Move the cursor down.

cursorLeft(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorRight(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorToRowEnd(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorToRowStart(boolean) - Method in class chemaxon.struc.graphics.MTextBox

cursorUp(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Moves the cursor up.

CUSTOM_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

custom name property

CustomDescriptor - Class in chemaxon.descriptors

The CustomDescriptor class implements a generic molecular descriptor class which supports third party or use defined descriptors.

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

Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.

CustomDescriptor(int, int) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.

CustomDescriptor(CDParameters) - Constructor for class chemaxon.descriptors.CustomDescriptor

Creates a new instance of CustomDescriptor according to the parameters given.

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

Copy constructor.

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

Creates a new instance of CustomDescriptor according to the parameters given.

CustomFunction - Interface in chemaxon.chemterms

Base interface for custom Chemical Terms functions.

CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "customizationEnabled".

customMatching(McsCustomMatcherFactory) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder

Sets the factory to be used to create a custom matcher.

CXON - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Object Notation.

CXSMARTS - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Extended SMARTS.

CXSMILES - Static variable in class chemaxon.formats.MFileFormat

Chemaxon Extended SMILES.

cyclomaticNumber() - Method in class chemaxon.core.calculations.TopologyAnalyzer

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 - Enum constant in enum class chemaxon.rendering.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 - Enum constant in enum class chemaxon.struc.SgroupType
DataExclusionList(String) - Constructor for class chemaxon.checkers.AttachedDataChecker.DataExclusionList
DataSgroup - Class in chemaxon.struc.sgroup: Data S-group.
DataSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.DataSgroup: Creates a Data S-group with the specified parent.
DataSgroup(DataSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.DataSgroup: Copy constructor.
DataSgroup(DataSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.DataSgroup: Copy constructor.
DataSgroupCheckerResult - Class in chemaxon.checkers.result: A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.
DataSgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DataSgroupCheckerResult: Constructor which initialize all the properties.
date() - Element in annotation interface chemaxon.common.annotations.SubjectToRemoval
DAYLIGHT_DOWNWEDGE_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Daylight style down wedge orientation flag.
DAYLIGHT_DOWNWEDGE_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Daylight style down wedge orientation.
Db - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Db.
DBS_ALL - Static variable in interface chemaxon.struc.StereoConstants: Double bond stereo checking for all double bonds.
DBS_MARKED - Static variable in interface chemaxon.struc.StereoConstants: Double bond stereo checking for marked double bonds only.
DBS_NONE - Static variable in interface chemaxon.struc.StereoConstants: No double bond stereo checking.
DEAROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph: General dearomatization.
DEAROM_HUCKELCHECK - Static variable in class chemaxon.struc.MoleculeGraph: Dearomatization method that dearomatizes a molecule only if it fulfills the Huckel's rule.
DEAROM_HUCKELCHECK_EX - Static variable in class chemaxon.struc.MoleculeGraph: Dearomatization method that dearomatizes a molecule only if it fulfills 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: Standardizer action that dearomatizes the molecule.
DearomatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DearomatizeAction: Initializes the action
DearomatizeFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which converts the aromatic rings in the molecule into Kekule representation.
DearomatizeFixer() - Constructor for class chemaxon.fixers.DearomatizeFixer
DEBUG - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "debug".
Debye - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit: Debye unit.
DEBYE_TO_EA - Static variable in class chemaxon.calculations.dipole.DipoleResult: Debye to eA conversion upon multiplication.
decForm - Variable in class chemaxon.descriptors.MDParameters: to format floating point output
Decomposition - Class in chemaxon.search: Class storing RgroupDecomposition results.
Decomposition(Molecule, Molecule, int[][], Molecule[], Molecule) - Constructor for class chemaxon.search.Decomposition: Constructor.
decompress(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Uncompresses input byte array and stores the uncompressed array in params.data.
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.
decValenceProp() - Method in class chemaxon.struc.MolAtom: Decrements the value of the valence property.
DEF_IONIC_STRENGTH - Static variable in class chemaxon.calculations.PkaPlugin: The default ionic strength of the pKa calculation models (small and large).
DEF_IONICSTRENGTH - Static variable in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.DEF_IONIC_STRENGTH instead. This constant will be removed in a future release.
DEF_MAX_IONS - Static variable in class chemaxon.calculations.PkaPlugin: The default value of the number of ionizable atoms to consider.
DEF_MAXIONS - Static variable in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.DEF_MAX_IONS instead. This constant will be removed in a future release.
DEF_TEMPERATURE - Static variable in class chemaxon.calculations.PkaPlugin: The default temperature in Kelvins.
DEF_TOLERANCE - Static variable in class chemaxon.reaction.Reactor: The default tolerance.
DEFAULT - Enum constant in enum class chemaxon.descriptors.MetricsType
DEFAULT - Enum constant in enum class chemaxon.search.api.options.HaltOnErrorOption: Default error handling.
DEFAULT - Static variable in class chemaxon.formats.Encoding: The system's default encoding.
DEFAULT - Static variable in class chemaxon.standardizer.StandardizerActionFactory: default factory id
DEFAULT - Static variable in class chemaxon.struc.graphics.MTextAttributes: Default attributes object.
DEFAULT - Static variable in class chemaxon.struc.ValenceCheckOptions: The default options: both ValenceCheckOptions.isLocalAromatic() and ValenceCheckOptions.isTraditionalNitrogensAllowed() return true.
DEFAULT - Static variable in class chemaxon.structurechecker.CheckerFixerFactory: default factory id
DEFAULT_ARROW_HEAD_LENGTH - Static variable in class chemaxon.struc.graphics.MPolyline: Default arrow head length.
DEFAULT_ARROW_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline: Default arrow head width.
DEFAULT_ASYMMETRY_FACTOR - Static variable in class chemaxon.descriptors.MDParameters
DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.CFParameters
DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.RFParameters
DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.CFParameters
DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.RFParameters
DEFAULT_CACHE_SIZE - Static variable in class chemaxon.reaction.mapper.AutoMapper: default cache size
DEFAULT_CACHE_SIZE_PROPERTY - Static variable in class chemaxon.reaction.mapper.AutoMapper: cache size property key
DEFAULT_CONFIG_FILE - Static variable in class chemaxon.calculations.gui.PluginFactory: The default config file name.
DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.standardizer.StandardizerActionFactory: Chemaxon's default standardizer action configuration path
DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.structurechecker.CheckerFixerFactory: Chemaxon's default checker configuration path
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.standardizer.StandardizerActionFactory: Chemaxon's default standardizer action configuration file schema path
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlReader: The default location of Chemaxon standard checker runner configuration
DEFAULT_DIAMETER - Static variable in class chemaxon.descriptors.ECFPParameters
DEFAULT_DISSIMILARITY_THRESHOLD - Static variable in interface chemaxon.search.api.SearchConstants: Default threshold value for similarity search.
DEFAULT_EQUILIBRIUM_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline: Default equilibrium head width.
DEFAULT_FUZZINESS_FACTOR - Static variable in class chemaxon.descriptors.PFParameters
DEFAULT_FUZZY_CUTOFF - Static variable in class chemaxon.descriptors.PFParameters
DEFAULT_FUZZY_LOWER_BOUND - Static variable in class chemaxon.descriptors.PFParameters
DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.CFParameters: default values for parameters
DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.ECFPParameters: default values for parameters
DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.RFParameters: default values for parameters
DEFAULT_LOWER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters: default values for parameters
DEFAULT_MAX_CONSIDERED_RING_SIZE - Static variable in class chemaxon.search.mcs.McsSearchOptions: Default value for McsSearchOptions.Builder.maxConsideredRingSize(int).
DEFAULT_MAX_CROSS_SIZE - Static variable in class chemaxon.struc.graphics.MPolyline: Default maximum cross size.
DEFAULT_OPTIONS - Static variable in interface chemaxon.struc.sgroup.Expandable: Default expansion/contraction options.
DEFAULT_OUTPUT_PRECISION - Static variable in class chemaxon.descriptors.MDParameters
DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.HBParameters: default values for parameters
DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.LDParameters
DEFAULT_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor: the default priority value
DEFAULT_RANDOM_SEED - Static variable in class chemaxon.search.mcs.MaxCommonSubstructure: Default random seed.
DEFAULT_RECURSION_LEVEL - Static variable in class chemaxon.search.util.HashCode
DEFAULT_RESOLUTION - Static variable in class chemaxon.descriptors.PFParameters: default values
DEFAULT_RETROSYNTHETIC_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline: Default retrosynthetic head width.
DEFAULT_RLOGIC_RANGE - Static variable in class chemaxon.struc.RgMolecule: Default R-logic range.
DEFAULT_SALT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.actions.StripSaltsAction: Default salt dictionary file path.
DEFAULT_SAMPLING_ACCURACY - Static variable in class chemaxon.alignment.AtropIsomerDetector: Default for parameter AtropIsomerDetector.setSamplingAccuracy(int).
DEFAULT_SAVE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "defaultSaveFormat".
DEFAULT_SCALE_FACTOR - Static variable in class chemaxon.descriptors.MDParameters: constants, default parameter values
DEFAULT_SEARCHTYPE - Static variable in interface chemaxon.search.api.SearchConstants: Default search type equals SUBSTRUCTURE.
DEFAULT_SERVICE_CONFIGURATION_PATH - Static variable in class chemaxon.calculations.services.ServiceDescriptorTools: Path to default services configuration xml
DEFAULT_SOLVENT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.actions.RemoveSolventsAction: Default solvent dictionary file path.
DEFAULT_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.StandardizerConfigurationReader: path to default standardizer action configuration list
DEFAULT_STEP_SIZE - Static variable in class chemaxon.descriptors.scalars.LDParameters
DEFAULT_SUPERSCRIPT_DELTAY - Static variable in class chemaxon.struc.graphics.MTextAttributes: Default value of the y shift attribute in superscripts
DEFAULT_SUPERSCRIPT_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes: Default value of the font scale attribute in superscripts
DEFAULT_SUPERSCRIPT_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes: Default value of the superscript level attribute in superscripts
DEFAULT_TAG_NAME - Static variable in class chemaxon.chemterms.ChemTermsEvaluator: Default SDFile tag to store the evaluation result.
DEFAULT_TAG_NAME - Static variable in class chemaxon.descriptors.pharmacophore.PMapper: Default SDFile tag to store the Pharmacophore Map.
DEFAULT_THICKNESS - Static variable in class chemaxon.struc.graphics.MPolyline: Default line thickness.
DEFAULT_TIMEOUT_LIMIT - Static variable in class chemaxon.search.api.options.SearchOptions
DEFAULT_TOOL - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "defaultTool".
DEFAULT_UNGROUP - Static variable in class chemaxon.struc.Molecule: Do not ungroup and do not expand S-group's children.
DEFAULT_UPPER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters
DEFAULT_USER_CHECKER_FILENAME - Static variable in interface chemaxon.structurechecker.configuration.StructureCheckerConfigurationReader: Default user-defined checker file name for fallback.
DEFAULT_USER_SERVICE_CONFIGURATION_FILENAME - Static variable in class chemaxon.calculations.services.ServiceDescriptorTools: name of default user service configuration file
DEFAULT_VALUE - Static variable in class chemaxon.struc.BondTable: The default (null) value in the matrix.
DEFAULT_WEIGHT - Static variable in class chemaxon.descriptors.MDParameters
DEFAULT_XML_CONFIG - Static variable in class chemaxon.descriptors.PFParameters
defaultCategories() - Static method in class chemaxon.calculations.solubility.SolubilityCategories: Creates default categories.
defaultChecker() - Static method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Creates a heavy atom limit checker using the default configuration.
DefaultExternalStructureCheckerResult - Class in chemaxon.checkers.result: This descendant of DefaultStructureCheckerResult also implements the ExternalStructureCheckerResult interface thus providing a default implementation base class for external structure checkers' results.
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult: Constructor which initialize all the properties.
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult: Deprecated.
use DefaultExternalStructureCheckerResult(StructureChecker, List, List, Molecule, String, String, String, String, String, Icon, int)
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult: Constructor which initialize all the properties.
defaultLimit() - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Returns the value of the defaultLimit record component.
DefaultSolubilityCategory - Enum Class in chemaxon.calculations.solubility: Default solubility categories.
DefaultStructureCheckerResult - Class in chemaxon.checkers.result: This class is the default implementation of StructureCheckerResult
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult: Deprecated.
use DefaultStructureCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) instead
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult: Constructor which initialize all the properties.
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult: Constructor which initialize all the properties.
defaultWeight - Variable in class chemaxon.descriptors.MDParameters: value for all missing weight parameters
deleteAllUserComparators() - Method in class chemaxon.search.api.options.SearchOptions: Deletes all comparator added by the user.
deleteChar() - Method in class chemaxon.struc.graphics.MTextBox: Removes the character under the cursor.
deleteCharBackward() - Method in class chemaxon.struc.graphics.MTextBox: Removes the character before the cursor (backspace).
deleteUserComparator(MolComparator) - Method in class chemaxon.search.api.options.SearchOptions: Deletes a given user defined comparator if found.
density - Variable in class chemaxon.descriptors.MDGenerator
DENY_IF_NOT_SPECIFIED - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColorNotSpecifiedCase
description() - Method in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory
description() - Method in class chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
description() - Method in interface chemaxon.calculations.solubility.SolubilityCategory: Description.
description() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the description of the checker
description() - Element in annotation interface chemaxon.fixers.FixerInfo: Returns the description of the fixer.
description() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the description of the action
DESCRIPTION - Static variable in class chemaxon.calculations.services.ServiceDescriptor: Property key for Service description as String
DESCRIPTION - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: description of checker
DESCRIPTION - Static variable in class chemaxon.fixers.StructureFixerDescriptor: description of fixer
DESCRIPTION - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: description of action
descriptor() - Method in record class chemaxon.core.calculations.stereo.CIPStereoCalculator.CIPStereoCalculatorResult: Returns the value of the descriptor record component.
DESCRIPTOR_URI - Static variable in class chemaxon.calculations.services.JsonServiceDescriptor: Property key for Service descriptor as String
DescriptorGenerator - Class in chemaxon.descriptors: Simple class for generating molecular descriptors (fingerprints).
DescriptorGenerator(String) - Constructor for class chemaxon.descriptors.DescriptorGenerator: Creates a new instance using the given descriptor type with its default configuration parameters.
DescriptorGenerator(String, String) - Constructor for class chemaxon.descriptors.DescriptorGenerator: Creates a new instance using the given descriptor type with the given XML configuration.
descrType - Variable in class chemaxon.descriptors.CDParameters: descriptor type
descrValue - Variable in class chemaxon.descriptors.ScalarDescriptor: descriptor value
desiredLength(int, int, int, int) - Static method in class chemaxon.struc.MolBond: Desired length of a bond between two atoms in Angstroms.
destroySketcher() - Method in class chemaxon.marvin.beans.MViewPane: Closes all detached sketcher windows.
DETACH - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "detach".
DETACHABLE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "detachable".
determinant() - Method in class chemaxon.struc.Transform3D: Computes the determinant of the matrix.
determinant2D() - Method in class chemaxon.struc.Transform3D: Computes the determinant of the 2D matrix.
determineArrowDistance(double, double, double, Point3D[]) - Static method in class chemaxon.struc.RxnMolecule: Project the point (x,y,z) to the line of the reaction arrow 'ar'.
determinePosition(Graphics, Point3D, boolean) - Method in class chemaxon.struc.graphics.MTextBox: Determines the character index based on the passed view coordinate.
determineType(double, double, double) - Method in class chemaxon.struc.RxnMolecule: Determines whether a point should be in a reactant, in a product or in an agent.
determineType(double, double, double, Point3D[]) - Static method in class chemaxon.struc.RxnMolecule: Determines whether a point should be in a reactant, in a product or in an agent.
DICE - Enum constant in enum class chemaxon.descriptors.MetricsType
DihedralRotator - Class in chemaxon.alignment: Rotates a dihedral in a 3D molecule
DihedralRotator(Molecule) - Constructor for class chemaxon.alignment.DihedralRotator: creates a rotator object
DihedralScanResult - Class in chemaxon.alignment: Results of a dihedral scan.
DihedralScanResult(DihedralScanResult.BondInfo) - Constructor for class chemaxon.alignment.DihedralScanResult: Construct for a dihedral.
DihedralScanResult.BondInfo - Class in chemaxon.alignment: Encapsulates bond info.
DihedralScanResult.ScanStep - Class in chemaxon.alignment: One step in a dihedral scan.
DIM_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Colors are dim if enabled.
DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph: Dimension bits in flags.
DIPOLE - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
DipoleCalculator - Class in chemaxon.calculations.dipole: Calculates the components of the dipole vector.
DipoleCalculator.Builder - Class in chemaxon.calculations.dipole: Builder class for dipole moment calculation.
DipoleResult - Class in chemaxon.calculations.dipole: Dipole moment calculation result.
DipoleResult(double, double, double, DipoleResult.Unit, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult: Constructor.
DipoleResult(double, double, double, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult: Constructor.
DipoleResult.Unit - Enum Class in chemaxon.calculations.dipole: Dipole moment units.
dirty - Variable in class chemaxon.search.api.options.SearchOptions: This flag is set to true whenever any of the options change.
DISABLE_ACCELERATOR - Static variable in class chemaxon.marvin.common.MAction: Disables the keyboard shortcut while still displaying its name in the menu.
DISABLE_SPECIAL_NODES - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "disableSpecialNodes".
disableNewEmfGenerator() - Static method in class chemaxon.marvin.util.ImageExportUtil: Disables the new .NET based EMF generator.
DisconnectMetalAtomsAction - Class in chemaxon.standardizer.actions: Standardizer action that disconnects metal atoms from other atoms of the molecule.
DisconnectMetalAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DisconnectMetalAtomsAction: Initializes the disconnect metal atoms action
displayInMarvinSpace - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: Display in MarvinSpace is enabled or not.
DispOptConsts - Interface in chemaxon.rendering.constants: Display option masks and offsets.
DISSIMILARITY - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: The dissimilarity score is shown and stored in the MPropertyContainer of the Molecule.
DISSIMILARITY_PROPERTY_NAME - Static variable in interface chemaxon.search.api.SearchConstants: Name of the mrv/sdf property which stores the dissimilarity values.
distance(Point3D) - Method in class chemaxon.struc.Point3D: Calculates the distance between two points.
distance2D(Point3D) - Method in class chemaxon.struc.Point3D: Calculates the distance between two points in the XY plane.
DistanceBasedMetalloceneFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which converts incorrectly drawn metallocenes into multicenter-based coordinate bond representation.
DistanceBasedMetalloceneFixer() - Constructor for class chemaxon.fixers.DistanceBasedMetalloceneFixer
distanceCount(int, int) - Method in class chemaxon.core.calculations.TopologyAnalyzer: Counts the given value in a row of the distance matrix.
distanceDegree(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
distanceFrom(double, double) - Method in class chemaxon.struc.MObject: Gets the 2D distance from the specified point.
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets the 2D distance from the specified point.
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.graphics.MEFlow
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets the 2D distance from the specified point.
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.graphics.MPolyline: Gets the 2D distance from the specified point.
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.graphics.MRectangle: Gets the 2D distance from the specified point.
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.MObject: Gets the 2D distance from the specified point.
distanceFrom(double, double, Transform3D) - Method in class chemaxon.struc.MPoint: Gets the 2D distance from the specified point.
distanceFrom(MoleculeGraph, double, double, Transform3D) - Static method in class chemaxon.struc.graphics.MChemicalStruct: Gets the 2D distance from the specified point.
DIVALENT - Enum constant in enum class chemaxon.struc.Radical: Divalent radical center.
DIVALENT_SINGLET - Enum constant in enum class chemaxon.struc.Radical: Divalent radical center with singlet electronic configuration.
DIVALENT_TRIPLET - Enum constant in enum class chemaxon.struc.Radical: Divalent radical center with triplet electronic configuration.
DNA - Static variable in class chemaxon.formats.MFileFormat: DNA sequence.
DO_NOT_FIX - Enum constant in enum class chemaxon.checkers.FixMode: on problem do nothing
doAction(ActionEvent) - Method in class chemaxon.marvin.common.MAction: Performs a custom action.
DOC_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: name of the principal author(s) of a document.
DOC_CREATION_DATE - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the date on which the document was created.
DOC_LAST_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: name of the last (most recent) author of a document.
DOC_PATENT_ASSIGNEES - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the assignees of the patent, separated by newline characters.
DOC_PATENT_ID - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the patent identifier.
DOC_PATENT_INVENTORS - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the inventors of the patent, separated by newline characters.
DOC_PATENT_IPC - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the IPC classification(s) for the patent, separated by newline characters.
DOC_PATENT_IPCR - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the IPCR classification(s) for the patent, separated by newline characters.
DOC_TITLE - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the title of the document.
docProduced(MDocStorage, MDocument, int) - Method in interface chemaxon.marvin.common.MDocStorage.Listener: Document retrieved from source.
document - Variable in class chemaxon.descriptors.MDParameters: contains the XML document
DOCUMENT - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the file name of the source document.
DocumentAnnotator - Class in chemaxon.naming.document: Generate a chemically annotated HTML view of a document.
DocumentAnnotator(File) - Constructor for class chemaxon.naming.document.DocumentAnnotator: Constructs a DocumentAnnotator to annotate the given document file.
DocumentAnnotator(InputStream) - Constructor for class chemaxon.naming.document.DocumentAnnotator: Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator(InputStream, DocumentAnnotator.DocumentType) - Constructor for class chemaxon.naming.document.DocumentAnnotator: Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator.DocumentType - Enum Class in chemaxon.naming.document: Document type enum for DocumentAnnotator.
DocumentAnnotator.Listener - Interface in chemaxon.naming.document: The interface for a DocumentAnnotator progress event listener.
DocumentAnnotator.ProgressInfo - Class in chemaxon.naming.document: Represents the state of progress during a document annotation process.
DocumentAnnotatorOptions - Class in chemaxon.naming.document: Represents various options regarding how a document should be annotated, both in terms of input and output.
DocumentAnnotatorOptions.Builder - Class in chemaxon.naming.document: A builder for DocumentAnnotatorOptions, allowing for options to be built using a fluent interface.
DocumentAnnotatorOptions.ImageFormat - Enum Class in chemaxon.naming.document: A list of supported image formats for popups in the annotated document.
DocumentToStructure - Class in chemaxon.naming.document: A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files.
DocumentToStructure() - Constructor for class chemaxon.naming.document.DocumentToStructure
DONOR_SIGN - Static variable in class chemaxon.calculations.HBDAPlugin: Donor sign displayed in GUI.
DONR - Static variable in class chemaxon.alignment.Pharmacophore3D
DONT_REMOVE_LAST_COMPONENT_KEY - Static variable in class chemaxon.standardizer.actions.StripSaltsAction: Property key for "Don't Remove Last Component" option
DOODLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains serious scanning or drawing issues, typically as a result of optical recognition process
doPaste() - Method in class chemaxon.marvin.beans.MarvinPane: Invokes Paste actions.
doPaste() - Method in class chemaxon.marvin.beans.MSketchPane: Invokes Paste action.
doPaste() - Method in class chemaxon.marvin.beans.MViewPane: Invokes Paste action.
doSetSetSeqs(Molecule[], int, String) - Method in class chemaxon.marvin.common.MDocStorage
DOT_DISCONNECTED_FRAGMENTS - Enum constant in enum class chemaxon.calculations.elemental.FormulaGenerationRule: Dot-disconnected molecular formula of a multifragment molecule.
For example: C7H5O2.Na for sodium benzoate.
DOTDISCONNECTED_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "dotdisconnectedformalchargeformula".
DOTDISCONNECTED_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "dotdisconnectedformula".
DOTDISCONNECTED_ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "dotdisconnectedisotopeformalchargeformula".
DOTDISCONNECTED_ISOTOPE_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "dotdisconnectedisotopeformula".
dotDisconnectedFormula() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the dot-disconnected molecular formula of a multifragment molecule.
dotDisconnectedIsotopeFormula() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the dot-disconnected isotope formula of a multifragment molecule.
dotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the dot-disconnected isotope formula of a multifragment molecule.
DOUBLE - Enum constant in enum class chemaxon.struc.BondType: Double bond type.
DOUBLE - Static variable in class chemaxon.struc.MolBond: Double bond type.
DOUBLE_BOND - Static variable in class chemaxon.calculations.StereoisomerPlugin: Deprecated.
DOUBLE_BOND_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains either double bonds which are not valid
DOUBLE_OR_AROMATIC - Enum constant in enum class chemaxon.struc.BondType: Double or aromatic query bond type.
DOUBLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond: Double or aromatic query bond type.
DoubleBondStereoErrorChecker - Class in chemaxon.checkers: Detects invalid either double bonds.
DoubleBondStereoErrorChecker() - Constructor for class chemaxon.checkers.DoubleBondStereoErrorChecker: Default constructor
doubleStringWidth(String, MFont, FontMetrics, Graphics) - Method in class chemaxon.struc.graphics.MTextDocument.Section: Gets the width of a string as a floating point number.
doubleValue() - Method in class chemaxon.struc.prop.MDoubleProp: Gets the double floating point value.
DOWN - Static variable in class chemaxon.struc.MolBond: Single bond down flag.
DOWN_WEDGE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "downWedge".
DOWNWEDGE_MODES - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Wedge bond display conventions.
DOWNWEDGE_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Down wedge orientation offset in display option flags.
DRAGGABLE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "draggable".
dropBinaryVector() - Method in class chemaxon.descriptors.ECFP: Drops the binary vector storage.
Ds - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ds.
DT_FORMATTED - Static variable in class chemaxon.struc.sgroup.DataSgroup: Field type: formatted.
DT_NUMERIC - Static variable in class chemaxon.struc.sgroup.DataSgroup: Field type: numeric.
DT_TEXT - Static variable in class chemaxon.struc.sgroup.DataSgroup: Field type: text.
DT_UNSPEC - Static variable in class chemaxon.struc.sgroup.DataSgroup: Field type: unspecified.
DT_URL - Static variable in class chemaxon.struc.sgroup.DataSgroup: Field type: url.
DUPLICATE - Static variable in interface chemaxon.search.api.SearchConstants: Duplicate search (formerly called perfect).
Dy - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Dy.
DYNAMIC_PKA_PREFIX - Static variable in class chemaxon.calculations.PkaPlugin: pKa's prefix (acidic/basic) does depend on the submitted microstate
DynamicArgument<CT,RT> - Class in chemaxon.calculations.services: ServiceArguments implementing this interface should support automatic evaluation of arguments before service call based on context.
DynamicArgument() - Constructor for class chemaxon.calculations.services.DynamicArgument
DynamicArgument(String) - Constructor for class chemaxon.calculations.services.DynamicArgument
DYNAMICpKaPREFIX - Static variable in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.DYNAMIC_PKA_PREFIX instead. This constant will be removed in a future release.

E

E - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue
E - Enum constant in enum class chemaxon.struc.EZConfiguration
E_OR_UNSPEC - Enum constant in enum class chemaxon.struc.EZConfiguration
E_OR_Z - Enum constant in enum class chemaxon.struc.EZConfiguration
E_SINK - Static variable in class chemaxon.struc.graphics.MEFlow: Electron sink.
E_SOURCE - Static variable in class chemaxon.struc.graphics.MEFlow: Electron source.
eA - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit: Atomic charge unit * Angstrom.
eccentricity(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
ECFP - Class in chemaxon.descriptors: The ECFP class implements Extended-Connectivity Fingerprints (ECFPs) as a type of MolecularDescriptors.
ECFP() - Constructor for class chemaxon.descriptors.ECFP: Creates a new, empty instance of ECFP without allocating internal storage.
ECFP(ECFP) - Constructor for class chemaxon.descriptors.ECFP: Copy constructor.
ECFP(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFP: Creates a new instance of ECFP according to the parameters given.
ECFP(String) - Constructor for class chemaxon.descriptors.ECFP: Creates a new instance of ECFP according to the parameters given.
ECFPFeature - Class in chemaxon.descriptors: Class for representing the substructural features of ECFP fingerprints.
ECFPFeatureLookup - Class in chemaxon.descriptors: Class for retrieving the substructural features of ECFP fingerprints.
ECFPFeatureLookup() - Constructor for class chemaxon.descriptors.ECFPFeatureLookup: Creates a new ECFPFeatureLookup instance with the default ECFP configuration parameters.
ECFPFeatureLookup(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup: Creates a new ECFPFeatureLookup instance with the given ECFP configuration parameters.
ECFPFeatureLookup(String) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup: Creates a new ECFPFeatureLookup instance with the given ECFP configuration parameters.
ECFPGenerator - Class in chemaxon.descriptors: The ECFPGenerator class generates ECFP fingerprints of molecular graphs.
ECFPGenerator() - Constructor for class chemaxon.descriptors.ECFPGenerator: Creates a new instance of ECFPGenerator, which can be used to generate ECFP fingerprints for an arbitrary number of molecules.
ECFPParameters - Class in chemaxon.descriptors: Manages ECFP fingerprint parameters.
ECFPParameters() - Constructor for class chemaxon.descriptors.ECFPParameters: Creates an empty object.
ECFPParameters(File) - Constructor for class chemaxon.descriptors.ECFPParameters: Creates a new object based on a given configuration file.
ECFPParameters(String) - Constructor for class chemaxon.descriptors.ECFPParameters: Creates a new object based on a given configuration string.
EDITABLE - Static variable in class chemaxon.marvin.beans.MViewPane: Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinView in a new window.
EDITABLE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "editable".
EDITOR_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: editor class name property of checker
EDITOR_CLASS_NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: editor class name property of standardizer action
editorClassName() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the name of the checker's editor
editorClassName() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the editor class name of the action
electronegOf(int) - Static method in class chemaxon.struc.MolAtom: Gets 10 times the electronegativity value for the specified element.
electronRadious - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
ELEMENT_COUNT - Static variable in class chemaxon.struc.MolAtom: Number of elements in the periodic table
ELEMENT_COUNT - Static variable in class chemaxon.struc.PeriodicTable: Number of elements in the periodic table
ElementalAnalysis - Class in chemaxon.calculations.elemental: Calculates molecular formula, mass, MS mass and composition.
ElementalAnalysisFactory - Class in chemaxon.calculations.elemental: Provides static factory methods for creating ElementalAnalysis instances from various input types.
ElementalAnalysisPlugin - Class in chemaxon.calculations: Calculates molecular formula, mass, MS mass and composition.
ElementalAnalysisPlugin() - Constructor for class chemaxon.calculations.ElementalAnalysisPlugin
ElementalAnalysisPlugin.ResultType - Enum Class in chemaxon.calculations: Represents the different result types of the elemental analysis plugin.
ElementalAnalyzer - Class in chemaxon.core.calculations: Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyzer() - Constructor for class chemaxon.core.calculations.ElementalAnalyzer
ELEMENTS - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "elements".
EMF - Static variable in class chemaxon.formats.MFileFormat: Windows Enhanced Metafiles.
EMPTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule is empty
EMPTY - Static variable in class chemaxon.chemterms.ConstantTable: An empty constant table.
EMPTY - Static variable in class chemaxon.struc.MolAtom: Empty atom type.
EmptyStructureChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting structures having no atoms.
EmptyStructureChecker() - Constructor for class chemaxon.checkers.EmptyStructureChecker: Default constructore
ENABLED_2D_VIEWER - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "2dviewerEnabled".
ENABLED_3D_VIEWER - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "3dviewerEnabled".
enableDefaultHeavyAtomLimits() - Static method in interface chemaxon.calculations.api.TaggedCalculator: Sets the global input checker to one that uses the default heavy atom limits.
enableRequiredHLBValue(boolean) - Method in class chemaxon.calculations.HLBPlugin: Sets whether the required HLB value (RHLB) is wanted or not.
enclosesPoint(double, double) - Method in class chemaxon.struc.graphics.MBracket: Checks if a specified point is enclosed by this bracket.
encode(MFont, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes: Returns the string representation of the attributes.
encoding - Variable in class chemaxon.formats.PositionedInputStream: The encoding.
Encoding - Class in chemaxon.formats: File encoding information.
Encoding() - Constructor for class chemaxon.formats.Encoding: Default constructor for serialization.
Encoding(String, int, ByteOrder) - Constructor for class chemaxon.formats.Encoding: Creates an Encoding for the specified name, word length and byte order.
END_CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: key of the molecule property which contains the ending character offset since the beginning of the document, for text formats (html, xml, txt).
endElement(String, String, String) - Method in class chemaxon.naming.document.XmlToHtmlConverter
endGrabLines() - Method in class chemaxon.formats.PositionedInputStream: Deprecated, for removal: This API element is subject to removal in a future version.
endHourglass() - Method in class chemaxon.marvin.beans.MarvinPane: Changes the hourglass cursor back to normal at the end of a long operation.
ENDO - Static variable in interface chemaxon.struc.StereoConstants: Non-CIP stereodescriptor, endo (relative configuration).
endReuse(int) - Method in class chemaxon.struc.Molecule: End reusing atoms.
endReuse(int) - Method in class chemaxon.struc.RgMolecule: End reusing atoms.
endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument: Tests whether the document ends with the specified character.
endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Tests whether this text portion ends with the specified character.
EnhancedStereo - Class in chemaxon.calculations.stereo.stereocenters: Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.
EnhancedStereo(EnhancedStereoType) - Constructor for class chemaxon.calculations.stereo.stereocenters.EnhancedStereo: Creates enhanced stereo representation.
EnhancedStereo(EnhancedStereoType, int) - Constructor for class chemaxon.calculations.stereo.stereocenters.EnhancedStereo: Creates enhanced stereo representation.
EnhancedStereoGroup - Class in chemaxon.calculations.stereo.stereocenters: Enhanced stereo descriptor class.
EnhancedStereoGroup(EnhancedStereo, List<TetrahedralStereoCenter>) - Constructor for class chemaxon.calculations.stereo.stereocenters.EnhancedStereoGroup: Creates enhanced stereo group.
EnhancedStereoType - Enum Class in chemaxon.calculations.stereo.stereocenters: Enhanced stereo flags.
enqueueUpdate() - Method in class chemaxon.marvin.common.TableSupport: Enqueues an update task.
ensureValidity() - Method in class chemaxon.struc.graphics.MElectronContainer
ENTRY_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringReader: Configuration entry separator token of the action string
ENTRY_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: Configuration entry separator token of the action string
ENTRY_SEPARATOR - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: Configuration entry separator token of the action string
ENUMERATION - Enum constant in enum class chemaxon.search.api.options.TautomerSubstructureMode
EPS - Static variable in class chemaxon.formats.MFileFormat: Encapsulated PostScript vector image format.
EPSILON - Static variable in class chemaxon.calculations.CalculatorPlugin: The microspecies is ignored if its distribution is less than EPSILON for all pH values.
EPSILON - Static variable in class chemaxon.calculations.HBDAPlugin
equals(Encoding) - Method in class chemaxon.formats.Encoding: Tests whether two encodings are equal.
equals(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes: Tests whether two attributes objects equal or not.
equals(Transform3D, double) - Method in class chemaxon.struc.Transform3D
equals(Object) - Method in record class chemaxon.calculations.admet.HergActivityPrediction: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class chemaxon.calculations.admet.HergClassPrediction: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class chemaxon.calculations.elemental.FormulaAtom: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class chemaxon.calculations.PkaTrainingResult
equals(Object) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
equals(Object) - Method in class chemaxon.checkers.AbstractStructureChecker
equals(Object) - Method in class chemaxon.checkers.AromaticityErrorChecker
equals(Object) - Method in class chemaxon.checkers.AtomLabels
equals(Object) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
equals(Object) - Method in class chemaxon.checkers.AttachedDataChecker.DataExclusionList
equals(Object) - Method in class chemaxon.checkers.AttachedDataChecker
equals(Object) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
equals(Object) - Method in class chemaxon.checkers.result.AromaticityCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
equals(Object) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.RgroupCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.SgroupCheckerResult
equals(Object) - Method in class chemaxon.checkers.result.SubstructureCheckerResult
equals(Object) - Method in class chemaxon.checkers.StructureCheckerDescriptor
equals(Object) - Method in class chemaxon.checkers.ValencePropertyChecker
equals(Object) - Method in class chemaxon.core.calculations.stereo.AtropStereoDescriptor
equals(Object) - Method in class chemaxon.core.calculations.stereo.AtropStereoIUPACDescriptor
equals(Object) - Method in class chemaxon.core.calculations.stereo.AxialStereoDescriptor
equals(Object) - Method in class chemaxon.core.calculations.stereo.AxialStereoIUPACDescriptor
equals(Object) - Method in record class chemaxon.core.calculations.stereo.CIPStereoCalculator.CIPStereoCalculatorResult: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class chemaxon.core.calculations.stereo.CisTransStereoDescriptor
equals(Object) - Method in class chemaxon.core.calculations.stereo.CisTransStereoIUPACDescriptor
equals(Object) - Method in class chemaxon.core.calculations.stereo.StereoActivePart
equals(Object) - Method in class chemaxon.core.calculations.stereo.TetrahedralStereoDescriptor
equals(Object) - Method in class chemaxon.core.calculations.stereo.TetrahedralStereoIUPACDescriptor
equals(Object) - Method in class chemaxon.fixers.StructureFixerDescriptor
equals(Object) - Method in class chemaxon.formats.Encoding: Tests whether two encodings are equal.
equals(Object) - Method in record class chemaxon.formats.Recognizer.RecognizerResult: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor
equals(Object) - Method in class chemaxon.reaction.AtomIdentifier
equals(Object) - Method in class chemaxon.search.api.SearchHit
equals(Object) - Method in class chemaxon.search.Decomposition: Returns true if this decomposition is equivalent to the specified decomposition.
equals(Object) - Method in class chemaxon.standardizer.actions.GroupDefinition
equals(Object) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
equals(Object) - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm
equals(Object) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.MElectron
equals(Object) - Method in class chemaxon.struc.graphics.MElectronContainer
equals(Object) - Method in class chemaxon.struc.graphics.MFont: Tests whether two font objects equal.
equals(Object) - Method in class chemaxon.struc.graphics.MMidPoint: Two midpoints equal if their parent lines are the same and the polyline point indices also equal.
equals(Object) - Method in class chemaxon.struc.graphics.MRectanglePoint: Two rectangle points equal if their parent rectangles are the same and they are on the same corner or edge.
equals(Object) - Method in class chemaxon.struc.graphics.MTextAttributes: Tests whether two attributes objects equal or not.
equals(Object) - Method in class chemaxon.struc.MPoint: Two points equal if their location equals.
equals(Object) - Method in class chemaxon.struc.Point3D: Two points equal if their coordinates equal.
equals(Object) - Method in class chemaxon.struc.prop.MBooleanProp
equals(Object) - Method in class chemaxon.struc.prop.MByteArrayProp
equals(Object) - Method in class chemaxon.struc.prop.MCollectionProp
equals(Object) - Method in class chemaxon.struc.prop.MDoubleArrayProp
equals(Object) - Method in class chemaxon.struc.prop.MDoubleProp
equals(Object) - Method in class chemaxon.struc.prop.MFontProp
equals(Object) - Method in class chemaxon.struc.prop.MHashProp
equals(Object) - Method in class chemaxon.struc.prop.MHCoords3DProp
equals(Object) - Method in class chemaxon.struc.prop.MIntegerArrayProp
equals(Object) - Method in class chemaxon.struc.prop.MIntegerProp
equals(Object) - Method in class chemaxon.struc.prop.MListProp
equals(Object) - Method in class chemaxon.struc.prop.MMoleculeProp
equals(Object) - Method in class chemaxon.struc.prop.MMoleculeStringProp
equals(Object) - Method in class chemaxon.struc.prop.MObjectProp
equals(Object) - Method in class chemaxon.struc.prop.MStringProp
equals(Object) - Method in class chemaxon.struc.RgroupBridgeId
equals(Object) - Method in class chemaxon.struc.Transform3D
equals(Object) - Method in class chemaxon.struc.ValenceCheckOptions
equalsHead(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Decides whether the head bonds equal the given bonds.
equalsNext(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes: Tests whether the attributes of two neighboring sections equal or not.
equalsTail(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Decides whether the tail bonds equal the given bonds.
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.AtropStereoDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.AtropStereoIUPACDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.AxialStereoDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.AxialStereoIUPACDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in interface chemaxon.core.calculations.stereo.CIPStereoDescriptor: Compares this value to the given other value with respect to the given search mapping.
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.CisTransStereoDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.CisTransStereoIUPACDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.TetrahedralStereoDescriptor
equalsTo(CIPStereoDescriptor, int[]) - Method in class chemaxon.core.calculations.stereo.TetrahedralStereoIUPACDescriptor
equalsTo(Object, int[]) - Method in class chemaxon.core.calculations.stereo.StereoActivePart
EQUILIBRIUM - Static variable in class chemaxon.struc.RxnMolecule: Resonance arrow, the same as the two-headed double reaction arrow.
Er - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Er.
error() - Method in record class chemaxon.calculations.admet.HergActivityPrediction: Returns the value of the error record component.
error() - Method in record class chemaxon.calculations.admet.HergClassPrediction: Returns the value of the error record component.
ERROR - Enum constant in enum class chemaxon.calculations.api.CalculatorLogger.Level
ERROR - Enum constant in enum class chemaxon.checkers.CheckerSeverity: This severity level should be used for StructureChecker implementations that search for serious problems in a Molecule.
ErrorProcessor - Interface in chemaxon.formats: Error processing interface.
ErrorReport - Class in chemaxon.calculations.stereo: Error reporting class.
ErrorReport(AtomSelection, String) - Constructor for class chemaxon.calculations.stereo.ErrorReport: Constructs new error report.
ErrorReport(AtomSelection, String, Optional<? extends StereoCenter>) - Constructor for class chemaxon.calculations.stereo.ErrorReport: Constructs new error report.
errors() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Error reports.
errorType - Variable in class chemaxon.checkers.AbstractStructureChecker: The error type of the current checker.
Es - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Es.
ESCAPE_CHAR - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "escapeChar".
estimateNumRecords() - Method in class chemaxon.calculations.CalculatorPluginMDocSource: Estimates the total number of records.
estimateNumRecords() - Method in class chemaxon.formats.MDocSource: Estimates the total number of records.
estimateNumRecords() - Method in class chemaxon.formats.MolImporter: Estimates the total number of records.
estimateProgress() - Method in interface chemaxon.formats.MoleculeIterator: Estimates the iteration progress.
Eu - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Eu.
euclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the Euclidean distance.
euclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the Euclidean distance.
EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType
evaluate(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Evaluates the expression.
evaluate(CT) - Method in class chemaxon.calculations.services.DynamicArgument: Evaluates the dynamic argument based on context
evaluate(Map<String, String>, List<Object>, ChemTermsContext) - Method in interface chemaxon.chemterms.CustomFunction: Evaluates this function.
evaluate_boolean(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Deprecated, for removal: This API element is subject to removal in a future version.
Use ChemTermsExpression.evaluateBoolean(C) instead.
evaluate_booleans(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Deprecated, for removal: This API element is subject to removal in a future version.
Use ChemTermsExpression.evaluateBooleanArray(C) instead.
evaluate_double(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Deprecated, for removal: This API element is subject to removal in a future version.
Use ChemTermsExpression.evaluateDouble(C) instead.
evaluate_doubles(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Deprecated, for removal: This API element is subject to removal in a future version.
Use ChemTermsExpression.evaluateDoubleArray(C) instead.
evaluateBoolean(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Evaluates the expression and converts the result boolean.
evaluateBooleanArray(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Evaluates the expression and converts the result to boolean[].
evaluateDouble(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Evaluates the expression and converts the result to double.
evaluateDoubleArray(C) - Method in class chemaxon.chemterms.ChemTermsExpression: Evaluates the expression and converts the result to double[].
EVALUATION_ERROR - Static variable in class chemaxon.chemterms.ChemTermsExpression: The evaluation error message.
EVALUATOR_DEFAULTS_FILE - Static variable in class chemaxon.chemterms.ChemTermsEvaluator: Default Function/Plugin settings filename.
EVALUATOR_SCRIPT_FILE - Static variable in class chemaxon.chemterms.ChemTermsEvaluator: Initial script filename.
EVEN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoValue
EVEN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoValue
EVEN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoValue
EVEN - Static variable in class chemaxon.core.calculations.stereo.Stereochemistry
EVERY_WEIGHT_IS_ONE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColorNotSpecifiedCase
EXACT - Static variable in class chemaxon.search.FormulaSearch: Constant value specifying the exact search type.
EXACT_KEY - Static variable in class chemaxon.standardizer.actions.TransformAction: Key of exact for parsing and property change
EXACT_MASS - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "exactmass".
EXACT_SUBFORMULA - Static variable in class chemaxon.search.FormulaSearch: Constant value specifying the exact sub formula search type.
exactMass() - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
exactMass() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.
exactMassPrecision() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the precision of the monoisitopic weight (number of significant decimal digits).
exactQueryAtomMatching(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether generic query atoms should be matched only to atoms of exactly the same type.
exactQueryBondMatching(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether generic query bonds should be matched only to bonds of exactly the same type.
EXCLUDE_KEY - Static variable in class chemaxon.standardizer.AbstractSgroupAction: Key of exclude for parsing and property change
EXCLUDE_XX - Enum constant in enum class chemaxon.search.api.options.TargetHomologyMatchingMode
excludeString - Variable in class chemaxon.standardizer.actions.ContractSgroupsAction
excludeString - Variable in class chemaxon.standardizer.actions.ExpandSgroupsAction
excludeString - Variable in class chemaxon.standardizer.actions.UngroupSgroupsAction
exit() - Method in class chemaxon.marvin.beans.MarvinPane: Closes all windows opened by this MarvinPane and saves user initialization file.
EXO - Static variable in interface chemaxon.struc.StereoConstants: Non-CIP stereodescriptor, exo (relative configuration).
expand(int) - Method in class chemaxon.struc.Sgroup: Sets the state to Sgroup.XSTATE_X or Sgroup.XSTATE_XC.
expand(int) - Method in interface chemaxon.struc.sgroup.Expandable: Expands the S-group.
expand(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Expands this S-group unless it has expandable child s-group because in that case our calculations' behaviour can not be predicted.
expand(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Expands this S-group.
Expandable - Interface in chemaxon.struc.sgroup: Expandable interface for S-groups.
ExpandAction - Class in chemaxon.standardizer.actions: Standardizer action that expands stoichiometry coefficients.
ExpandAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ExpandAction: Initializes the action with parameters
ExpandGroupFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which expands all abbreviated groups in the molecule
ExpandGroupFixer() - Constructor for class chemaxon.fixers.ExpandGroupFixer
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker: This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureChecker: Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BondAngleChecker
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.BracketsChecker: This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker: This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker: This implementation does nothing.
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.OverlappingAtomsChecker
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.OverlappingBondsChecker
expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker: This implementation does nothing.
expandOther(int, Molecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Deprecated.
as of Marvin 6.2. use SuperatomSgroup.expand(int) instead on the S-groups desired to be expanded
expandSgroups() - Method in class chemaxon.struc.Molecule: Expands all S-groups.
expandSgroups(int) - Method in class chemaxon.struc.Molecule: Expands all S-groups.
ExpandSgroupsAction - Class in chemaxon.standardizer.actions: Standardizer action that expands S-groups of the molecule.
ExpandSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ExpandSgroupsAction: Initializes the action
EXPLICIT_H - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that explicit hydrogens have been found in the molecule
EXPLICIT_LONE_PAIR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that explicit lone pairs have been found in the molecule
explicitHIndex - Variable in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
ExplicitHydrogenChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting explicit hydrogens.
ExplicitHydrogenChecker() - Constructor for class chemaxon.checkers.ExplicitHydrogenChecker: Default constructor All types of explicit hydrogens will be searched.
ExplicitHydrogenChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ExplicitHydrogenChecker: Parameterized constructor If map contains lonely/charged/mapped/isotopic/radical/wedged keys with value false then hydrogens with these types won't be detected.
ExplicitHydrogenResult - Class in chemaxon.checkers.result: A descendant of DefaultStructureCheckerResult for identifying explicit hydrogen problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.
ExplicitHydrogenResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.ExplicitHydrogenResult: Constructor which initialize all the properties.
explicitHydrogens - Variable in class chemaxon.calculations.CalculatorPlugin: explicit hydrogens of the input molecule stored here key: index of the "parent" atom on the input molecule value: the hydrogen atom
ExplicitLonePairChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting lone pair type atoms.
ExplicitLonePairChecker() - Constructor for class chemaxon.checkers.ExplicitLonePairChecker: Default constructor
export(NMRSpectrum, double, double, double) - Static method in class chemaxon.calculations.nmr.NMRExporter: Returns the x-y point pairs of an NMR spectrum.
exportToBinFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter: Creates a binary representation of the document.
exportToBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter: Creates a binary representation of the molecule.
exportToFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter: Creates a string representation of the document.
exportToFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter: Creates a string representation of the molecule.
exportToJcampDX(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.NMRExporter: Exports the NMR spectrum into JCAMP-DX format.
exportToJcampDX(NMRSpectrum, int) - Static method in class chemaxon.calculations.nmr.NMRExporter: Exports the NMR spectrum into JCAMP-DX format.
exportToMol(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.NMRExporter: Returns a molecule with its NMR spectrum property.
exportToMol(NMRSpectrum, String) - Static method in class chemaxon.calculations.nmr.NMRExporter: Returns a molecule with its NMR spectrum property.
exportToObject(MDocument, String) - Static method in class chemaxon.formats.MolExporter: Creates a String, byte[] or Image representation of the document.
exportToObject(Molecule[], String, MolExportModule) - Static method in class chemaxon.formats.MolExporter: Creates a String, byte[] or Image representation of the given molecules.
exportToObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter: Creates a String, byte[] or Image representation of the molecule.
EXTENDED_ATOMTYPES - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColoringScheme
EXTERNAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Error type for externally developed StructureChecker classes
EXTERNAL_CHECKER_CONFIGURATION_PATH_PROPERTY_KEY - Static variable in class chemaxon.structurechecker.CheckerFixerFactory: Java System Property key to globally override default configuration path.
ExternalStructureChecker - Class in chemaxon.checkers: ExternalStructureChecker class provides a super class for externally implemented structure checkers.
ExternalStructureChecker(String) - Constructor for class chemaxon.checkers.ExternalStructureChecker: This constructor creates an external structure checker instance with the given error code
ExternalStructureCheckerResult - Interface in chemaxon.checkers.result: This interface is an extension of StructureCheckerResult that supports external StructureChecker development.
EXTRA_BONDS - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "extraBonds".
EXTRA_TEMPLATES - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "xtmpls".
extraFlavor - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable
EZ_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains double bonds that can be cis or trans
EZ_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: E/Z visibility flag.
EZ_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "ezVisible".
EZConfiguration - Enum Class in chemaxon.struc: Enumeration of possible E/Z stereo values.
EZDoubleBondChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting double bonds, that can be cis or trans.
EZDoubleBondChecker() - Constructor for class chemaxon.checkers.EZDoubleBondChecker: Initializes the EZ double bond checker

F

F - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element F.
F_ARCHIVE - Static variable in class chemaxon.formats.MFileFormat: General archive format that stores a file in another format.
F_BINARY - Static variable in class chemaxon.formats.MFileFormat: Import/export module handles binary (byte array) data.
F_COORDS - Static variable in class chemaxon.formats.MFileFormat: The format can store atom coordinates if this flag is set.
F_EXPORT - Static variable in class chemaxon.formats.MFileFormat: Export is possible if this flag is set.
F_GRAPHICS - Static variable in class chemaxon.formats.MFileFormat: File format readable by a graphics program (image viewer, ray tracer etc.).
F_IMAGE - Static variable in class chemaxon.formats.MFileFormat: 2D image file format, readable by image viewers.
F_IMPORT - Static variable in class chemaxon.formats.MFileFormat: Import is possible if this flag is set.
F_MIXED - Static variable in class chemaxon.formats.MFileFormat: Storage of records in different formats is possible if this flag is set.
F_MOLECULE - Static variable in class chemaxon.formats.MFileFormat: The format can store molecule(s) if this flag is set.
F_MULTIPLE_RECORDS_LEGAL - Static variable in class chemaxon.formats.MFileFormat: The format is designed to store multiple records if this flag is set.
F_MULTIPLE_RECORDS_POSSIBLE - Static variable in class chemaxon.formats.MFileFormat: The import/export modules can handle files with multiple records if this flag is set, but according to the format definition it is not legal.
F_OBJECT - Static variable in class chemaxon.formats.MFileFormat: Import/export module creates or reads a java object.
F_REACTION - Static variable in class chemaxon.formats.MFileFormat: The format can store reaction(s) if this flag is set.
F_RECOGNIZER - Static variable in class chemaxon.formats.MFileFormat: Format recognizer exists if this flag is set.
F_SINGLE_LINE - Static variable in class chemaxon.formats.MFileFormat: Format uses one line per structure.
F_USER_DEFINED - Static variable in class chemaxon.formats.MFileFormat: User defined format.
F_XML - Static variable in class chemaxon.formats.MFileFormat: The format is XML based if this flag is set.
Factory() - Constructor for class chemaxon.alignment.MCSAlignment.Factory
FALSE - Static variable in class chemaxon.chemterms.ChemTermsExpression: Logical result value: FALSE.
FALSE - Static variable in interface chemaxon.chemterms.CustomFunction: Possible result with the value of 0.0.
FAST - Enum constant in enum class chemaxon.alignment.AlignmentAccuracyMode: Atomic contribution, only for some selected atoms and ring centers.
FAST - Enum constant in enum class chemaxon.alignment.AtropIsomerDetector.Accuracy
FAST - Enum constant in enum class chemaxon.search.mcs.McsSearchMode: Fast search mode.
FAST_COORDS - Static variable in interface chemaxon.struc.sgroup.Expandable: Fast coordinate calculation in expand.
FASTA - Static variable in class chemaxon.formats.MFileFormat: FASTA file format
FASTA_DNA - Static variable in class chemaxon.formats.MFileFormat: FASTA file format with DNA sequence
FASTA_PEPTIDE - Static variable in class chemaxon.formats.MFileFormat: FASTA file format with peptide sequence
FASTA_RNA - Static variable in class chemaxon.formats.MFileFormat: FASTA file format with RNA sequence
Fe - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Fe.
fillInStackTrace() - Method in exception class chemaxon.naming.NameFormatException
fillOptionList(ArrayList<String>, SearchOptions) - Method in class chemaxon.search.api.options.SearchOptions: Fills ret with "optionname:optionvalue" pairs.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.Molecule: Adds all atoms and bonds to the specified molecule.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RgMolecule: Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RxnMolecule: Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
fillWithNulls() - Method in class chemaxon.marvin.common.MDocStorage: Set all stored document entries to null.
FILTER_DIM0 - Static variable in class chemaxon.formats.MolExporter: Molecule filter for cleaning 0D molecules only.
FILTER_VALENCE - Static variable in class chemaxon.calculations.MarkushEnumerationPlugin: Filter constant: valence filter.
FilteredCase(String) - Constructor for exception class chemaxon.naming.NameFormatException.FilteredCase
FilteredCase(String, Throwable) - Constructor for exception class chemaxon.naming.NameFormatException.FilteredCase
filterGroups(StandardizerConfiguration, String[]) - Static method in class chemaxon.standardizer.configuration.ConfigurationUtility: Deprecated.
Use StandardizerConfiguration.filterGroups(String...) instead
filterGroups(String...) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Filters the action list of this configuration to only contain the actions that are in the given target groups.
find() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Performs MCS search according to the specified options.
findAll() - Method in class chemaxon.search.AbstractSearch: Looks for all matching patterns in the molecule.
findAllGroups() - Method in class chemaxon.search.AbstractSearch: Returns the group hits corresponding to all hits.
findAllHits() - Method in class chemaxon.search.AbstractSearch: Looks for all matching patterns in the molecule.
findAllHits() - Method in class chemaxon.search.MolSearch
findAllSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Deprecated, for removal: This API element is subject to removal in a future version.
Use Molecule.findSmallestSgroupsContaining(MolAtom)
findAllSgroupsContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Finds all S-groups containing the specified atom.
findAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Finds an atom in the atoms array.
findAtomClone(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated for removal, no replacement.
findAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicTable: Returns the atomic number of the element in the periodic table specified by its symbol.
findAttachAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the attachment atom of attachment point with the smallest order.
findBasicFrags(Class<C>) - Method in class chemaxon.struc.MoleculeGraph: Determines the disconnected fragments and puts them into an array.
findBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Finds a bond in the bonds array.
findComponentIds(int[]) - Method in class chemaxon.struc.MoleculeGraph: Assigns a component ID to each connected component formed by the specified atom indexes.
findContainingMulticenterSgroup(MolAtom) - Method in class chemaxon.struc.Molecule: Gets the containing multicenter S-group of a multicenter atom.
findCrossingBonds() - Method in class chemaxon.struc.Sgroup: Finds the crossing bonds.
findCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Finds the crossing bonds.
findCrossingBonds() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Finds the crossing bonds.
findDecomposition() - Method in class chemaxon.search.RgroupDecomposition: Finds the first decomposition result.
findDecomposition(boolean) - Method in class chemaxon.search.RgroupDecomposition: Finds a decomposition result.
findFirst() - Method in class chemaxon.alignment.AlignOnPairedAtoms: Overlays the molecule to align on the reference using the predefined atom pairs.
findFirst() - Method in class chemaxon.search.AbstractSearch: Looks for the first matching pattern in the target molecule.
findFirstDecomposition() - Method in class chemaxon.search.RgroupDecomposition: Finds the first decomposition result.
findFirstGroup() - Method in class chemaxon.search.AbstractSearch: Returns the group hit corresponding to the first hit.
findFirstHit() - Method in class chemaxon.search.AbstractSearch: Looks for the first matching pattern in the target molecule.
findFirstHit() - Method in class chemaxon.search.MolSearch
findFormats(String, long, long) - Static method in class chemaxon.formats.MFileFormatUtil: Gets a list of formats.
findFrag(int, int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Determines the subgraph connected to the specified atom.
findFragById(int, int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Determines the subgraph corresponding to the specific fragment ID.
findFrags() - Method in class chemaxon.struc.Molecule: Determines the disconnected fragments and puts them into an array.
findFrags(Class<C>, int) - Method in class chemaxon.struc.Molecule: Determines the disconnected fragments and puts them into an array.
findFrags(Class<C>, int) - Method in class chemaxon.struc.MoleculeGraph: Determines the disconnected fragments and puts them into an array.
findInArray(Object[], int[], int, Object) - Static method in class chemaxon.struc.MoleculeGraph: Finds an object in an array.
findLigandTable(int, int) - Method in class chemaxon.search.RgroupDecomposition: Returns the ligand table.
findLigandTable(int, int, String) - Method in class chemaxon.search.RgroupDecomposition: Returns the ligand table.
findLigandTableRow(int) - Method in class chemaxon.search.RgroupDecomposition: Returns a ligand table row with ligands corresponding to a the first search hit.
findLigandTableRow(int, String) - Method in class chemaxon.search.RgroupDecomposition: Returns a ligand table row with ligands corresponding to a the first search hit.
findMcs() - Method in class chemaxon.search.mcs.BuildupMcs
findMcs() - Method in class chemaxon.search.mcs.MaxCliqueMcs
findNext() - Method in class chemaxon.alignment.AlignOnPairedAtoms: Randomizes dihedral angles of the input conformation for flexible molecules and aligns.
findNext() - Method in class chemaxon.search.AbstractSearch: Looks for the next matching pattern in the target molecule.
findNextDecomposition() - Method in class chemaxon.search.RgroupDecomposition: Finds the next decomposition result.
findNextGroup() - Method in class chemaxon.search.AbstractSearch: Returns the group hit corresponding to the next hit.
findNextHit() - Method in class chemaxon.search.AbstractSearch: Searches for the next hit.
findNextHit() - Method in class chemaxon.search.MolSearch
findRgroupBridgeId(int) - Method in class chemaxon.struc.RgMolecule: Finds the corresponding RgroupBridgeId for an R-group index.
findRgroupIndex(int) - Method in class chemaxon.struc.RgMolecule: Finds the index of an R-group based on the R-group number.
findRgroupIndex(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Finds R-group R#.
findScriptLastSectionIndex(int, int) - Method in class chemaxon.struc.graphics.MTextDocument: Finds the end of a subscript or superscript.
findSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Deprecated.
Use Molecule.findAllSgroupsContaining(MolAtom), as there can be multiple largest S-groups containing a certain atom
findSgroupOf(MolAtom) - Method in class chemaxon.struc.Molecule: Deprecated.
Use Molecule.findSmallestSgroupsContaining(MolAtom), as there can be multiple smallest S-groups containing a certain atom
findSmallestSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Deprecated.
Use Molecule.findSmallestSgroupsContaining(MolAtom), as there can be multiple smallest S-groups containing a certain atom
findSmallestSgroupContaining(MolAtom) - Method in class chemaxon.struc.Sgroup: Finds the smallest S-group containing the specified atom.
findSmallestSgroupOf(MolAtom) - Method in class chemaxon.struc.Sgroup: Finds the smallest S-group that has the specified node.
findSmallestSgroupsContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Finds all smallest (minimal) S-groups containing the specified atom.
FINGERPRINT - Static variable in class chemaxon.chemterms.MolContext
FingerprintGenerator - Interface in chemaxon.chemterms: Interface for fingerprint generators used in Chemical Terms match functions.
finishCalculation() - Method in class chemaxon.calculations.api.ProgressableCalculator
finishCancel() - Method in exception class chemaxon.marvin.common.MDocStorage.CancellationException: This method should be called after catching the exception.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MAnalysisBox
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MElectronContainer
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MPolyline: Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.MObject: Finish cloning a document.
firstPage - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions: The first page of the document that should be annotated.
firstPage(Integer) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
fix() - Method in class chemaxon.structurechecker.AdvancedCheckerRunner: Checks the structure, then fixes the problems based on configuration.
NOTE: FixMode and fixerClassName from configuration is used to choose best fixer.
fix() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
fix() - Method in interface chemaxon.structurechecker.CheckerRunner: Runs all StructureChecker on the given molecule and after that fixes all identified problems with the first StructureFixer which is associated with the current problem.
fix(StructureCheckerResult) - Method in class chemaxon.fixers.AddChiralFlagFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.BondAngleFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.BondLengthFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.CleanFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ClearWedgeFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ContractGroupFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertAliasToGroupFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertPseudoToGroupFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToAtomFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToCarbonFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToElementalFormFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToIonicFormFixer: Checker results contain atoms from the alkali metal and alkaline earth metal groups and their ionic counterparts of N, O, S atoms.
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToPlainDoubleBondFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToSingleBondFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ConvertToWigglyDoubleBondFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.DearomatizeFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.DistanceBasedMetalloceneFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ExpandGroupFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.FlipWedgeBondFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MapMoleculeFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MapReactionFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MarkAsMajorFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MarkAsUnknownFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.MetalloceneFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.NeutralizeChargeFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.PartialCleanFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RearomatizeFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RearrangeWedgesFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAliasFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomMapFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomQueryPropertyFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAtomValueFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveAttachedDataFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBondFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBondTopologyFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveBracketsFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveChiralFlagFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveExplicitHydrogenFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveRadicalFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveReactingCenterBondMarkFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveStereoCareBoxFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveValencePropertyFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RemoveZCoordinateFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.RgroupAttachmentFixer
fix(StructureCheckerResult) - Method in interface chemaxon.fixers.StructureFixer: Fixes one molecule problem identified by the result
fix(StructureCheckerResult) - Method in class chemaxon.fixers.SubstructureFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.UngroupFixer
fix(StructureCheckerResult) - Method in class chemaxon.fixers.ValenceFixer
fix(StructureCheckerResult) - Method in class chemaxon.structurechecker.AdvancedCheckerRunner: Fixes the given result based on the fixer defined for the checker.
fix(StructureCheckerResult) - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
fix(StructureCheckerResult) - Method in interface chemaxon.structurechecker.CheckerRunner: Fixes the problem identified by result with the first StructureFixer which is associated with the StructureCheckerErrorType of the result.
fix(StructureChecker, StructureCheckerResult) - Method in class chemaxon.structurechecker.AdvancedCheckerRunner: Tries to fix the problem detected by the specified checker, or falls back to result based behavior.
FIX - Enum constant in enum class chemaxon.checkers.FixMode: on problem applies preferred fix if possible
FIX_CHARGE - Static variable in class chemaxon.struc.MolAtom: Valence checking will replace radicals with charges if this flag is set.
FIX_MODE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: fix mode property
fix2D(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.Cleaner: Fixes or cleans the given structure in 2D.
fix2D(MoleculeGraph, String) - Static method in class chemaxon.core.calculations.clean.Cleaner: Fixes or cleans the given structure in 2D.
fixable(StructureCheckerResult) - Method in class chemaxon.fixers.PartialCleanFixer: Gets whether the result is fixable.
fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.graphics.MPolyline
fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.graphics.MRectangle
fixClonedPoints(MObject[], MObject[], int) - Method in class chemaxon.struc.MObject: Sets the parent object for this object.
FIXED - Enum constant in enum class chemaxon.alignment.AlignmentProperties.DegreeOfFreedomType: Do not move this molecule
fixElectronContainers(MDocument, boolean, boolean) - Static method in class chemaxon.struc.MDocument: Removes unnecesarry MElectronContainers from the give MDocument corresponding to lone pair display options, if an electron of a MEFlow arrow has been removed the arrow is removed as well.
FIXER_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: fixer class name property
FixerClassDescriptor() - Constructor for class chemaxon.structurechecker.CheckerFixerFactory.FixerClassDescriptor: Initializes an empty fixer class descriptor
FixerClassDescriptor(String, String, String) - Constructor for class chemaxon.structurechecker.CheckerFixerFactory.FixerClassDescriptor: Initializes a fixer class descriptor
FixerInfo - Annotation Interface in chemaxon.fixers: This annotation is responsible for adding GUI-related metadata for StructureFixer implementations.
Fixes - Annotation Interface in chemaxon.fixers: This annotation is used to annotate the StructureFixer implementations which StructureCheckerErrorType can be fixed by the current fixer
FixesExternal - Annotation Interface in chemaxon.fixers: This annotation is used to annotate the StructureFixer implementations which error codes (identified by a unique String) can be fixed by the current fixer
fixMidPointClones(MObject[], MObject[]) - Static method in class chemaxon.struc.graphics.MPolyline: Fixes the parents of the cloned MMidPoints.
FixMode - Enum Class in chemaxon.checkers: Fix mode options
fixProperties() - Method in class chemaxon.struc.MoleculeGraph: Delegates to tracker's fixProperties().
fixProperties() - Method in class chemaxon.struc.RxnMolecule
fixRectanglePointClones(MObject[], MObject[]) - Static method in class chemaxon.struc.graphics.MRectangle: Fixes the parents of the cloned MRectanglePoints.
fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.Molecule: Fix a property containing reference to the molecule.
fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.MoleculeGraph: Fix a property containing a reference to the molecule.
fixSelfReferringProperty(MProp) - Method in class chemaxon.struc.RgMolecule: Fix a property containing reference to the molecule.
Fl - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Fl.
flag() - Method in class chemaxon.calculations.stereo.stereocenters.EnhancedStereo: Returns the enhanced stereo flag (eg.
flatten() - Method in class chemaxon.struc.MPropertyContainer: Flattens hierarchically specified RDF properties.
flavor - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable: The DataFlavor represented by the implementation.
FlipWedgeBondFixer - Class in chemaxon.fixers: Flips wedge bonds.
FlipWedgeBondFixer() - Constructor for class chemaxon.fixers.FlipWedgeBondFixer
FLOAT_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
floatDescr - Variable in class chemaxon.descriptors.CustomDescriptor: storage for the floating point descriptors
flush() - Method in class chemaxon.formats.MolExporter: Flushes the output stream and forces any buffered output bytes to be written out.
Fm - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Fm.
FOG_FACTOR - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "fogFactor".
FONT_DEFAULT_SCALE - Static variable in class chemaxon.struc.graphics.MTextBox
forIntValue(int) - Static method in enum class chemaxon.struc.EZConfiguration
forIntValue(int) - Static method in enum class chemaxon.struc.Radical: Gets the Radical that's int value is the given parameter.
FORMAL_CHARGE - Enum constant in enum class chemaxon.calculations.elemental.FormulaGenerationRule: Show the formal (total) charge at the end of the molecular formula, instead of showing the charge of each atom separately.
If FormulaGenerationRule.DOT_DISCONNECTED_FRAGMENTS is also applied, then the charge of each fragment will be shown separately.
This rule has no effect if FormulaGenerationRule.IGNORE_CHARGE is also applied.
For example: [O-]NO -> NO2[-]
FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "formalchargeformula".
formalCharge() - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the formal (total) charge of the molecule.
format - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable: The format string.
format() - Element in annotation interface chemaxon.checkers.PersistentProperty: Returns the format of the annotated property
format() - Element in annotation interface chemaxon.standardizer.PersistentProperty: Returns the serialization format of the annotated property
format(double) - Method in class chemaxon.calculations.CalculatorPlugin: Converts a double into String, applying the maximum number of fractional digits specified.
format(double[][], int) - Method in class chemaxon.calculations.CalculatorPlugin: Converts a double[][] 2xN table to a 2-column tab-separated string representation of the table.
format(double, int) - Method in class chemaxon.calculations.CalculatorPlugin: Converts a double into String, applying the maximum number of fractional digits specified.
format(double, StringBuffer) - Method in class chemaxon.calculations.CalculatorPlugin: Converts a double into String, applying the maximum number of fractional digits specified.
format(String) - Method in interface chemaxon.struc.graphics.MAnalysisBoxTerm.Formatter
FORMAT_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction: The key of the molecule format parameter of the abstract action.
formula() - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
formula() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
formula(int) - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates a fixed digit sortable molecular formula.
formula(FormulaGenerationRule...) - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
formula(Set<FormulaGenerationRule>) - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "formula".
FormulaAtom - Record Class in chemaxon.calculations.elemental: Represents an atom in an ElementalAnalysis.
FormulaAtom(String, int) - Constructor for record class chemaxon.calculations.elemental.FormulaAtom: Creates a new instance with the given symbol and charge.
FormulaAtom(String, int, int) - Constructor for record class chemaxon.calculations.elemental.FormulaAtom: Creates a new instance with the given symbol, mass number and charge.
FormulaAtom(String, Optional<Integer>, int) - Constructor for record class chemaxon.calculations.elemental.FormulaAtom: Creates an instance of a FormulaAtom record class.
FormulaGenerationRule - Enum Class in chemaxon.calculations.elemental: Molecular formula generation settings.
FormulaSearch - Class in chemaxon.search: Chemical formula based search class.
FormulaSearch() - Constructor for class chemaxon.search.FormulaSearch
FORMULATION - Enum constant in enum class chemaxon.struc.SgroupType
forName(String) - Static method in class chemaxon.formats.Encoding: Creates an Encoding for the specified name, with unknown byte order (endianness).
fp - Variable in class chemaxon.descriptors.ChemicalFingerprint: storage for the fingerprint
fp - Variable in class chemaxon.descriptors.ECFP: Binary vector storage of the fingerprint
fp - Variable in class chemaxon.descriptors.PharmacophoreFingerprint: storage for the fingerprint
fp - Variable in class chemaxon.descriptors.ReactionFingerprint: storage for the fingerprint
Fr - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Fr.
FRAG_BASIC - Static variable in class chemaxon.struc.MoleculeGraph: Basic fragmentation, only atom - atom connections (bond) are considered.
FRAG_KEEPING_MULTICENTERS - Static variable in class chemaxon.struc.MoleculeGraph: Fragmentation without breaking multicenter S-groups.
FRAG_KEEPING_SGROUPS - Static variable in class chemaxon.struc.MoleculeGraph: Fragmentation without breaking S-groups.
FRAG_TYPE_COUNT - Static variable in class chemaxon.struc.MoleculeGraph: Number of fragmentation types.
fragmentCount() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the number of fragments (disconnected parts) of the molecule.
freqCount - Variable in class chemaxon.descriptors.MDGenerator
fromData(byte[]) - Method in class chemaxon.descriptors.BCUT: Builds a BCUT descriptor from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ChemicalFingerprint: Builds a fingerprint from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.CustomDescriptor: Builds a CustomDescriptor from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ECFP: Builds an ECFP fingerprint from an external data format created by toData().
fromData(byte[]) - Method in class chemaxon.descriptors.MolecularDescriptor: Builds a MolecularDescriptor object from its external (database) representation.
fromData(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Builds a PharmacophoreFingerprint from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ReactionFingerprint: Builds a fingerprint from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ScalarDescriptor: Builds a descriptor from an external data format, created by a previous call to toData().
fromData(byte[]) - Method in class chemaxon.descriptors.ShapeDescriptor
fromFile(File) - Method in class chemaxon.descriptors.CDParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.CFParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.ECFPParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.MDParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.PFParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.RFParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.SDParameters: Sets parameters from an XML file.
fromFile(File) - Method in class chemaxon.descriptors.ShapeParameters: Sets parameters from an XML file.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.BCUT: Builds a BCUT descriptor from its float array representation (generated by toFloatArray()).
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ChemicalFingerprint: Builds fingerprint from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.CustomDescriptor: Builds a molecular descriptor from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ECFP: Builds an ECFP fingerprint from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.MolecularDescriptor: Builds a molecular descriptor from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Builds a molecular descriptor from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ReactionFingerprint: Builds fingerprint from its float array representation.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ScalarDescriptor: Builds the descriptor from a float array of one element.
fromFloatArray(float[]) - Method in class chemaxon.descriptors.ShapeDescriptor
fromId(int) - Static method in enum class chemaxon.calculations.admet.HergClass: Converts the given integer ID to the appropriate hERG class: 0 to HergClass.SAFE and 1 to HergClass.TOXIC.
fromIdentiferSet(Set<Integer>) - Method in class chemaxon.descriptors.ECFP: Deprecated, for removal: This API element is subject to removal in a future version.
Use ECFP.fromIdentifierSet(Set) instead.
fromIdentifierSet(Set<Integer>) - Method in class chemaxon.descriptors.ECFP: Builds an ECFP fingerprint from a set of Integer identifiers.
fromIntArray(int[]) - Method in class chemaxon.descriptors.ECFP: Builds an ECFP fingerprint from an array of int identifiers.
fromPlainText(Reader) - Static method in class chemaxon.naming.document.DocumentAnnotator: Constructs a DocumentAnnotator to annotate the given text.
fromProperties(InputStream) - Static method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Parses the given input stream into a Properties object and passes that to HeavyAtomLimitChecker.fromProperties(Properties).
fromProperties(Properties) - Static method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Creates a heavy atom limit checker from the given configuration.
fromString(String) - Method in class chemaxon.descriptors.BCUT: Builds a BCUT descriptor from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.BCUTParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.CDParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.CFParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.ChemicalFingerprint: Builds a fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.CustomDescriptor: Builds a descriptor from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.ECFP: Builds an ECFP fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.ECFPParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.MDParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.MolecularDescriptor: Builds a molecular descriptor from its string representation.
fromString(String) - Method in class chemaxon.descriptors.PFParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Builds a fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.ReactionFingerprint: Builds a fingerprint from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.RFParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.ScalarDescriptor: Builds a descriptpr from its string representation created by toString().
fromString(String) - Method in class chemaxon.descriptors.SDParameters: Sets parameters from a string representation.
fromString(String) - Method in class chemaxon.descriptors.ShapeDescriptor
fromString(String) - Method in class chemaxon.descriptors.ShapeParameters
fromString(String) - Static method in enum class chemaxon.search.api.options.HaltOnErrorOption: Gets the halt on error option value for the string representation.
fromString(String) - Static method in enum class chemaxon.search.api.options.HomologyTranslationOption
fromString(String) - Static method in class chemaxon.struc.graphics.MAnalysisBoxTerm: Parses a string into a list of MAnalysisBoxTerms.
FULL - Enum constant in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Full clean
FULL - Static variable in interface chemaxon.search.api.SearchConstants: Full structure search.
FULL_FRAGMENT - Static variable in interface chemaxon.search.api.SearchConstants: Full fragment search (formerly called exact fragment).
functionScale - Variable in class chemaxon.calculations.nmr.NMRSpectrum: Scale factor for NMR spectrum function scaling.
fuse(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Adds those atoms and bonds of another molecule to this one that are not already elements.
fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.MoleculeGraph: Adds atoms and bonds of another molecule to this one.
fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.RgMolecule: Add the atoms and bonds of another molecule.
fuse(MoleculeGraph, boolean) - Method in class chemaxon.struc.RxnMolecule: Add the atoms and bonds of another molecule.
fuse(RxnMolecule) - Method in class chemaxon.struc.RxnMolecule: Fuse and RxnMolecule to this RxnMolecule.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.Molecule: Adds those atoms and bonds of a molecule graph to this one that are not already elements.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.MoleculeGraph: Adds the atoms and bonds of another molecule to this one.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.RgMolecule: Add those nodes and edges of a graph that are not already elements.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.RxnMolecule: Add those nodes and edges of a graph that are not already elements.
fuse0(MoleculeGraph, boolean) - Method in class chemaxon.struc.SelectionMolecule: Adds those atoms and bonds of a graph to this one that are not already elements.
FUSED_REACTION_OUTPUT - Static variable in class chemaxon.reaction.Reactor: Output type: fused reaction output.
fusedAliphaticRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
fusedAliphaticRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of fused aliphatic rings in the molecule (rings s).
fusedAliphaticRings() - Method in class chemaxon.core.calculations.Ring: Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
fusedAliphaticRings(int) - Method in class chemaxon.core.calculations.Ring: Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).
fusedAromaticRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
fusedAromaticRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of fused aromatic rings in the molecule (rings s).
fusedAromaticRings() - Method in class chemaxon.core.calculations.Ring: Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
fusedAromaticRings(int) - Method in class chemaxon.core.calculations.Ring: Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).
fusedRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.

G

Ga - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ga.
gatherBaseColors() - Static method in class chemaxon.marvin.util.ColorGenerator: Creates a Collection of the base colors.
These colors are:

- black
- white
- red
- green
- blue
- cyan
- magenta
- yellow.
gatherBaseColorsAndBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator: Creates a Collection of the base Molecule RGB colors and base colors.
These colors are the atom label RGB colors of:
- H
- C
- N
- O
- S
- F
- P
- Cl
- Br
- I.
gatherBaseMoleculeColors(boolean) - Static method in class chemaxon.marvin.util.ColorGenerator: Creates a Collection of the base Molecule RGB colors.
These colors are the atom label RGB colors of:

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

and

- black
- white
gatherBlackAndWhite() - Static method in class chemaxon.marvin.util.ColorGenerator: Creates a Collection of black and white color
GAUSS_44_SAME - Enum constant in enum class chemaxon.alignment.AlignmentProperties
GAUSS_FAST_EXTENDED_ATOMTYPE - Enum constant in enum class chemaxon.alignment.AlignmentProperties
GAUSS_FAST_EXTENDED_ATOMTYPE_MCS - Enum constant in enum class chemaxon.alignment.AlignmentProperties: Deprecated.
GAUSS_FAST_PHARMACOPHORE - Enum constant in enum class chemaxon.alignment.AlignmentProperties
GAUSS_FAST_SHAPE_ONLY - Enum constant in enum class chemaxon.alignment.AlignmentProperties
GAUSS_VOLUME_SIMPLE_44 - Enum constant in enum class chemaxon.alignment.AlignmentProperties.NodeType
GAUSS_VOLUME_SIMPLE_45 - Enum constant in enum class chemaxon.alignment.AlignmentProperties.NodeType
GAUSS_VOLUME_SIMPLE_FAST - Enum constant in enum class chemaxon.alignment.AlignmentProperties.NodeType
GAUSS_VOLUME_SIMPLE_FULL - Enum constant in enum class chemaxon.alignment.AlignmentProperties.NodeType
GAUSSIAN_CUBE - Static variable in class chemaxon.formats.MFileFormat: Gaussian Cube files.
GAUSSIAN_INPUT - Static variable in class chemaxon.formats.MFileFormat: Gaussian Input Format.
GAUSSIAN_INPUTZ - Static variable in class chemaxon.formats.MFileFormat: Gaussian Input Format: Z-matrix.
GAUSSIAN_OUTPUT - Static variable in class chemaxon.formats.MFileFormat: Gaussian output format.
Gd - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Gd.
Ge - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ge.
GENERAL - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type: General aromatization
generate() - Method in class chemaxon.search.MarkushGenerator: Generates the RgMolecule with the specified scaffold (see MarkushGenerator.setQuery(chemaxon.struc.Molecule)) covering the specified targets (see MarkushGenerator.setTargets(chemaxon.struc.Molecule[])).
generate(int, Molecule, boolean, boolean) - Method in class chemaxon.alignment.AlignmentMoleculeFactory: Deprecated.
Use AlignmentMoleculeFactory.create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.
generate(Molecule) - Method in class chemaxon.descriptors.BCUT: Creates the BCUT descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ChemicalFingerprint: Creates the ChemicalFingerprint descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.DescriptorGenerator: Generates descriptor for the given molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ECFP: Creates the ECFP fingerprint for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.MolecularDescriptor: Creates the descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Creates the PharmacophoreFingerprint descriptor from the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ReactionFingerprint: Creates the ReactionFingerprint descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ScalarDescriptor: Creates the ScalarDescriptor descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.HAcc: Calculates the HAcc descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.HBParameters: Calculates the descriptor value for the given molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.HDon: Creates the HDon descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.Heavy: Creates the HeavyAtomCount descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.LDParameters
generate(Molecule) - Method in class chemaxon.descriptors.scalars.LogD: Creates the LogD descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.LogP: Creates the LogP descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.Mass: Creates the Mass descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.scalars.TPSA: Creates the TPSA descriptor for the given Molecule.
generate(Molecule) - Method in class chemaxon.descriptors.ShapeDescriptor
generate(Molecule, int[]) - Method in class chemaxon.descriptors.DescriptorGenerator: Generates partial descriptor for the given molecule.
generate(Molecule, int[], MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator: Generates the partial chemical fingerprint for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.BCUTGenerator: Generates the BCUT descriptors for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.BCUTParameters: Calls the descriptor generator for the molecule provided and stores result (the descriptor) in the MolecularDescriptor object.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator: Generates the chemical fingerprint for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.CFParameters: Calls CFGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator: Generates the ECFP fingerprint for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPParameters: Calls ECFPGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator: Generates the molecular descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator: Generates the pharmacophore fingerprint of the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator: Generates the reaction fingerprint for the given reaction molecule object.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.RFParameters: Calls RFGenerator and generates the descriptor for the given molecule.
generate(Molecule, MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeGenerator
generate(String) - Method in class chemaxon.descriptors.MolecularDescriptor: Creates the descriptor for the given Molecule.
generateBracketCoords(Sgroup, int) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Generates brackets with coordinates for a specified S-group.
generateBracketCoords(Sgroup, int, boolean) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Generates brackets with coordinates for a specified S-group.
generateColors(int) - Static method in class chemaxon.marvin.util.ColorGenerator: Generates the specified number of different Colors, with no forbidden colors.
generateColors(int, Collection<Color>) - Static method in class chemaxon.marvin.util.ColorGenerator: Generates the specified number of different Colors, which are different enough from the specified forbidden colors.
generateEMFToFile(String, String, String) - Static method in class chemaxon.marvin.util.ImageExportUtil: Creates a new .NET based EMF picture and saves it to the given file.
generateMultiplet() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Generates the line positions and intensities of this multiplet.
generator - Variable in class chemaxon.descriptors.MDParameters: generates MolecularDescriptors
GENERIC - Enum constant in enum class chemaxon.search.api.options.TautomerEqualityMode
GENERIC - Enum constant in enum class chemaxon.search.api.options.TautomerSubstructureMode
GENERIC - Enum constant in enum class chemaxon.search.api.options.TautomerTransformationMode
GENERIC - Enum constant in enum class chemaxon.struc.SgroupType
GEOMETRY - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
GEOMETRY_PROJECTION - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
GeometryPlugin - Class in chemaxon.calculations: Plugin class for geometric properties calculations.
GeometryPlugin() - Constructor for class chemaxon.calculations.GeometryPlugin: Constructor.
get(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the content of the specified hitogram bin.
get(int) - Static method in enum class chemaxon.rendering.constants.AnyBondStyle
get(int) - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
get(int) - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle
get(int) - Static method in enum class chemaxon.rendering.constants.RenderingStyle
get(int) - Method in class chemaxon.standardizer.actions.CreateGroupAction: Returns the group definition at specified index.
get(int) - Method in class chemaxon.struc.prop.MHashProp: Gets a value.
get(int) - Method in class chemaxon.struc.prop.MListProp: Gets the specified element.
get(int, int, float) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
get(int, int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the histogram bar height of two features ('fa'-'fb') corresponding to the given ditance 'dist'.
get(String) - Method in class chemaxon.struc.MPropertyContainer: Gets a property object.
get(String) - Method in class chemaxon.struc.prop.MHashProp: Gets a value.
GET - Enum constant in enum class chemaxon.calculations.services.JsonServiceDescriptor.Method: HTTP GET method
get3DMolecule() - Method in class chemaxon.calculations.MSAPlugin: Returns the 3D molecule used in 3D surface area calculation.
getAbbreviation() - Method in class chemaxon.standardizer.actions.GroupDefinition: Gets the abbreviation of the group.
getAbbreviation(int) - Method in class chemaxon.standardizer.actions.CreateGroupAction: Gets the abbreviation at the provided index
getAbbreviationAsMolecule(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: If the given atom is an abbreviation returns the expanded structure, otherwise returns null.
getAbsoluteCellIndex(int) - Method in class chemaxon.marvin.beans.MViewPane: Determines the absolute cell index of a visible cell
getAbsoluteCellIndex(JComponent) - Method in class chemaxon.marvin.beans.MViewPane: Determines in which cell the specified component is located.
getAbsoluteLabelVisible() - Method in class chemaxon.marvin.common.UserSettings: Are Absolute labels visible?
getAbsoluteXY() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
getAbundance(int, int) - Static method in class chemaxon.struc.PeriodicTable: Natural abundance of the isotope
getAcceptorAtomCount() - Method in class chemaxon.calculations.HBDAPlugin: Returns the overall acceptor atom count (without multiplicity) in the molecule.
getAcceptorSiteCount() - Method in class chemaxon.calculations.HBDAPlugin: Returns the overall acceptor count (with multiplicity) in the molecule.
getAcceptorSiteCount(int) - Method in class chemaxon.calculations.HBDAPlugin: Returns the atomic acceptor count corresponding to the specified atom index.
getAccuracyMode() - Method in class chemaxon.alignment.MMPAlignmentProperties
getAction() - Method in class chemaxon.standardizer.Changes: Gets the base StandardizerAction of the changes
getActionCommand() - Method in class chemaxon.marvin.common.MAction: Gets the action command string.
getActionCount() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets the action count of the configuration
getActionIndexes(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets the indexes of actions defined by the provided action string
getActionName() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction: Gets the name of the original action
getActions() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets all actions of the configuration
getActions(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets actions of a group of the configuration
getActions(String...) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets actions of a group of the configuration
getActionString() - Method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
getActionStringTokens() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Gets the action string token of the checker
getActionStringTokens() - Method in class chemaxon.fixers.StructureFixerDescriptor: Gets the action string token of the fixer
getActionStringTokens() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the action string tokens of the action
getActiveAtomIndex() - Method in class chemaxon.core.calculations.stereo.StereoActivePart: Get the active atom index.
getActiveAtomReference() - Method in class chemaxon.core.calculations.stereo.StereoActivePart: For internal use only.
getAddedAtoms() - Method in class chemaxon.standardizer.Changes: Gets the list of atoms added during the standardization procedure
getAgent(int) - Method in class chemaxon.struc.RxnMolecule: Gets an agent.
getAgentCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of agents.
getAgents() - Method in class chemaxon.struc.RxnMolecule: Gets all agents in an array.
getAlias() - Method in class chemaxon.calculations.services.ServiceArgument: Returns the argument alias.
getAlias() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the service alias.
getAliasNames() - Method in class chemaxon.descriptors.BCUT
getAliasNames() - Method in class chemaxon.descriptors.ChemicalFingerprint
getAliasNames() - Method in class chemaxon.descriptors.CustomDescriptor
getAliasNames() - Method in class chemaxon.descriptors.ECFP
getAliasNames() - Method in class chemaxon.descriptors.MolecularDescriptor
getAliasNames() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getAliasNames() - Method in class chemaxon.descriptors.ReactionFingerprint
getAliasNames() - Method in class chemaxon.descriptors.ScalarDescriptor
getAliasNames() - Method in class chemaxon.descriptors.ShapeDescriptor
getAliasstr() - Method in class chemaxon.struc.MolAtom: Gets the alias string or pseudo atom type string for pseudo atoms.
getAlignedMoleculesAsFragments() - Method in class chemaxon.alignment.Alignment
getAlignedMoleculesAsFragments() - Method in class chemaxon.alignment.PairwiseAlignment
getAlignedMoleculesAsFragments() - Method in interface chemaxon.alignment.PairwiseComparison: After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.
getAlignedMoleculesAsFragments() - Method in class chemaxon.alignment.PairwiseSimilarity3D
getAlignedQuery() - Method in class chemaxon.alignment.PairwiseAlignment
getAlignedQuery() - Method in interface chemaxon.alignment.PairwiseComparison
getAlignedQuery() - Method in class chemaxon.alignment.PairwiseSimilarity3D
getAlignedTarget() - Method in class chemaxon.alignment.PairwiseAlignment
getAlignedTarget() - Method in interface chemaxon.alignment.PairwiseComparison
getAlignedTarget() - Method in class chemaxon.alignment.PairwiseSimilarity3D
getAlignedWithNewCoordinates() - Method in class chemaxon.alignment.AlignOnPairedAtoms
getAlignmentMode() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the alignment mode.
getAlignScaffold() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Gets the scaffold aligning mode
getAliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the aliphatic atom count.
getAliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the aliphatic bond count.
getAliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the aliphatic ring count.
getAliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
getAliphaticRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the aliphatic rings in the molecule.
getAliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Indentifies aliphatic rings in the molecule having a given size (number of atoms).
getAllAtomCount() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the atom count (including implicit hydrogens).
getAllAtomCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the atom count.
getAllAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the attachment atoms (atoms having attachment point).
getAllFragments() - Method in class chemaxon.struc.RxnMolecule: Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
getAllFromDocument(MDocument) - Static method in class chemaxon.struc.NoStructure: Returns all NoStructure labels from the document.
getAllMolecules() - Method in class chemaxon.struc.MDocument: Gets an array containing all molecule objects.
getAllNonEmptyMolecules() - Method in class chemaxon.struc.MDocument: Gets an array containing all non-empty molecule objects.
getAllObjects() - Method in class chemaxon.struc.MDocument: Gets all objects stored in this document and from the chemical structure of the document.
getAllObjects() - Method in class chemaxon.struc.Molecule: Gets all MObjects that belong to this molecule.
getAllObjects() - Method in class chemaxon.struc.RgMolecule
getAllObjects() - Method in class chemaxon.struc.RxnMolecule
getAllOptionsAsString() - Method in class chemaxon.search.api.options.SearchOptions: Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
getAllOptionsAsString(String) - Method in class chemaxon.search.api.options.SearchOptions: Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
getAnalysisBoxTerms() - Method in class chemaxon.marvin.common.UserSettings
getAngle() - Method in class chemaxon.alignment.DihedralScanResult.ScanStep: Represented angle.
getAngle(int[]) - Method in class chemaxon.calculations.GeometryPlugin: Returns the angle of 3 atoms.
getAngle(int, int, int) - Method in class chemaxon.calculations.GeometryPlugin: Returns the angle of 3 atoms.
getAnimated() - Method in class chemaxon.marvin.beans.MViewPane: Gets index of animated cells of the table (or simple viewer).
getAnimDelay() - Method in class chemaxon.marvin.beans.MViewPane: Gets the repeat delay for animations.
getAnimFPS() - Method in class chemaxon.marvin.beans.MViewPane: Gets the frames per second for animations.
getAnyBondStyles() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the any bond style.
getAppliedActions() - Method in class chemaxon.standardizer.Standardizer: Returns the applied tasks to the last input molecule.
getAppliedTaskIDs() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor: Returns the IDs of tasks applied to the last input molecule.
getAppliedTaskIDs() - Method in class chemaxon.standardizer.Standardizer: Returns the IDs of tasks applied to the last input molecule.
getAppliedTaskIndexes() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor: Returns the indexes of tasks applied to the last input molecule.
getAppliedTaskIndexes() - Method in class chemaxon.standardizer.Standardizer: Returns the indexes of tasks applied to the last input molecule.
getArcAngle() - Method in class chemaxon.struc.graphics.MPolyline: Gets the central angle of the arc.
getArcCenter(Point3D, Point3D, double) - Static method in class chemaxon.struc.graphics.MPolyline: Returns the arc center.
getArcHeight() - Method in class chemaxon.struc.graphics.MRoundedRectangle
getArcRadius(Point3D, Point3D, double) - Static method in class chemaxon.struc.graphics.MPolyline
getArcRadius(Transform3D) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arc radius.
getArcWidth() - Method in class chemaxon.struc.graphics.MRoundedRectangle
getArgument(int) - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the type of the specified argument
getArgumentCount() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the number of arguments
getArguments() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns an unmodifiable list of the argument types
getAromataType() - Method in class chemaxon.checkers.result.AromaticityCheckerResult: Returns the type of the aromatization
getAromaticAndAliphaticRings(int, boolean, boolean, int, int) - Method in class chemaxon.struc.MoleculeGraph: Returns the aromatic and or aliphatic ring atom indexes.
Note: This method does not aromatize the already aromatized rings.
getAromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the aromatic atom count.
getAromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the aromatic bond count.
getAromaticRingCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the total partial charge of the smallest aromatic ring containing the specified atom.
getAromaticRingCharge(int, int) - Method in class chemaxon.calculations.ChargePlugin: Returns the partial charge of the smallest aromatic ring containing the specified atom.
getAromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the aromatic ring count.
getAromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
getAromaticRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the aromatic rings in the molecule.
getAromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Indentifies aromatic rings in the molecule having a given size (number of rings).
getAromaticSystemCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the total partial charge of the aromatic system containing the specified atom.
getAromaticSystemCharge(int, int) - Method in class chemaxon.calculations.ChargePlugin: Returns the partial charge of the aromatic system containing the specified atom.
getAromatizedStructures() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the enumerated structures in aromatized form.
getAromatizeMethod() - Method in class chemaxon.marvin.common.UserSettings: Gets the aromatize method.
getAromType() - Method in class chemaxon.checkers.AromaticityErrorChecker: Returns the aromType
getArrowAsProperty() - Method in class chemaxon.struc.RxnMolecule: Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.
getArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arrow flags.
getArrowLength(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arrow head length.
getArrowWidth(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arrow head width.
getASA() - Method in class chemaxon.calculations.MSAPlugin: Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule.
getASAHydrophobic() - Method in class chemaxon.calculations.MSAPlugin: Returns water accessible surface area of all hydrophobic (|qi|invalid input: '<'0.125) atoms.
getASANegative() - Method in class chemaxon.calculations.MSAPlugin: Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0).
getASAPlus() - Method in class chemaxon.calculations.MSAPlugin: Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0).
getASAPolar() - Method in class chemaxon.calculations.MSAPlugin: Returns water accessible surface area of all polar (|qi|>=0.125) atoms.
getAsBitSet() - Method in class chemaxon.descriptors.DescriptorGenerator: Returns the generated descriptor in a BitSet representation if it is available.
getAscent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the ascent of this portion.
getAsFloatArray() - Method in class chemaxon.descriptors.DescriptorGenerator: Returns the generated descriptor in a float array representation if it is available.
getAsIntArray() - Method in class chemaxon.descriptors.DescriptorGenerator: Returns the generated descriptor in an int array representation if it is available.
getAsMolecule() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the found common substructure as a Molecule object.
getAssignedAtoms() - Method in class chemaxon.struc.graphics.MAssigner: Gets the atoms which are assigned by this object.
getAssociatedNonQueryFormat() - Method in class chemaxon.formats.MFileFormat: Gets the associated non-query format.
getAssociatedQueryFormat() - Method in class chemaxon.formats.MFileFormat: Gets the associated query format.
getAsString() - Method in class chemaxon.descriptors.DescriptorGenerator: Returns the generated descriptor in its native string representation.
getAsymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of asymmetric atoms.
getAsymmetricAtoms() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Determines the asymmetric atoms.
getAsymmetricEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the asymmetric Euclidean distance.
getAsymmetricEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Calculates the asymmetric Euclidean distance.
getAsymmetricEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP: Calculates the asymmetric Euclidean distance.
getAsymmetricEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getAsymmetricFBPA(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the asymmetric FBPA convolution product based distance of the fingerprint from an other (given as parameter).
getAsymmetryFactor() - Method in class chemaxon.descriptors.MDParameters: Gets the asymmetry factor used in the current parametrized asymmetric metrics.
getAtno() - Method in class chemaxon.struc.MolAtom: Gets the atomic number.
getAtom() - Method in class chemaxon.chemterms.AtomContext: Returns the input atom index.
getAtom() - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Gets the atom.
getAtom() - Method in class chemaxon.struc.graphics.MElectron
getAtom() - Method in class chemaxon.struc.graphics.MElectronContainer: All MElectron should belong to the same MolAtom, this returns the MolAtom reference of the first MElectron.
getAtom() - Method in class chemaxon.struc.sgroup.AttachmentPoint: Gets the atom on which the attachment point was placed.
getAtom() - Method in exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
getAtom(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the atom with the given index in this molecule.
getAtom(int) - Method in class chemaxon.struc.RgMolecule: Gets a node in the graph union.
getAtom(int) - Method in class chemaxon.struc.RxnMolecule: Gets a node.
getAtom(int) - Method in class chemaxon.struc.Sgroup: Gets an atom in the S-group.
getAtom(Molecule[]) - Method in class chemaxon.reaction.AtomIdentifier: Gets the MolAtom representation of the identified atom based on the provided output molecules of the reaction
getAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow: Gets the atom at the terminus of an arrow.
getAtom1() - Method in class chemaxon.struc.MolBond: Gets the first endpoint.
getAtom1Index() - Method in class chemaxon.alignment.DihedralScanResult.BondInfo: Atom index for first end atom.
getAtom2() - Method in class chemaxon.struc.MolBond: Gets the second endpoint.
getAtom2Index() - Method in class chemaxon.alignment.DihedralScanResult.BondInfo: Atom index for second end atom.
getAtomArray() - Method in class chemaxon.struc.graphics.MAtomSetPoint
getAtomArray() - Method in class chemaxon.struc.MoleculeGraph: Returns an array containing all atoms of the molecule in the order of their indices.
getAtomArray() - Method in class chemaxon.struc.Sgroup: Gets the array of atoms in the S-group.
getAtomCount() - Method in class chemaxon.alignment.AlignmentMolecule
getAtomCount() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the number of atoms in the input molecule.
getAtomCount() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the number of atoms in the multiplet.
getAtomCount() - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the number of atoms.
getAtomCount() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the number of atoms in the found common substructure.
getAtomCount() - Method in class chemaxon.struc.BondTable: Returns the number of atoms in the molecule this bond table represents.
getAtomCount() - Method in class chemaxon.struc.MoleculeGraph: Gets the number of atoms in this molecule.
getAtomCount() - Method in class chemaxon.struc.RgMolecule: Gets the number of nodes in the root structure.
getAtomCount() - Method in class chemaxon.struc.RxnMolecule: Returns the number of nodes in the graph union.
getAtomCount() - Method in class chemaxon.struc.Sgroup: Gets the number of atoms in the S-group.
getAtomCount(int) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the number of atoms with given atomic number (including its isotopes).
getAtomCount(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the number of atoms with the given atomic number.
getAtomCount(int) - Method in class chemaxon.struc.RgMolecule: Gets the number of atoms with the given atomic number in the root structure.
getAtomCount(int) - Method in class chemaxon.struc.RxnMolecule: Gets the number of atoms with the given atomic number in the unified molecule graph of the reaction.
getAtomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the number of atoms with given atomic number in the molecule isotope with the specified mass number.
getAtomFont() - Method in class chemaxon.marvin.common.UserSettings: Gets the atom symbol font name.
getAtomicNumber(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets the atomic number of the given atom.
getAtomicNumber(String) - Static method in class chemaxon.struc.MolAtom: Deprecated.
As of Marvin 5.9, replaced by a similar method PeriodicTable.findAtomicNumber(String).
The recommended method does not work for symbol not representing a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
getAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicTable: Returns the atomic number of the element in the periodic table specified by its symbol or -1 if not found.
getAtomicRadius(int) - Static method in class chemaxon.struc.PeriodicTable: Atomic radius of the element Angstroms.
getAtomicSurfaceAreaIncrement(int) - Method in class chemaxon.calculations.MSAPlugin: Returns the 3D surface area increments.
getAtomIndex() - Method in class chemaxon.calculations.CalculatorPlugin.HydrogenData
getAtomIndex() - Method in class chemaxon.calculations.nmr.NMRShift: Returns the atom index.
getAtomIndex() - Method in class chemaxon.reaction.AtomIdentifier: Gets the index of the atom in the molecule
getAtomIndex(int) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the atom index in the standardized molecule, or the atom index itself if the input molecule has not been standardized.
getAtomIndex(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the index of the ith atom of this multiplet.
getAtomIndexes() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the atom indices of the NMR active nuclei.
getAtomIndexMap() - Method in class chemaxon.calculations.CalculatorPlugin
getAtomIndexMapping() - Method in class chemaxon.calculations.CalculatorPlugin: Returns an immutable function of the current atom index mapping from the original molecule to standardized one.
getAtomIndices() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the indices of the atoms of this multiplet.
getAtomIterator() - Method in class chemaxon.struc.MoleculeGraph: Deprecated, for removal: This API element is subject to removal in a future version.
use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
getAtomIterator() - Method in class chemaxon.struc.RgMolecule: Deprecated, for removal: This API element is subject to removal in a future version.
use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
getAtomIterator() - Method in class chemaxon.struc.RxnMolecule: Deprecated, for removal: This API element is subject to removal in a future version.
use MoleculeGraph.atoms() or MoleculeGraph.getAtomArray() instead.
getAtomlogPIncrement(int) - Method in class chemaxon.calculations.LogPPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPPlugin.getAtomLogPIncrement(int) instead. This method will be removed in a future version.
getAtomLogPIncrement(int) - Method in class chemaxon.calculations.LogPPlugin: Returns the logP increment for the specified atom.
getAtomMap() - Method in class chemaxon.calculations.nmr.NMRMultiplet
getAtomMap() - Method in class chemaxon.struc.MolAtom: Gets the atom-atom mapping number.
getAtomMapping() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the atom mapping of the found common substructure.
getAtomMappingMethod() - Method in class chemaxon.marvin.common.UserSettings: Gets the atom mapping method.
getAtomNumberingType() - Method in class chemaxon.marvin.beans.MarvinPane: Determines the atom numbering.
getAtomNumberingType() - Method in class chemaxon.marvin.beans.MolPrinter: Returns atom numbering type.
getAtomNumberingType() - Method in class chemaxon.marvin.common.UserSettings: Gets the atom numbering type.
getAtomOf(MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
getAtomReverseMapping() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the reverse atom mapping of the found common substructure.
getAtoms() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getAtoms() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getAtoms() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the atoms.
getAtoms() - Method in class chemaxon.struc.MDocument.CheckerMark
getAtoms(int) - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the atom indices of the atoms having the given feature.
getAtoms(int, int[]) - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the atom indices of the atoms having the given feature.
getAtoms(Object) - Static method in class chemaxon.struc.graphics.MEFlow: Gets the atom or atoms at the terminus of an arrow.
getAtomSetColor(int) - Method in class chemaxon.marvin.beans.MarvinPane: Gets the color of an atom set.
getAtomSetColor(int) - Method in class chemaxon.struc.MDocument: Gets an atom set color.
getAtomSetColorMode(int) - Method in class chemaxon.struc.MDocument: Gets the atom set coloring mode.
getAtomSetColors() - Method in class chemaxon.descriptors.MolecularDescriptor: Determines the coloring of atoms.
getAtomSetColors() - Method in class chemaxon.descriptors.PFParameters: Gets the coloring of atoms as defined in the XML configuration file.
getAtomSetColors() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Determines the coloring of atoms.
getAtomSetFont(int) - Method in class chemaxon.struc.MDocument: Gets an atom set font.
getAtomSetIndexes(Molecule) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the individual atom color indexes.
getAtomSetIndexes(Molecule) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the individual atom colors by pharmcophore point type.
getAtomSetIndexes(Molecule, PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PFParameters: Gets the individual atom colors by pharmcophore point type.
getAtomSetNames() - Method in class chemaxon.descriptors.MolecularDescriptor
getAtomSetNames() - Method in class chemaxon.descriptors.PFParameters: Gets the name of atom sets (pharmacophore point type set), as defined in the configuration file/string.
getAtomSetNames() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getAtomSetRGB(int) - Method in class chemaxon.struc.MDocument: Gets an atom set color.
getAtomSetSize() - Method in class chemaxon.struc.MDocument: Gets the size of the atom set.
getAtomsize() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the atom size.
getAtomSize() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the atom size in units of regular bond length.
getAtomSize() - Method in class chemaxon.marvin.common.UserSettings: Gets the atom size in C-C bond length units.
getAtomSymbol(int, int, int[], Transform3D) - Method in class chemaxon.struc.MolAtom: Gets the string representation of the atom symbol.
getAtomSymbol(int, int, int[], Transform3D) - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the string representation of the atom symbol.
getAtomSymbolListAsString(MolAtom[]) - Static method in class chemaxon.struc.Sgroup
getAtropBonds() - Method in class chemaxon.alignment.AtropIsomerDetector: After the calculate method finished.
getAttach() - Method in class chemaxon.struc.MolAtom: Deprecated.
as of Marvin 6.0 replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom).
If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.
getAttach(MolAtom) - Static method in class chemaxon.struc.Sgroup: Gets the attachment point information from the ExtraAtomProperties
getAttachCount(Integer) - Method in class chemaxon.standardizer.actions.GroupDefinition: Gets the attachment point count for the atom specified by the index
getAttachedData() - Method in class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter
getAttachedData() - Method in class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter
getAttachedData() - Method in class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter
getAttachedData() - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenter: Gets the attached data.
getAttachedData() - Method in class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter
getAttachedDataMatch() - Method in class chemaxon.search.api.options.SearchOptions: Returns whether attached data (in data sgroups) should be used when comparing structures.
getAttachedDataPrefixes() - Method in class chemaxon.search.api.options.SearchOptions: Returns the prefixes of the names of those data sgroups that will be used during structure comparison or null if all data sgroups should be checked.
getAttachFromExtraAtomProp() - Method in class chemaxon.struc.MolAtom: Gets the attachment information stored in the extra atom properties
getAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the attachment point that's order is given as parameter
getAttachmentPointCount() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the number of the attachment points.
getAttachmentPointOrders() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the orders with which attachment point exists
getAttachmentPointOrders(int) - Method in class chemaxon.standardizer.actions.GroupDefinition: Returns the attachment point orders of the atom specified by atomIndex.
getAttachmentPointOrders(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the attachment orders of the given attachment atom.
getAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the sorted copy of the attachment point list.
getAttachParentSgroup() - Method in class chemaxon.struc.MolAtom: Gets the smallest containing sgroup which can have the attachment point information of this atom.
getAttrFont(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument: Gets the font for the specified attribute object.
getAttribute(String) - Method in class chemaxon.struc.graphics.MAnalysisBox
getAttribute(String) - Method in class chemaxon.struc.graphics.MBracket: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MEFlow
getAttribute(String) - Method in class chemaxon.struc.graphics.MElectron
getAttribute(String) - Method in class chemaxon.struc.graphics.MElectronContainer
getAttribute(String) - Method in class chemaxon.struc.graphics.MNameTextBox: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MPolyline: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MRectangle: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MRoundedRectangle: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MTextBox: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.MObject: Gets the value of an attribute.
getAttributes() - Method in class chemaxon.struc.graphics.MTextDocument.Section: Gets the attributes.
getAttributes(int, int, int) - Method in class chemaxon.struc.graphics.MTextDocument: Gets attributes of the text of len length from start that are supposed to be set even if their values are "default".
getAutoScale() - Method in class chemaxon.marvin.beans.MSketchPane: Returns autoscale property.
getAutoTabScale() - Method in class chemaxon.marvin.beans.MViewPane: Is tab scale automatically changed?
getAvailableCheckers() - Method in class chemaxon.structurechecker.CheckerFixerFactory: This method returns all StructureChecker instances available by the current configuration
getAvailableFixers() - Method in class chemaxon.structurechecker.CheckerFixerFactory: This method returns all StructureFixer instances available by the current configuration
getAvailableStandardizerActions() - Method in class chemaxon.standardizer.StandardizerActionFactory: Returns the list of standardizer actions that are available
getAverageNonZeroRatio() - Method in class chemaxon.descriptors.MDGenerator: Gets the average percentage of cells that have non-zero value taken all descriptors generated since the initialization of the generator into account.
getAveragePolarizabilityComponent() - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the average polarizability component (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
getAWTFont() - Method in class chemaxon.struc.graphics.MFont: Gets an AWT font instance.
getBackground() - Method in class chemaxon.struc.MObject: Gets the background color of the object.
getBackgroundColor() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the current background color.
getBalabanIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
getBallRadius() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the ball radius in units of covalent radius.
getBallRadius() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the ball radius for "ball and stick" mode.
getBallRadius() - Method in class chemaxon.marvin.common.UserSettings: Gets the ball radius for ball and stick mode.
getBaseElectronContainerIndex() - Method in class chemaxon.struc.graphics.MEFlow
getBaseElectronIndexInContainer() - Method in class chemaxon.struc.graphics.MEFlow
getBaseFont() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the base font.
getBaseFont() - Method in class chemaxon.struc.graphics.MTextBox: Gets the base font.
getBaseFontFamily() - Method in class chemaxon.struc.graphics.MTextBox: Gets the base font family.
getBaseFontStyle() - Method in class chemaxon.struc.graphics.MTextBox: Gets the base font style.
getBasicElectronCount() - Method in enum class chemaxon.struc.BondType: Returns the electron count given by an atom at the end of bond into the bond if it can be determined unambiguously, otherwise returns 0.
getBestTabScale() - Method in class chemaxon.marvin.beans.MViewPane: Gets the smallest best scale value in the molecule table.
getBestTabScale(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the best scale value for a molecule cell.
getBicycloStereo() - Method in class chemaxon.struc.MolAtom: Gets the previously stored bicyclo stereo information of this atom.
getBit(int) - Method in class chemaxon.descriptors.CustomDescriptor
getBitCount() - Method in class chemaxon.descriptors.CFParameters: Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.
getBitCount() - Method in class chemaxon.descriptors.RFParameters: Gets the preset bit count (number of fingerprint bits to be set to 1) parameter.
getBitPosition() - Method in class chemaxon.descriptors.ECFPFeature: Gets the generated bit position for this ECFP feature.
getBitPosition(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup: Returns the corresponding bit position for the given integer identifier.
getBitPosition(MolAtom, int) - Method in class chemaxon.descriptors.ECFPFeatureLookup: Returns the corresponding bit position for the given atom neighborhood.
getBoldBondWidth() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the C-C bold bond width in pt units.
getBoldBondWidth() - Method in class chemaxon.marvin.common.UserSettings: Gets the bold bond width in pt.
getBond() - Method in class chemaxon.alignment.DihedralScanResult: Represented bond info.
getBond() - Method in class chemaxon.struc.sgroup.AttachmentPoint: Gets the bond that is binded to this attachment point (crossing bond).
getBond(int) - Method in class chemaxon.struc.IteratorFactory.BondIterator: Deprecated.

Returns a bond of a specified index.
getBond(int) - Method in class chemaxon.struc.IteratorFactory.NeighbourIterator: Deprecated.

Returns a bond of a specified index.
getBond(int) - Method in class chemaxon.struc.MolAtom: Gets the i-th bond.
getBond(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the bond with the given index in this molecule.
getBond(int) - Method in class chemaxon.struc.RgMolecule: Gets an edge in the graph union.
getBond(int) - Method in class chemaxon.struc.RxnMolecule: Gets an edge.
getBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow: Gets the bond at the terminus of an arrow.
getBondArray() - Method in class chemaxon.struc.MolAtom: Gets the bonds connected to this atom.
getBondArray() - Method in class chemaxon.struc.MoleculeGraph: Returns an array containing all bonds of the molecule in the order of their indices.
getBondArray() - Method in class chemaxon.struc.Sgroup: Gets all bonds connecting two atoms that are both in the Sgroup
getBondConnectionInfo() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Gets a bond triplet which stores the crossing bond and flip information.
getBondCorrespondence() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Gets four bonds that store the crossing bond and flip information.
getBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the bond count.
getBondCount() - Method in class chemaxon.descriptors.CFParameters: Gets the preset path length (number of adjacent bonds) parameter.
getBondCount() - Method in class chemaxon.descriptors.RFParameters: Gets the preset path length (number of adjacent bonds) parameter.
getBondCount() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the number of bonds in the found common substructure.
getBondCount() - Method in class chemaxon.struc.MolAtom: Gets the number of bonds/ligands.
getBondCount() - Method in class chemaxon.struc.MoleculeGraph: Gets the number of bonds in this molecule.
getBondCount() - Method in class chemaxon.struc.RgMolecule: Gets the number of edges in the root structure.
getBondCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of edges in the graph union.
getBondFlags() - Method in class chemaxon.calculations.CalculatorPlugin.HydrogenData
getBondHashSpacing() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the bond hash spacing that is the distance hashes in a hashed bond.
getBondHashSpacing() - Method in class chemaxon.marvin.common.UserSettings: Gets the bond hash spacing.
getBondIndex() - Method in class chemaxon.alignment.DihedralScanResult.BondInfo: Bond index.
getBondIndex(int, int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the index of the bond connecting two atoms, -1 if the two atoms are not connected by bond.
getBondIndex(int, int) - Method in class chemaxon.struc.BondTable: Returns the index of the bond connecting two atoms, or -1 if the two atoms are not connected.
getBondIterator() - Method in class chemaxon.struc.MoleculeGraph: Deprecated, for removal: This API element is subject to removal in a future version.
use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
getBondIterator() - Method in class chemaxon.struc.RgMolecule: Deprecated, for removal: This API element is subject to removal in a future version.
use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
getBondIterator() - Method in class chemaxon.struc.RxnMolecule: Deprecated, for removal: This API element is subject to removal in a future version.
use MoleculeGraph.bonds() or MoleculeGraph.getBondArray() instead.
getBondLength() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the C-C bond length in pt units.
getBondLength() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the actual bond length in pt.
getBondLength() - Method in class chemaxon.marvin.common.UserSettings: Gets the bond length in pt.
getBondMapping() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the bond mapping of the found common substructure.
getBondReverseMapping() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the reverse bond mapping of the found common substructure.
getBonds() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getBonds() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getBonds() - Method in class chemaxon.struc.MDocument.CheckerMark
getBonds(MolAtom) - Method in class chemaxon.struc.Molecule: Returns the bonds attached to the given atom.
getBonds(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Returns the bonds attached to the given atom in this molecule graph.
getBondSetColor(int) - Method in class chemaxon.struc.MDocument: Gets a bond set color.
getBondSetColorMode(int) - Method in class chemaxon.struc.MDocument: Gets the bond set coloring mode.
getBondSetRGB(int) - Method in class chemaxon.struc.MDocument: Gets a bond set color.
getBondSetSize() - Method in class chemaxon.struc.MDocument: Gets the bond set size.
getBondSetThickness(int) - Method in class chemaxon.struc.MDocument: Gets a bond set thickness.
getBondSpacing() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the bond spacing.
getBondSpacing() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the double bond spacing that is the distance of the two lines representing a double bond.
getBondSpacing() - Method in class chemaxon.marvin.common.UserSettings: Gets the double bond spacing.
getBondTable() - Method in class chemaxon.struc.MoleculeGraph: Gets the bond (edge) table.
getBondTable() - Method in class chemaxon.struc.RgMolecule: Gets the bond table of the root structre.
getBondTable() - Method in class chemaxon.struc.RxnMolecule: Gets the bond table for the graph union.
getBondTo(MolAtom) - Method in class chemaxon.struc.MolAtom: Finds the bond that connects this atom to another atom.
getBondType() - Method in class chemaxon.struc.MolBond: Gets the type of the bond.
getBondType(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Determines the type of a bond (aromatic bonds are automatically recognized)
getBoolean(String) - Static method in class chemaxon.search.api.options.SearchOptions: Returns value as a boolean flag.
getBorderWidth() - Method in class chemaxon.marvin.beans.MViewPane: Gets the width of the border between cells.
getBottomMargin() - Method in class chemaxon.struc.PageSettings
getBoundAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets atoms with attachment point having crossing bond.
getBoundingRectangle(MoleculeGraph[]) - Method in class chemaxon.marvin.beans.MolPrinter: Returns the bounding rectangle of the specified molecules using the current scale factor.
getBoundRectSize() - Method in class chemaxon.marvin.beans.MSketchPane: Gets the size of the bounding rectangle.
getBracketCount() - Method in class chemaxon.struc.Sgroup: Gets the number of brackets in this S-group.
getBracketOrientation() - Method in class chemaxon.struc.graphics.MBracket: Gets the orientation of the bracket.
getBrackets() - Method in class chemaxon.struc.Sgroup: Gets all graphic brackets from this Sgroup
getBreakingChars() - Method in class chemaxon.struc.graphics.MNameTextBox: Gets the breaking characters after that the text in the text box can be broken if it doesn't fit into the text box.
getBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox: Gets the breaking characters after that the text in the text box can be broken if it doesn't fit into the text box.
getBrightestMolId() - Method in class chemaxon.descriptors.MDGenerator: Gets the id of that molecule which had the maximum number of non-zero cells among all descriptors generated since the initialization of the generator object.
getBrightness() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the brightness of the fingerprint.
getBrightness() - Method in class chemaxon.descriptors.ECFP: Gets the brightness of the fingerprint.
getBrightness() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the brightness of the fingerprint.
getBuildDate() - Static method in class chemaxon.common.version.VersionInfo: Returns the build date as string (in local time zone).
getBuildTime() - Static method in class chemaxon.common.version.VersionInfo: Returns the build time as string (in local time zone).
getBuildTimestamp() - Static method in class chemaxon.common.version.VersionInfo: Returns the build date and time.
getBuildTimestampStr() - Static method in class chemaxon.common.version.VersionInfo: Returns the build date and time as string in UTC time zone.
getBuildYear() - Static method in class chemaxon.common.version.VersionInfo: Returns the year of the build date as string.
getByIndex(int) - Static method in enum class chemaxon.calculations.PkaTrainingResult.PkaType
getByteArray() - Method in class chemaxon.struc.prop.MByteArrayProp: Gets the byte array value.
getC(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the state of a checkbox in a GridBagView table.
getCacheCapacity() - Method in class chemaxon.marvin.common.MDocStorage: Gets the maximum number of cached documents.
getCachedDoc(int, String) - Method in class chemaxon.marvin.common.MDocStorage: Gets the specified document if it is present in the memory.
getCachedDocIndices() - Method in class chemaxon.marvin.common.MDocStorage: Gets the indices of cached records.
getCachedResults(Molecule, boolean) - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns cached results, separated from the plugin object, so that no further enqueries needed to the plugin to get the result.
getCacheLock() - Method in class chemaxon.marvin.common.MDocStorage: Gets the synchronization lock for caching operations.
getCalcMolecule() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the molecule used in the calculation.
getCanvasComponent() - Method in class chemaxon.marvin.beans.MSketchPane: Determines canvas component of MarvinSketch.
getCapacity() - Method in class chemaxon.marvin.common.MDocStorage: Gets the total capacity.
getCarboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
getCarboaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
getCarbonVisibility() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the visibility style of the C labels on Carbon atoms.
getCarboRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the carbo ring count.
getCarboRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
getCarboRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
getCarboRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
getCASNumber() - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns the CAS number via public web service.
getCategory(Molecule, double) - Method in class chemaxon.calculations.solubility.SolubilityCategories: Calculates the solubility category of molecule.
getCellCount() - Method in class chemaxon.marvin.beans.MViewPane: Gets the number of molecule cells in the table.
getCellEditorValue() - Method in class chemaxon.marvin.beans.MViewCellEditor: Returns the edited molecule that is a Molecule instance.
getCellSize() - Method in class chemaxon.descriptors.MDParameters: Gets the number of bits of an atomic cell in the descriptor.
getCenter(int, int) - Method in class chemaxon.struc.RxnMolecule: Gets the geometrical center of a reaction component.
getCenterAtom() - Method in class chemaxon.descriptors.ECFPFeature: Gets the center atom of the represented substructure.
getCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup: Gets the central atom of this sgroup.
getCentralAtomIndex() - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor: Returns the index of the central atom.
getCentralAtomReference() - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor: For internal use only.
getChainAtomCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the chain atom count.
getChainBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the chain bond count.
getChangedAtomIndexes() - Method in class chemaxon.calculations.TautomerPlugin: Returns the indexes of the atoms changed during tautomerization.
getCharge() - Method in class chemaxon.struc.MolAtom: Returns the formal charge of the atom.
getCharge() - Method in class chemaxon.struc.sgroup.SgroupAtom: Returns the sum of the charges in the corresponding superatom s-group.
getCharge(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets the charge of the given atom.
getChargeAngle() - Method in class chemaxon.struc.MolAtom: Returns the charge angle of the atom or Double.NaN if it is not specified explicitly.
getChargeCategory() - Method in class chemaxon.calculations.LogDPlugin
getChargeDensity(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
getChargeDistribution() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the charge distribution array over pH values.
getChargeFont() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the charge's font.
getChargeLocation() - Method in class chemaxon.struc.Sgroup: Returns the charge location attribute of the S-group.
getChargeMatching() - Method in class chemaxon.search.api.options.SearchOptions: Get the charge matching option value
getChargePlusMinusDistribution() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the plus and the minus parts of the charge distribution array over pH values.
getChartComponent() - Method in class chemaxon.calculations.gui.MChart
getChartImage(int, int) - Method in class chemaxon.calculations.gui.MChart
getCheckerConfiguration() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
getCheckerConfiguration() - Method in interface chemaxon.structurechecker.CheckerRunner: Gets the list of available checkers
getCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings: Returns the URL of configuration for Checkers in marvin sketch.
getCheckerList() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Returns the checkerList
getCheckerList() - Method in class chemaxon.structurechecker.configuration.StructureCheckerActionStringReader
getCheckerList() - Method in interface chemaxon.structurechecker.configuration.StructureCheckerConfigurationReader: Returns the list of StructureChecker instances, which can be run by a CheckerRunner instance.
getCheckerList() - Method in class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlReader
getCheckerMarks() - Method in class chemaxon.struc.MDocument: Returns the array of checker marks NOTE: checker marks will be reset on any molecule change
getCheckSpHyb() - Method in class chemaxon.search.api.options.SearchOptions: Get the sp-hybridization state option
getChemicalHashedFingerprint(int[], int) - Static method in class chemaxon.descriptors.ReactionFingerprint: Creates chemical hashed fingerpint from reaction fingerprint.
getChemTermsFilter() - Method in class chemaxon.search.api.options.SearchOptions: Gets the Chemical Terms filtering expression
getChemTermsFilterConfig() - Method in class chemaxon.search.api.options.SearchOptions: Gets the configuration string for Chemical Terms filter.
getChild() - Method in interface chemaxon.core.util.MProgressMonitor: Deprecated.

Gets the child of this progress monitor.
getChildSgroup(int) - Method in class chemaxon.struc.Sgroup: Gets a child S-group.
getChildSgroupCount() - Method in class chemaxon.struc.Sgroup: Gets the number of child S-groups.
getChildSgroups() - Method in class chemaxon.struc.Sgroup: Gets the children of this S-group.
getChiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of tetrahedral stereogenic centers.
getChiralCenters() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Determines the chiral center atoms.
getChirality(int) - Method in class chemaxon.struc.MoleculeGraph: Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getChiralityOfOriginalLigand() - Method in class chemaxon.calculations.CalculatorPlugin.HydrogenData
getChiralitySupport() - Method in class chemaxon.marvin.beans.MarvinPane: Gets chirality support level.
getChiralitySupport() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the current chirality display mode.
getChiralitySupport() - Method in class chemaxon.marvin.common.UserSettings: Gets the chirality support parameter.
getCIPValue() - Method in class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter
getCIPValue() - Method in class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter
getCIPValue() - Method in class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter
getCIPValue() - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenter: Returns the stereo center value.
getCIPValue() - Method in class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter
getClassName() - Method in class chemaxon.calculations.services.LocalServiceDescriptor: Returns the full class name of the service
getClassName() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor: Gets the name of the standardizer class
getClassName() - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor: Gets the name of the checker class
getClean2dOpts() - Method in class chemaxon.marvin.common.UserSettings: Gets the 2D cleaning options.
getClean3dOpts() - Method in class chemaxon.marvin.common.UserSettings: Gets the 3D cleaning options.
getCleanDim() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the number of space dimensions for cleaning.
getCleanRelevantAtoms() - Method in class chemaxon.standardizer.Changes: Gets the list of atoms changed during the standardization procedure, and needs to be cleaned
getClip(Transform3D) - Method in class chemaxon.struc.graphics.MRectangle: Gets the clipping rectangle.
getClonedValue(String) - Method in class chemaxon.chemterms.ConstantTable: Returns the value of a constant.
getClosestMElectronRef(Point3D) - Method in class chemaxon.struc.graphics.MElectronContainer
getClosestMElectronRef(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
getCoarseReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint: Returns the tanimoto distance of the reaction centers.
getCode() - Method in enum class chemaxon.standardizer.actions.AromatizeAction.Type: Gets the MoleculeGraph constant value of the aromatization
getColor() - Method in enum class chemaxon.alignment.AlignmentProperties
getColor() - Method in class chemaxon.struc.MDocument.CheckerMark
getColor() - Method in class chemaxon.struc.MObject: Gets the color of the object.
getColoredLargestConjugatedSystem() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns a Molecule in which the atoms of largest conjugated system are colored.
getColoring() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the hit coloring options.
getColoringScheme() - Method in class chemaxon.alignment.ShapeData
getColors() - Method in class chemaxon.alignment.Pharmacophore3D
getColorScheme() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the color scheme.
getColorScheme() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the current color scheme.
getColumn(int) - Static method in class chemaxon.struc.MolAtom: The column or group of an element in the periodic table.
getColumn(int) - Static method in class chemaxon.struc.PeriodicTable: The column or group of an element in the periodic table.
getColumnCount() - Method in class chemaxon.struc.PageSettings
getColumnWidth() - Method in class chemaxon.marvin.common.TableOptions: Gets the default column width.
getColumnWidth(int) - Method in class chemaxon.marvin.common.TableOptions: Gets the default width of a specified column.
getColumnWidthsString() - Method in class chemaxon.marvin.common.TableOptions: Gets a parameter string containing column widths.
getCommandKeyStroke(int) - Static method in class chemaxon.marvin.util.SwingUtil: Gets the command keystroke preferred on the current platform.
getComment() - Method in class chemaxon.struc.Molecule: Gets the comment.
getComment() - Method in class chemaxon.struc.RgMolecule: Gets the comment of the root molecule.
getCommonActions() - Method in class chemaxon.marvin.beans.MarvinPane: Deprecated.
getCommonActions() - Method in class chemaxon.marvin.beans.MSketchPane: Deprecated.
getCommonActions() - Method in class chemaxon.marvin.beans.MViewPane: Deprecated.
getCommonBitCount(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint
getCommonBitCount(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint
getComponent() - Method in interface chemaxon.calculations.gui.ParameterPanelHandler: Returns the parameter panel component.
getComponent(int, int) - Method in class chemaxon.struc.RxnMolecule: Gets a reactant, product or agent.
getComponent(long) - Method in class chemaxon.struc.RxnMolecule: Gets a reactant, product or agent.
getComponent(Molecule, int) - Method in class chemaxon.checkers.AtomChecker
getComponent(Molecule, int) - Method in class chemaxon.checkers.BondChecker
getComponent(Molecule, int) - Method in class chemaxon.checkers.ComponentChecker: Gets the component from the molecule with index i.
getComponentCount(int) - Method in class chemaxon.struc.RxnMolecule: Gets the number of reactants, products or agents.
getComponentCount(Molecule) - Method in class chemaxon.checkers.AtomChecker
getComponentCount(Molecule) - Method in class chemaxon.checkers.BondChecker
getComponentCount(Molecule) - Method in class chemaxon.checkers.ComponentChecker: Gets the number of the components in the molecule
getComponentFlags(long) - Method in class chemaxon.struc.RxnMolecule: Gets the reaction component type flags from the ID.
getComponentID(MolAtom) - Method in class chemaxon.struc.RxnMolecule: Gets the reaction component ID of an atom.
getComponentID(MolBond) - Method in class chemaxon.struc.RxnMolecule: Gets the reaction component ID of a bond.
getComponentID(Molecule) - Method in class chemaxon.struc.RxnMolecule: Gets the ID of a reaction component.
getComponentIndex(long) - Method in class chemaxon.struc.RxnMolecule: Gets the reactant, product or agent index from the ID.
getComponents(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction: A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.ExpandAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.MapAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.MapReactionAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.NeutralizeAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RearrangeReactionAction: Every action that needs to do something on a reaction as a whole needs this, otherwise reaction components will be processed one-by-one.
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.StripSaltsAction
getComponents(Molecule) - Method in class chemaxon.standardizer.actions.TransformAction
getComponentType(long) - Method in class chemaxon.struc.RxnMolecule: Gets the reaction component type from the ID.
getComposition() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
getConfiguration() - Method in class chemaxon.standardizer.configuration.StandardizerActionStringReader
getConfiguration() - Method in interface chemaxon.standardizer.configuration.StandardizerConfigurationReader: Gets the configuration defined by the pre-set configuration file.
getConfiguration() - Method in class chemaxon.standardizer.configuration.StandardizerConfigurationXmlReader
getConfiguration() - Method in class chemaxon.standardizer.Standardizer: Gets the configuration of the standardizer.
getConformer(int) - Method in class chemaxon.calculations.ConformerPlugin: Returns a conformer.
getConformerCount() - Method in class chemaxon.calculations.ConformerPlugin: Returns the number of different conformers.
getConformers() - Method in class chemaxon.calculations.ConformerPlugin: Returns all conformers in a Molecule[] array.
getConformerWithConformerInfoProperty(int) - Method in class chemaxon.calculations.ConformerPlugin: Deprecated.
Only intended for internal use.
getConfTryCountLimit() - Method in class chemaxon.alignment.MMPAlignmentProperties
getConnectedObject(int) - Method in class chemaxon.struc.MDocument: Gets an object from the document or from the chemical structure of the document.
getConnectedObjectCount() - Method in class chemaxon.struc.MDocument: Gets the number of objects in this document and in the chemical structure of this document.
getConnectionAtom() - Method in class chemaxon.struc.BicycloStereoDescriptor: Returns the ring atom connected to the ligand.
getConnectionAtomIndex() - Method in class chemaxon.struc.BicycloStereoDescriptor: Returns the ring atom index connected to the ligand.
getConnectionAtoms() - Method in class chemaxon.standardizer.actions.GroupDefinition: Gets the indexes of atoms connection to any atoms
getConnectivity() - Method in class chemaxon.struc.Sgroup: Gets S-group connectivity.
getContainerMObject(MDocument) - Method in class chemaxon.struc.MObject
getContainerOfMelectron(MElectron) - Static method in class chemaxon.struc.graphics.MElectronContainer
getContext() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the context of the data sgroup.
getContextId() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the id of the context of the data sgroup.
getCoordinateBondStyle() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the coordinate bond line style when both atoms are single.
getCoordinateBondStyle() - Method in class chemaxon.marvin.common.UserSettings: Gets the "coordinative" bond line style when both atoms are single.
getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the coordinate bond line style.
getCoordinateBondStyleAtMulticenter() - Method in class chemaxon.marvin.common.UserSettings: Gets the "coordinative" bond line style when one of the atoms is multicenter.
getCoordinatesOfAligned() - Method in class chemaxon.alignment.AlignOnPairedAtoms
getCoordinatesOfReference() - Method in class chemaxon.alignment.AlignOnPairedAtoms
getCopyAsFormat() - Method in class chemaxon.marvin.common.UserSettings: Gets the selected format from the Copy As dialog.
getCorrectionFactor(String[], int, int) - Method in class chemaxon.calculations.PkaTrainingResult
getCorrectionLibraryIds() - Static method in class chemaxon.calculations.PkaPlugin: Returns the id's of available pKa correction libraries.
getCount() - Method in class chemaxon.calculations.gui.PluginFactory: Returns the number of plugin records.
getCouplingConstants() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns coupling constants.
getCouplingConstants(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the coupling constants of the ith atom in this multiplet.
getCouplingConstants(int, NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the coupling constants of the ith atom in this multiplet.
getCouplingConstants(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns coupling constants in the given unit.
getCouplingNeeded() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns whether spin-spin couplings are taken into account.
getCovalentRadius(int) - Static method in class chemaxon.struc.PeriodicTable: Covalent radius of the element in Angstroms.
getCovalentRadius(int, int) - Static method in class chemaxon.struc.PeriodicTable: Covalent radius of the element in specific bond type in Angstroms.
getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.Sgroup: Gets the atoms that have crossing bonds.
getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the atoms from the S-group that have crossing bonds.
getCSSR() - Method in class chemaxon.struc.MoleculeGraph: Gets the Complete Set of Smallest Ring atom indexes array.
getCSSRIdxesForAtoms() - Method in class chemaxon.struc.MoleculeGraph: Get the cssr ring indexes in which the atom (specified with its index) can be located.
getCtab() - Method in class chemaxon.struc.MoleculeGraph: Gets the connection table.
getCtab() - Method in class chemaxon.struc.RgMolecule: Gets the connection table of the root structure.
getCtab() - Method in class chemaxon.struc.RxnMolecule: Gets the connection table for the graph union.
getCTAtom1() - Method in class chemaxon.struc.MolBond: Gets the first atom for cis/trans stereo calculation.
getCTAtom4() - Method in class chemaxon.struc.MolBond: Gets the fourth atom for cis/trans stereo calculation.
getCurrent() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
getCurrent() - Method in interface chemaxon.structurechecker.CheckerRunner
getCurrentCheckerName() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
getCurrentCheckerName() - Method in interface chemaxon.structurechecker.CheckerRunner
getCurrentDefaultFontMetrics() - Method in class chemaxon.struc.graphics.MTextBox: Gets the current default FontMetrics.
getCurrentForeground() - Method in class chemaxon.struc.graphics.MTextBox: Gets the current color.
getCurrentFrameIndex() - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets the current frame index.
getCurrentHeight() - Method in class chemaxon.struc.graphics.MTextBox: Gets the current height of the text.
getCurrentMetricIndex() - Method in class chemaxon.descriptors.MDParameters
getCurrentMolecule() - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets the stored molecule graph.
getCurrentScriptCount(int) - Method in class chemaxon.struc.graphics.MTextBox: Gets the number of subscripts or superscripts on the last normal character.
getCurrentSubLevel() - Method in class chemaxon.struc.graphics.MTextBox: Gets the current subscript/superscript level.
getCurrentTarget() - Method in class chemaxon.marvin.common.MAction: Is the current action coming from a pop-up menu item?
getCurrentTextAttributes(int) - Method in class chemaxon.struc.graphics.MTextBox: Gets the common attributes of the selected text or attributes for the next character to be typed.
getCurrentWidth() - Method in class chemaxon.struc.graphics.MTextBox: Gets the current width of the text.
getCursorColumn() - Method in class chemaxon.struc.graphics.MTextBox: Gets the cursor's column number.
getCursorPos() - Method in class chemaxon.struc.graphics.MTextBox: Gets the cursor position.
getCursorRow() - Method in class chemaxon.struc.graphics.MTextBox: Gets the cursor's row number.
getCustomFuzzyIncrements(int, int) - Method in class chemaxon.descriptors.PFParameters: Gets fuzzy increments for the fuzzy smoothing with a user-defined custom distribution (fuzzy smoothing vector).
getCustomMatching() - Method in class chemaxon.search.mcs.McsSearchOptions: Returns the factory that is used to create custom matcher (if specified).
getCustomName() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the customName
getCyclomaticNumber() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the smallest number of graph edges which must be removed such that no circuit remains.
getDarkestMolId() - Method in class chemaxon.descriptors.MDGenerator: Gets the id of that molecule which had the minimum number of non-zero cells among all descriptors generated since the initialization of the generator object.
getData() - Method in class chemaxon.calculations.stereo.stereocenters.AttachedData: Gets the data field.
getData() - Method in class chemaxon.descriptors.MDParameters: Gets the byte array which is used for conversions between internal and external data formats.
getData() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the data value to be set.
getDataFromClipboard(DataFlavor) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable: Returns the Molecule from the Transferable object.
getDataLine(int) - Method in class chemaxon.struc.sgroup.DataSgroup: Gets a line of data.
getDataLineCount() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the number of data lines.
getDataToClipboard(DataFlavor) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable: Returns the clipboard representation of the given Molecule.
getDaviesHlbValue() - Method in class chemaxon.calculations.HLBPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, use HLBPlugin.getDaviesHLBValue() instead.
getDaviesHLBValue() - Method in class chemaxon.calculations.HLBPlugin: Returns the HLB value calculated by Davies method.
getDebug() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the debugging level.
getDecForm() - Method in class chemaxon.descriptors.MDParameters: Gets the formatter object that is capable of formatting fractions with given precision.
getDecompositions() - Method in class chemaxon.search.RgroupDecompositionResults: Returns the Decomposition objects corresponding to the targets.
getDefault() - Static method in enum class chemaxon.search.api.options.TautomerEqualityMode
getDefault() - Static method in enum class chemaxon.search.api.options.TautomerTransformationMode
getDefault() - Static method in class chemaxon.search.mcs.McsSearchOptions: Returns the default search options object.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.BCUT: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.CustomDescriptor: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ECFP: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ScalarDescriptor: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDissimilarityMetricThresholds() - Method in class chemaxon.descriptors.ShapeDescriptor: Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.BCUTParameters: Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.CDParameters: Gets the XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.CFParameters: Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.ECFPParameters: Get the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.MDParameters: Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.PFParameters: Gets the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.RFParameters: Get the default XML configuration string.
getDefaultDocumentFrame() - Method in class chemaxon.descriptors.ShapeParameters: Get the default XML configuration string.
getDefaultFont() - Method in class chemaxon.struc.graphics.MTextDocument: Gets the default font.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the index of the default metric.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.ECFP: Gets the index of the default metric.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the index of the default metric.
getDefaultMetricIndex() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the index of the default metric.
getDefaultProperty(String) - Method in class chemaxon.marvin.common.UserSettings: Gets the value of the given key in the default configuration or null if the key does not exist.
getDefaultSaveFormat() - Method in class chemaxon.marvin.common.UserSettings: Gets the default molecule format in the "Save As" dialog.
getDefaultScale() - Static method in class chemaxon.marvin.beans.MSketchPane: Returns the default scale factor which is equivalent to 100% magnification.
getDefaultServiceDescriptorReader() - Static method in class chemaxon.calculations.services.ServiceDescriptorTools: Returns the default ServiceDescriptorReader instance
getDefaultServiceDescriptorWriter() - Static method in class chemaxon.calculations.services.ServiceDescriptorTools: Returns the default ServiceDescriptorWriter instance
getDefaultSize() - Method in class chemaxon.marvin.common.TableSupport: Gets the default size of an MViewPane containing the generated table.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.ECFPParameters: Gets the default configuration of the standardizer.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.MDParameters: Gets the default configuration of the standardizer.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.PFParameters: Gets the default configuration of the standardizer.
getDefaultStandardizerConfiguration() - Static method in class chemaxon.descriptors.ShapeParameters: Gets the default configuration of the standardizer.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ECFP: Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ReactionFingerprint: Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ScalarDescriptor: Gets a metric dependent default threshold value.
getDefaultThreshold(int) - Method in class chemaxon.descriptors.ShapeDescriptor: Gets a metric dependent default threshold value.
getDefaultValue() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the default value of the multiplet function.
getDefaultValue() - Method in class chemaxon.calculations.nmr.NMRSpectrum: The default value of the function.
getDensityCounts() - Method in class chemaxon.descriptors.MDGenerator: Gets the array of bit density.
getDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule: Gets the R-group definition's index which depends on the referenced R-group definition.
getDescent(Graphics, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the descent of this portion.
getDescription() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the description (tooltip) of service descriptor
getDescription() - Method in class chemaxon.checkers.AbstractStructureChecker
getDescription() - Method in class chemaxon.checkers.InvalidChecker
getDescription() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getDescription() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getDescription() - Method in interface chemaxon.checkers.StructureChecker
getDescription() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the description
getDescription() - Method in class chemaxon.fixers.StructureFixerDescriptor: Returns the description
getDescription() - Method in class chemaxon.formats.MFileFormat: Gets the format description.
getDescription() - Method in class chemaxon.formats.OptionDescriptor: Gets the description.
getDescription() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the description of the action
getDescriptor() - Method in class chemaxon.checkers.AbstractStructureChecker
getDescriptor() - Method in class chemaxon.checkers.InvalidChecker
getDescriptor() - Method in interface chemaxon.checkers.StructureChecker: Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker
getDescriptor() - Method in class chemaxon.fixers.AbstractStructureFixer
getDescriptor() - Method in interface chemaxon.fixers.StructureFixer: Gets the descriptor object of the fixer.
getDescriptor() - Method in class chemaxon.standardizer.AbstractStandardizerAction
getDescriptor() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
getDescriptor() - Method in interface chemaxon.standardizer.StandardizerAction: Gets the descriptor of the standardizer action.
getDescriptorLongName(String) - Static method in class chemaxon.descriptors.DescriptorGenerator: Returns the long name for the given molecular descriptor type.
getDescriptorTypeName(String) - Static method in class chemaxon.descriptors.MDParameters: Takes the descriptor type name from the root element of the XML configuration.
getDescriptorTypes() - Static method in class chemaxon.descriptors.DescriptorGenerator: Returns the list of the built-in molecular descripor types.
getDescriptorURI() - Method in class chemaxon.calculations.services.JsonServiceDescriptor: Gets the URI of the JSON RPC descriptor file
getDescrType() - Method in class chemaxon.descriptors.CDParameters: Gets the type of the descriptor.
getDf1() - Method in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode
getDf2() - Method in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode
getDiameter() - Method in class chemaxon.descriptors.ECFPFeature: Gets the diameter of the represented substructure.
getDiameter() - Method in class chemaxon.descriptors.ECFPParameters: Gets the preset diameter parameter.
getDihedral(int[]) - Method in class chemaxon.calculations.GeometryPlugin: Returns the dihedral of 4 atoms.
getDihedral(int, int, int, int) - Method in class chemaxon.calculations.GeometryPlugin: Returns the dihedral of 4 atoms.
getDihedralScanResults() - Method in class chemaxon.alignment.AtropIsomerDetector: Get results of executed dihedral scans.
getDim() - Method in class chemaxon.struc.MoleculeGraph: Gets the dimension.
getDipole() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the length of the dipole moment vector.
getDipoleVector() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the dipole moment vector.
getDipoleX() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the x component of the dipole moment vector.
getDipoleY() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the y component of the dipole moment vector.
getDipoleZ() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the z component of the dipole moment vector.
getDirectory() - Method in class chemaxon.marvin.beans.MarvinPane: Sets the working directory.
getDisabledGroupTypes() - Method in class chemaxon.marvin.beans.MSketchPane
getDisplay() - Method in class chemaxon.calculations.gui.PluginFactory.PluginRecord
getDisplay(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets a display object, loads it if needed.
getDisplayedChars() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the number of characters to be displayed(1...999 or 0 for all)
getDisplayedLines() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the number of lines to be displayed (0: show all)
getDisplayMolecule() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the molecule object to be used for GUI display.
getDisplayMolecule() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the molecule object to be used for GUI display.
getDisplayMolecule() - Method in class chemaxon.calculations.MSAPlugin: Returns the molecule object to be used for GUI display.
getDisplayVersion() - Static method in class chemaxon.common.version.VersionInfo: Returns the display version.
getDispopts() - Method in class chemaxon.marvin.beans.MarvinPane: Gets display options.
getDispopts() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the actual display options.
getDispoptsExt() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the actual extended display options.
getDispOptsMask() - Static method in enum class chemaxon.rendering.constants.AnyBondStyle
getDispOptsMask() - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
getDispOptsMask() - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle
getDispOptsMask() - Static method in enum class chemaxon.rendering.constants.RenderingStyle
getDispOptsOffset() - Static method in enum class chemaxon.rendering.constants.AnyBondStyle: Get the offset used to store the settings in the dispopts integer.
getDispOptsOffset() - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle: Get the offset used to store the settings in the dispopts integer.
getDispOptsOffset() - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle: Get the offset used to store the settings in the dispopts integer.
getDispOptsOffset() - Static method in enum class chemaxon.rendering.constants.RenderingStyle: Get the offset used to store the settings in the dispopts integer.
getDissimilarity() - Method in class chemaxon.search.mcs.McsSearchResult: Returns a Tanimoto-like dissimilarity metric score of the input molecules based on the found maximum common substructure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.BCUT: Calculates the dissimilarity ratio between two BCUT objects using the current default metric.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the dissimilarity between two chemical fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFP: Calculates the dissimilarity ratio between two ECFP objects using the current default metric.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.MolecularDescriptor: Calculates the dissimilarity ratio between two MolecularDescriptor objects using the default metric.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ReactionFingerprint: Calculates the dissimilarity between two reaction fingerprints using the default distance measure.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ScalarDescriptor: Calculates the dissimilarity between two scalar descriptor using the default metrics In the present implementation it is always the absolute difference between them.
getDissimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.BCUT: Calculates the dissimilarity between two BCUT objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the dissimilarity between two chemical fingerprints using the specified distance metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.CustomDescriptor: Calculates the dissimilarity between two descriptors using the specified parametrized dissimilarity metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ECFP: Calculates the dissimilarity between two ECFP objects using the specified metric, apart from that it is the same as getDissimilarity(final MolecularDescriptor other).
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.MolecularDescriptor: Calculates the dissimilarity between two MolecularDescriptor objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the dissimilarity between two pharmacophore fingerprints using the specified parametrized distance metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ReactionFingerprint: Calculates the dissimilarity between two reaction fingerprints using the specified distance metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ScalarDescriptor: Calculates the dissimilarity between two scalar descriptor using the specified metric.
getDissimilarity(MolecularDescriptor, int) - Method in class chemaxon.descriptors.ShapeDescriptor
getDissimilarity(T) - Method in class chemaxon.descriptors.SimilarityCalculator: Gets the dissimilarity value according to previously defined metric and its parameters.
getDissimilarityMetricIndex(String) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the internal index of the given metric.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.BCUT: Gets the dissimilarity metric names introduced for this class of MolecularDescriptor.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the dissimilarity metric names
getDissimilarityMetrics() - Method in class chemaxon.descriptors.CustomDescriptor: Gets the dissimilarity metric names.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ECFP: Gets the dissimilarity metric names introduced for this class of MolecularDescriptor.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the dissimilarity metric names in an array.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the dissimilarity metric names.
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the dissimilarity metric names
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ScalarDescriptor: Gets the dissimilarity metric names
getDissimilarityMetrics() - Method in class chemaxon.descriptors.ShapeDescriptor
getDissimilarityMetricsParamDefault() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the dissimilarity metric parameter names -> no parameters.
getDissimilarityMetricsParamHelp() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the dissimilarity metric parameter names -> no parameters.
getDissimilarityMetricsParamNames() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the dissimilarity metric parameter names -> no parameters.
getDissimilarityMetricsParamNum() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the dissimilarity metric parameter number -> no parameters.
getDissimilarityMetricsParamRanges() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the dissimilarity metric parameter ranges -> no parameters.
getDistance(int[]) - Method in class chemaxon.calculations.GeometryPlugin: Returns the distance of 2 atoms.
getDistance(int, int) - Method in class chemaxon.calculations.GeometryPlugin: Returns the distance of 2 atoms.
getDistanceCount(int, int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Counts the given value in a row of the distance matrix.
getDistanceDegree(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
getDoc(int, String) - Method in class chemaxon.marvin.common.MDocStorage: Gets the specified document.
getDoc(int, String, ProgressMonitor) - Method in class chemaxon.marvin.common.MDocStorage: Gets the specified document.
getDocLabel(int, MDocument) - Method in class chemaxon.formats.MDocSource: Returns the display label for the given document and document index.
getDocLabel(int, MDocument) - Method in class chemaxon.marvin.common.MDocStorage: Returns the display label for the given document and document index.
getDocSource() - Method in class chemaxon.marvin.common.MDocStorage: Gets the document source.
getDocSourcePosition() - Method in class chemaxon.marvin.common.MDocStorage: Gets the current position in the input.
getDocStorage() - Method in class chemaxon.marvin.beans.MViewPane: Gets the sparse dynamic document storage.
getDocStorage() - Method in class chemaxon.marvin.common.TableSupport: Gets the sparse dynamic document storage.
getDocument() - Method in class chemaxon.marvin.beans.MSketchPane: Gets the document.
getDocument() - Method in class chemaxon.struc.MoleculeGraph: Gets the document object.
getDocument(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the nth document.
getDocument(Molecule) - Static method in class chemaxon.calculations.CalculatorPlugin: Returns encapsulating document, creates it if needed.
getDocumentForChild(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Gets the parent document for a child molecule graph.
getDocuments() - Method in class chemaxon.marvin.beans.MViewPane: Gets the array of documents.
getDocumentStyleName() - Method in class chemaxon.marvin.common.UserSettings
getDomainMax() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the upper end of this multiplet.
getDomainMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the upper end of the spectrum.
getDomainMin() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the lower end of this multiplet.
getDomainMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the lower end of the spectrum.
getDominantTautomerDistribution(int) - Method in class chemaxon.calculations.TautomerPlugin: Returns the distribution of the dominant tautomer.
getDonorAtomCount() - Method in class chemaxon.calculations.HBDAPlugin: Returns the overall donor atom count (without multiplicity) in the molecule.
getDonorSiteCount() - Method in class chemaxon.calculations.HBDAPlugin: Returns the overall donor count (with multiplicity) in the molecule.
getDonorSiteCount(int) - Method in class chemaxon.calculations.HBDAPlugin: Returns the atomic donor count corresponding to the specified atom index.
getDotDisconnectedFormalChargeFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the dot-disconnected molecular formula of a multifragment molecule with its formal charge.
getDotDisconnectedFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the dot-disconnected molecular formula of a multifragment molecule.
getDotDisconnectedIsotopeFormalChargeFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.
getDotDisconnectedIsotopeFormalChargeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.
getDotDisconnectedIsotopeFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the dot-disconnected isotope formula of a multifragment molecule.
getDotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the dot-disconnected isotope formula of a multifragment molecule.
getDoubleArray() - Method in class chemaxon.struc.prop.MDoubleArrayProp: Gets the integer value.
getDoubleBondStereoMatchingMode() - Method in class chemaxon.search.api.options.SearchOptions: Get the double bond stereo matching mode.
getDoublePrecision() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the precision.
getDownWedge() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the wedge bond display convention.
getDownWedge() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the down wedge orientation.
getDownWedge() - Method in class chemaxon.marvin.common.UserSettings: Gets the wedge bond display convention.
getDraggedObject() - Method in class chemaxon.struc.MDocument: Gets the dragged object
getDreidingEnergy() - Method in class chemaxon.calculations.GeometryPlugin: Returns the energy of the conformer.
getDx() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the x shift.
getDy() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the y shift.
getEccentricity(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
getEditable() - Method in class chemaxon.marvin.beans.MViewCellEditor: Returns the mode that determines if the structure is editable.
getEditable() - Method in class chemaxon.marvin.beans.MViewPane: Returns the mode that determines if the structure is editable.
getEditorClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the editorClassName
getEditorClassName() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Returns the editorClassName
getEditorClassName() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor: Gets the name of the editor of the standardizer class
getEditorClassName() - Method in class chemaxon.structurechecker.CheckerFixerFactory.CheckerClassDescriptor: Gets the name of the editor of the checker class
getEditorComponent() - Method in class chemaxon.marvin.beans.MViewCellEditor: Returns the editor component.
getEFlowsFromAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow: Returns all the EFlow from this atom.
getEFlowsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow: Returns all the EFlows that are started from this atom or pointing to this atom.
getEFlowsToAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MEFlow: Returns all the EFlows to this atom.
getEigenVector() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Deprecated.
Use HuckelAnalysisPlugin.getHMOEigenVector()
getElectronContainersOf(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
getElectronCount() - Method in class chemaxon.struc.MDocument: Returns the number of electrons.
getElectronDensity(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the electron density of an atom calculated with HMO, Double.NaN for no value.
getElectronProp() - Method in class chemaxon.struc.MolAtom: Returns the number of lone pairs on this atom.
getElectrophilicEnergy(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
getElectrophilicOrder(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Deprecated.
Use HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)
getElementCount() - Static method in class chemaxon.struc.PeriodicTable: Number of elements in the periodic table
getEnableStandardization() - Method in class chemaxon.descriptors.RFParameters: Shows if standardization should be applied of not.
getEnantiomer(T) - Static method in class chemaxon.core.calculations.stereo.Stereochemistry: Get the enantiomer pair of the given molecule
getEnclosingCube() - Method in class chemaxon.struc.MoleculeGraph: Gets the cube that encloses the atoms of the molecule graph.
getEncoding() - Method in class chemaxon.formats.MolExportModule: Gets the output encoding.
getEncoding() - Method in class chemaxon.formats.PositionedInputStream: Gets the encoding.
getEncodingFromOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil: Gets the encoding that was explicitly given as an import option.
getEndDx() - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the x shift at the end.
getEndPos() - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the position of the last character + 1.
getEndPosition() - Method in class chemaxon.struc.MDocument: Gets the end position of this document in the input file.
getEndPosition() - Method in class chemaxon.struc.Molecule: Gets the end position of this molecule in the input file.
getEnergy() - Method in class chemaxon.alignment.DihedralScanResult.ScanStep: Represented energy.
getEnergy() - Method in class chemaxon.calculations.ConformerPlugin: Returns the energy of the lowest energy conformer in kcal/mol.
getEnergy(int) - Method in class chemaxon.calculations.ConformerPlugin: Returns the energy of the i-th conformer in kcal/mol.
getEnergyDifference() - Method in class chemaxon.alignment.DihedralScanResult: Observed rotational energy barrier.
getEnhancedStereo() - Method in class chemaxon.calculations.stereo.stereocenters.EnhancedStereoGroup
getEnhancedStereo() - Method in class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter: Returns the enhanced stereo group (optional).
getEnhancedStereoFlags() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Returns the enhanced stereo flags of the molecule.
getEnhancedStereoGroup(String) - Method in class chemaxon.calculations.stereo.StereoAnalysis: Gets the EnhancedStereoGroup to which the specified flag is mapped.
getEnumCodeNeeded() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Tests whether unique Markush enumeration code should be generated
getEnumerateMarkush() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns true if markush structures should be hit enumerated according to the query structure.
getError() - Method in class chemaxon.alignment.MolAligner: Get the error for the best alignment
getErrorCode() - Method in class chemaxon.checkers.AbstractStructureChecker
getErrorCode() - Method in class chemaxon.checkers.ExternalStructureChecker
getErrorCode() - Method in class chemaxon.checkers.InvalidChecker
getErrorCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
getErrorCode() - Method in interface chemaxon.checkers.result.ExternalStructureCheckerResult: This function returns a String which identifies the problems thus this must be unique for each class that implements this interface
getErrorCode() - Method in interface chemaxon.checkers.StructureChecker: Returns the String represented error code of the checker (this error code should be used for external implementation support instead of StructureChecker.getErrorType())
getErrorComponent() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns a component with the appropriate error message.
getErrorCount() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult: Return the error count.
getErrorDescription(int) - Method in class chemaxon.checkers.AbstractStructureChecker: Generate the error description depends on erroCount
getErrorDescription(StructureCheckerDescriptor, int) - Static method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getErrorMessage() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).
getErrorMessage() - Method in class chemaxon.calculations.ChargePlugin: Returns the calculation error information message if ChargePlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.ChemicalNamePlugin
getErrorMessage() - Method in class chemaxon.calculations.ElementalAnalysisPlugin
getErrorMessage() - Method in class chemaxon.calculations.HBDAPlugin: Returns the calculation error information message if HBDAPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the calculation error information message if HuckelAnalysisPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.IonChargePlugin: Returns the calculation error information message if IonChargePlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the calculation error information message if IsoelectricPointPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.LogDPlugin: Returns the calculation error information message if LogDPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.LogPPlugin: Returns the calculation error information message if LogPPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin: Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.calculations.MSAPlugin: Returns the calculation error information message if MSAPlugin.run() returned false (calculation error).
getErrorMessage() - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the calculation error information message if OrbitalElectronegativityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.PkaPlugin: Returns the calculation error information message if PkaPlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the calculation error information message if PolarizabilityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.RefractivityPlugin: Returns the calculation error information message if RefractivityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.calculations.ResonancePlugin: Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.calculations.TautomerPlugin: Returns the calculation error information message or the empty string if there is no error.
getErrorMessage() - Method in class chemaxon.calculations.TPSAPlugin: Returns the calculation error information message if TPSAPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.checkers.InvalidChecker: Gets the error message of the checker instance
getErrorMessage() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction: Gets the error message of the standardizer instance
getErrorMessage(List<CalculatorError>) - Method in class chemaxon.calculations.api.ProgressableCalculator
getErrorType() - Method in class chemaxon.checkers.AbstractStructureChecker
getErrorType() - Method in class chemaxon.checkers.InvalidChecker
getErrorType() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getErrorType() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getErrorType() - Method in interface chemaxon.checkers.StructureChecker
getErrorType() - Method in class chemaxon.checkers.SubstructureChecker
getErrorTypeDefaultFixerMap() - Method in class chemaxon.structurechecker.configuration.StructureCheckerActionStringReader
getErrorTypeDefaultFixerMap() - Method in interface chemaxon.structurechecker.configuration.StructureCheckerConfigurationReader: Returns a map that contains the association between StructureCheckerErrorType and StructureFixer instances.
getErrorTypeDefaultFixerMap() - Method in class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlReader
getEstimatedStereoisomerCount() - Method in class chemaxon.calculations.stereo.StereoisomerEnumeration: Gets the number of stereoisomers, if molecule does not contain pseudo stereocenters.
# of stereoisomer = 2 ^ stereocenter count
getEuclidean(BCUT) - Method in class chemaxon.descriptors.BCUT: Calculates the Euclidean distance.
getEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the Euclidean distance.
getEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Calculates the Euclidean distance.
getEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP: Calculates the Euclidean distance.
getEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the Euclidean distance.
getEuler() - Method in class chemaxon.struc.Transform3D: Gets the Euler angles from the rotation transformation.
getExactMass() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
getExactMass() - Method in class chemaxon.struc.MoleculeGraph: Calculates the molecular weight of the molecule using the mass of the most frequent natural isotope of the atoms.
getExactSpecialAtomMatching() - Method in class chemaxon.search.api.options.SearchOptions: Get the identifiers of those special atoms that should match exactly during structure comparison.
getException() - Method in exception class chemaxon.calculations.CalculatorPluginException: Returns the wrapped exception.
getExcluded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker: Gets the excluded abbreviations
getExcluded() - Method in class chemaxon.checkers.AttachedDataChecker: Any attached data that matches this descriptor won't appear as the result of this checker.
getExcluded() - Method in class chemaxon.checkers.PseudoAtomChecker
getExcludeString() - Method in class chemaxon.standardizer.AbstractSgroupAction: Gets the exclude string of action
getExcludeString() - Method in class chemaxon.standardizer.actions.ContractSgroupsAction
getExcludeString() - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction
getExcludeString() - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction
getExhaustiveModeLimit() - Method in class chemaxon.search.api.options.SearchOptions: Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
getExplicitHcount() - Method in class chemaxon.struc.MolAtom: Gets number of hydrogen connections.
getExplicitHcount() - Method in class chemaxon.struc.MoleculeGraph: Gets the total number of explicit hydrogens attached to the molecule.
getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.calculations.CalculatorPlugin
getExplicitHydrogenData(Molecule, int) - Method in class chemaxon.calculations.TautomerPlugin
getExplicitHydrogenIndex() - Method in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
getExplicitLonePairCount() - Method in class chemaxon.struc.MDocument: Returns the number of Lone Pair electrons set by the user.
getExplicitLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph: Deprecated.
For internal use only.
getExpression() - Method in class chemaxon.calculations.services.DynamicArgument: Returns the expression used for evaluations
getExtensionList() - Method in class chemaxon.formats.MFileFormat: Gets the extension list.
getExternalCheckerConfigURL() - Method in class chemaxon.marvin.common.UserSettings: Returns the URL of the configuration file containing the list of external Checkers in marvin sketch.
getExternalConnections(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the number of bonds of a specified atom where the neighbor atom doesn't belong to the S-group.
getExtraLabel() - Method in class chemaxon.struc.MolAtom: Gets the label string (also called atom value): "result" or "result1|result2".
getExtraLabelColor() - Method in class chemaxon.struc.MolAtom: Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
getExtraLabelColor(int) - Method in class chemaxon.struc.MolAtom: Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue).
getExtraLabelColor(long, int) - Static method in class chemaxon.struc.MolAtom: Gets extra label color from composed color value.
getExtraLabelSetColorMode(int) - Method in class chemaxon.struc.MDocument: Gets the coloring mode of extra label set sequences.
getExtraLabelSetFont(int) - Method in class chemaxon.struc.MDocument
getExtraLabelSetRGBs(int) - Method in class chemaxon.struc.MDocument
getExtraLabelSetSeq() - Method in class chemaxon.struc.MolAtom
getExtraLabelSetSize() - Method in class chemaxon.struc.MDocument
getEZStereo(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Gets E/Z stereo information for the given double bond.
getFamily() - Method in class chemaxon.struc.graphics.MFont: Gets the font family name.
getFeatureCount() - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the number of features.
getFeatureCount(int) - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the number of features corresponding to the given atom index.
getFeatures(int) - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the feature indices corresponding to the given atom index.
getFeaturesFromBitPosition(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup: Returns the substructural features represented by the given bit position.
getFeaturesFromIdentifier(int) - Method in class chemaxon.descriptors.ECFPFeatureLookup: Returns the substructural features represented by the given integer identifier.
getFieldAccessor() - Method in class chemaxon.marvin.common.MDocStorage: Deprecated, for removal: This API element is subject to removal in a future version.
designed for MarvinView, do not use.
getFieldFont(String) - Method in class chemaxon.marvin.beans.MViewPane: Gets the font of a named field in a table.
getFieldFontSize() - Method in class chemaxon.marvin.common.TableOptions: Gets the field font size.
getFieldName() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the data field name.
getFieldsShown() - Method in class chemaxon.marvin.common.TableOptions: Are SDfile fields shown in table?
getFieldType() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the field type.
getFile() - Method in class chemaxon.formats.MolImporter: Gets the file object for the input.
getFile() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the current molecule file.
getFileExtensionLC(File) - Static method in class chemaxon.formats.MFileFormatUtil: Gets the file extension in lower case.
getFileExtensionLC(String) - Static method in class chemaxon.formats.MFileFormatUtil: Gets the file extension in lower case.
getFileName() - Method in class chemaxon.formats.MolImporter: Gets the name of the input file
getFilePointer() - Method in class chemaxon.formats.PositionedInputStream: Get the file pointer.
getFinalCause() - Method in exception class chemaxon.formats.MolFormatException: Gets the final cause of the exception.
getFingerprint() - Method in class chemaxon.chemterms.MolContext: Returns the input molecule fingerprint.
getFingerprint(Molecule) - Method in interface chemaxon.chemterms.FingerprintGenerator: Returns the fingerprint of the structure.
getFingerprint(Object) - Method in class chemaxon.chemterms.MolContext: Returns the input molecule fingerprint if argument is the input molecule, null otherwise.
getFiveLongRings() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult: This method returns the five long rings in the molecule represented by a List of List of MolAtom
getFixedLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MMidPoint: Gets the fixed location in the polyline.
getFixerClassName() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the fixerClassName
getFixers(StructureCheckerResult) - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
getFixers(StructureCheckerResult) - Method in interface chemaxon.structurechecker.CheckerRunner: Returns all the StructureFixer instances which associated with the StructureCheckerErrorType of the result
getFixMode() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the fixMode
getFlags() - Method in class chemaxon.formats.MFileFormat: Gets the format descriptor flags.
getFlags() - Method in class chemaxon.struc.graphics.MPolyline: Gets the flags.
getFlags() - Method in class chemaxon.struc.MolAtom: Gets flags.
getFlags() - Method in class chemaxon.struc.MolBond: Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits), bond set (5 bits) and reacting center (7 bits) information.
getFlags() - Method in class chemaxon.struc.MoleculeGraph: Gets the dimension and chiral flags.
getFlags() - Method in class chemaxon.struc.RgMolecule: Gets the dimension and chiral flags.
getFlexibilityMode() - Method in class chemaxon.alignment.MMPAlignmentProperties
getFlexibleRingRotatableBondCount() - Method in class chemaxon.alignment.AlignmentMoleculeFactory
getFlexibleRingSize() - Method in class chemaxon.alignment.AlignmentMoleculeFactory
getFloat(int) - Method in class chemaxon.descriptors.CustomDescriptor
getFocus() - Method in class chemaxon.struc.MDocument: Gets the focused object
getFogFactor() - Method in class chemaxon.marvin.common.UserSettings: Gets the fog factor.
getFont() - Method in class chemaxon.struc.prop.MFontProp
getFontFamily() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the font family name.
getFontMetrics(Graphics, MFont) - Method in class chemaxon.struc.graphics.MTextDocument.Section: Gets and updates the font metrics of a document section.
getFontScale() - Method in class chemaxon.struc.graphics.MTextBox: Gets the font scaling factor.
getForefather() - Method in class chemaxon.struc.MoleculeGraph: Gets the first parent.
getForeground() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the foreground color.
getFormalCharge() - Method in class chemaxon.calculations.ChargePlugin: Returns the formal charge of the molecule.
getFormalCharge() - Method in class chemaxon.struc.MoleculeGraph: Gets the (total) formal charge of the molecule.
getFormalCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the formal charge of a specified atom.
getFormalChargeFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular formula with formal charge.
getFormalChargeFormula(int) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates a fixed digit sortable molecular formula with formal charge.
getFormat() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder: Dipole export format.
getFormat() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder: Spectrum export format.
getFormat() - Method in class chemaxon.formats.MolExporter: Gets the output file format.
getFormat() - Method in class chemaxon.formats.MolExportModule: Returns the output format.
getFormat() - Method in class chemaxon.formats.MolImporter: Get the file format.
getFormat() - Method in class chemaxon.formats.MolInputStream: Get the molecule file format.
getFormat() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the default molecule file format.
getFormat() - Method in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: Gets the string value of the format of molecule export used by the writer
getFormat() - Method in class chemaxon.standardizer.configuration.StandardizerConfigurationXmlWriter: Gets the string value of the format of molecule export used by the writer
getFormat() - Method in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: Gets the string value of the format of molecule export used by the writer
getFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil: Gets the file format descriptor for the specified codename.
getFormatNamesWithExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil
getFormatter() - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm: Returns the formatter of this term, which is used to format the value of this term.
getFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
getFormula() - Method in class chemaxon.struc.MoleculeGraph: Gets the molecular formula.
getFormula() - Method in class chemaxon.struc.RgMolecule: Gets the molecular formula in Hill order.
getFormula() - Method in class chemaxon.struc.RxnMolecule: Gets the molecular formula in Hill order.
getFormula(int) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates a fixed digit sortable molecular formula.
getFragCount(int) - Method in class chemaxon.struc.MoleculeGraph: Returns the number of fragments for the given fragmentation type.
getFragIds(int) - Method in class chemaxon.struc.MoleculeGraph: Gets an array containing the fragment id for each atom for the given fragmentation type.
getFragmentCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of fragments (disconnected parts) of the molecule.
getFragmentCount() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the number of fragments in the found common substructure.
getFreeAtomSetIndex() - Method in class chemaxon.struc.MDocument: Returns the first unused atomset index.
getFreeAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the atoms with free attachment points.
getFreeAttachmentPointCount() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the number of free attachment points.
getFreeAttachmentPointOrders() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the increasingly sorted orders of the free attachment points.
getFreeAttachmentPointOrders(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the sorted free attachment orders of the given attachment atom.
getFreeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Returns the number of the free attachment points for the given atom.
getFreeBondSetIndex() - Method in class chemaxon.struc.MDocument: Returns the first unused bondset index.
getFreeElectronCount() - Method in class chemaxon.struc.graphics.MElectronContainer
getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder: Gets the NMR frequency.
getFrequency() - Method in class chemaxon.calculations.nmr.NMRCalculator: Returns NMR measurement frequency.
getFrequency() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the freuency in MHz.
getFrequency() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the NMR measurement frequency in MHz unit.
getFrequencyCounts() - Method in class chemaxon.descriptors.MDGenerator: Gets the absolute frequence count array for all descriptors generated.
getFromFlag(int) - Static method in enum class chemaxon.rendering.constants.AnyBondStyle
getFromFlag(int) - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
getFromFlag(int) - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle
getFromFlag(int) - Static method in enum class chemaxon.rendering.constants.RenderingStyle
getFsp3() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Fsp3 value of the given molecule.
Fsp3 = number of sp3 carbons / number of carbons
getFsp3() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Fsp3 value of the molecule.
getFunctionScale() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the scaling parameter for the function of this multiplet.
getFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum
getFusedAliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
getFusedAliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of fused aliphatic rings in the molecule (rings s).
getFusedAliphaticRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
getFusedAliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).
getFusedAromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
getFusedAromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of fused aromatic rings in the molecule (rings s).
getFusedAromaticRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
getFusedAromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).
getFusedRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.
getFuzzyExponents() - Method in class chemaxon.descriptors.PFParameters: Gets the precalculated fuzzy exponent used in the Fuzzy Bipolar Autocorrelogram (FBPA) metric.
getFuzzyLowerBound() - Method in class chemaxon.descriptors.PFParameters
getFuzzySmoothingFactor() - Method in class chemaxon.descriptors.PFParameters: Gets the fuzzy smoothing factor used in the construction of fuzzy fingerprints.
getGaussianFuzzyIncrements() - Method in class chemaxon.descriptors.PFParameters: Gets fuzzy increments for the fuzzy smoothing with a normal distribution.
getGenerator() - Method in class chemaxon.descriptors.MDParameters: Gets the MolecularDescriptor generator object.
getGenNameFontSize() - Method in class chemaxon.marvin.common.TableOptions: Gets the IUPAC name font size.
getGlobalChecker() - Static method in interface chemaxon.calculations.api.TaggedCalculator: Returns the global input checker that will be used by all calculators implementing this interface.
getGlobalGUIProperties() - Method in class chemaxon.marvin.common.MDocStorage: Gets the Global GUI properties.
getGlobalProperties() - Method in class chemaxon.formats.MolImporter: Gets the global properties in a container that was retrieved from the input stream, earlier.
getGrabbedLines() - Method in class chemaxon.formats.PositionedInputStream: Deprecated, for removal: This API element is subject to removal in a future version.
getGrabbedMoleculeString() - Method in class chemaxon.formats.MolImporter: Gets the last grabbed molecule string with LF style line endings by default.
getGraphUnion() - Method in class chemaxon.struc.MoleculeGraph: Gets a molecule graph containing all the atoms and bonds.
getGraphUnion() - Method in class chemaxon.struc.RgMolecule: Gets a graph containing all the atoms and bonds.
getGraphUnion() - Method in class chemaxon.struc.RxnMolecule: Gets a graph containing all the atoms and bonds.
getGraphUnionAsSelection() - Method in class chemaxon.struc.Molecule: Gets a selection molecule containing all the atoms and bonds.
getGriffinHlbValue() - Method in class chemaxon.calculations.HLBPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, use HLBPlugin.getGriffinHLBValue() instead.
getGriffinHLBValue() - Method in class chemaxon.calculations.HLBPlugin: Returns the HLB value calculated by Griffin method.
getGrinv() - Method in class chemaxon.struc.graphics.MNameTextBox: Gets an invariant the text box depends on.
getGrinv() - Method in class chemaxon.struc.MoleculeGraph: Gets the graph invariants array.
getGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph: Gets the graph invariants (canonical labels).
getGrinv(int[], int) - Method in class chemaxon.struc.MoleculeGraph: Gets the graph invariants (canonical labels).
getGrinvCC() - Method in class chemaxon.struc.MoleculeGraph: Gets the graph invariant change count.
getGrinvCC() - Method in class chemaxon.struc.MProp: Gets the graph invariant change count at the moment of creation.
getGrinvOptions() - Method in class chemaxon.struc.MoleculeGraph: Gets graph invariant calculation options passed to the module.
getGroup() - Method in class chemaxon.standardizer.actions.GroupDefinition: Gets the definition of the group.
getGroup(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the menu group for a plugin.
getGroupCount() - Method in class chemaxon.standardizer.actions.CreateGroupAction: Gets the count of the groups of the action
getGroupedDotDisconnectedFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the grouped dot-disconnected molecular formula of a multifragment molecule.
getGroupHit() - Method in class chemaxon.search.api.SearchHit: Returns the group hit view of the hit object.
getGroupHit() - Method in class chemaxon.search.Decomposition: Returns the group hit corresponding to the R-group decomposition.
getGroupIndices() - Method in class chemaxon.checkers.result.DataSgroupCheckerResult
getGroupList() - Method in class chemaxon.standardizer.actions.CreateGroupAction: Gets the list of groups set for the action
getGroupMnemonic(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the group mnemonic for a plugin.
getGroups() - Method in class chemaxon.standardizer.actions.AliasToGroupAction: Gets the abbreviated groups of the action
getGroupsOf(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets the group names associated to an action separated by , character
getGroupsOf(String, List<GroupDefinition>) - Static method in class chemaxon.standardizer.actions.GroupDefinition: Gets the group from a list of group definitions, based on the abbreviation.
getGUIPropertyContainer() - Method in class chemaxon.struc.MDocument
getHalfWidth() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the half-width of the NMR lines.
getHalfWidth() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns NMR half-width.
getHararyIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
getHashCode(Molecule) - Method in class chemaxon.search.util.HashCode: Gets hash code with default recursion level.
getHashCode(Molecule, int) - Method in class chemaxon.search.util.HashCode: Gets the hash code.
getHashCode(Molecule, int[]) - Method in class chemaxon.search.util.HashCode: Gets hash code with default recursion level.
getHashCode(Molecule, int[], int) - Method in class chemaxon.search.util.HashCode: Gets the hash code.
getHBond(int) - Method in class chemaxon.calculations.GeometryPlugin: Returns a hydrogen bond.
getHBondCount() - Method in class chemaxon.calculations.GeometryPlugin: Returns the number of intramolecular hydrogen bonds.
getHCountMatching() - Method in class chemaxon.search.api.options.SearchOptions: Get the interpretation of H count in the query.
getHeadCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Gets the head crossing bonds of a ladder-type polymer.
getHeader() - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the table header.
getHeader() - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the table header.
getHeight() - Method in class chemaxon.struc.PageSettings
getHelpText() - Method in class chemaxon.checkers.AbstractStructureChecker
getHelpText() - Method in class chemaxon.checkers.InvalidChecker
getHelpText() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getHelpText() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getHelpText() - Method in interface chemaxon.checkers.StructureChecker: Gets the help text of the checker
getHelpText() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the help text
getHelpText() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the help text of the action
getHeteroaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
getHeteroaliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroaliphaticRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
getHeteroaliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the heteroaromatic ring count.
getHeteroaromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroaromaticRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).
getHeteroaromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
getHeteroRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the hetero ring count.
getHeteroRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
getHeteroRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
getHeteroRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Indentifies hetero rings in the molecule having a given size (number of atoms).
getHidrophobicity() - Method in class chemaxon.calculations.LogDPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
getHighBridgeAtomIndexes() - Method in class chemaxon.struc.BicycloStereoDescriptor: Return the atom indexes of the atoms of the bridge with the higher index.
getHighBridgeAtoms() - Method in class chemaxon.struc.BicycloStereoDescriptor: Return the atoms of the bridge with the higher index.
getHighestEigenvalue(int, int) - Method in class chemaxon.descriptors.BCUT: Gets the specified highest eigenvalue.
getHighestEigenvaluesCount(int) - Method in class chemaxon.descriptors.BCUTParameters: Gets the number of highest eigenvalues calculated.
getHit(Molecule) - Method in class chemaxon.search.hitdisplay.HitDisplayTool: Processes the next target structure.
getHitColor() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the color to be used when coloring the substructure hit.
getHitHomologyColor() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the color used for highlighting user defined homologies in a substructure hit.
getHitIndexes() - Method in class chemaxon.search.hitdisplay.HitDisplayTool: Returns the hit indexes for the last target.
getHitIndexType() - Method in class chemaxon.search.api.options.MolSearchOptions: Returns the representation on which the hit indexes are given in case of Markush search.
getHitOrdering() - Method in class chemaxon.search.api.options.SearchOptions: Returns the hit ordering type.
getHits(int) - Method in class chemaxon.search.hitdisplay.HitDisplayTool: Processes the next target structure.
getHits(Molecule, Molecule, int) - Method in class chemaxon.search.hitdisplay.HitDisplayTool: Deprecated, for removal: This API element is subject to removal in a future version.
This method will be removed in a future release, use HitDisplayTool.getHits(int) instead.
getHitsAsMarkush() - Method in class chemaxon.search.RgroupDecompositionResults: Returns a single RgMolecule that consists of the scaffold and all the possible ligands as rgroup-definitions.
getHitsAsRgDecomp() - Method in class chemaxon.search.RgroupDecompositionResults: Returns All ligands of all targets.
getHitsAsTable() - Method in class chemaxon.search.RgroupDecompositionResults: Returns the table elements in Molecule[][] format.
getHlbValue() - Method in class chemaxon.calculations.HLBPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, use HLBPlugin.getHLBValue() instead.
getHLBValue() - Method in class chemaxon.calculations.HLBPlugin: Returns the HLB value.
getHMOChargeDensity(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
getHMOEigenVector() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the eigenvector.
getHMOElectronDensity(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the electron density of an atom calculated with HMO, Double.NaN for no value.
getHMOElectrophilicEnergy(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
getHMOElectrophilicOrder(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the electrophilic order of an atom, -1 for no value.
getHMOHuckelOrbitalCoefficients() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the huckel orbital coefficients.
getHMONucleophilicEnergy(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
getHMONucleophilicOrder(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the nucleophilic order of an atom, -1 for no value.
getHMORealEigenValue() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the real part of the eigenvalue.
getHMOTotalPiEnergy() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the total pi energy of the input molecule.
getHomologyBroadTranslation() - Method in class chemaxon.search.api.options.SearchOptions: Get target-side homology matching option.
getHomologyNarrowTranslation() - Method in class chemaxon.search.api.options.SearchOptions: Get query-side homology matching option, which homology atoms can match specific atoms.
getHorizontalAlignment() - Method in class chemaxon.struc.graphics.MTextBox: Gets the horizontal alignment.
getHPolarizability(int) - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the sum of the implicit H atom polarizability values around the given heavy atom.
getHResult(int) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns the sum result of the H neighbours of the given atom.
getHuckelOrbitalCoefficients() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Deprecated.
Use HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()
getHybridizationState() - Method in class chemaxon.struc.MolAtom: Gets the hybridization state.
getHydrogen() - Method in class chemaxon.calculations.CalculatorPlugin.HydrogenData
getHydrophobicity() - Method in class chemaxon.calculations.LogDPlugin
getHyperWienerIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the hyper Wiener index of the molecule.
getIcon() - Method in class chemaxon.calculations.services.ServiceDescriptor: Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, always returns null.
getIcon() - Method in class chemaxon.checkers.AbstractStructureChecker
getIcon() - Method in class chemaxon.checkers.InvalidChecker
getIcon() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getIcon() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getIcon() - Method in interface chemaxon.checkers.StructureChecker: Gets the Icon of the current checker
getIcon() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the Icon related to iconPath property
getIcon() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Returns the Icon related to iconPath property
getIcon(int) - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo: Returns a MarvinSketch icon in 16x16 or 32x32 size.
getIcon(int) - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo: Returns a MarvinView icon in 16x16 or 32x32 size.
getIconPath() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the icon path
getIconPath() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the path of icon associated to the action
getId() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the id of the action
getId() - Method in class chemaxon.struc.Molecule
getId() - Method in class chemaxon.struc.Sgroup
getId(String) - Static method in class chemaxon.calculations.services.JsonServiceDescriptor: Gets an ID for a method name, to make sure the client can identify the answer for the request.
getID() - Method in class chemaxon.standardizer.AbstractStandardizerAction: Gets the identifier string of the standardizer action.
getID() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
getID() - Method in interface chemaxon.standardizer.StandardizerAction: Gets the identifier of the standardizer task
getID() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor: Gets the id of the standardizer class
getID() - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor: Gets the id of the checker class
getID(String) - Method in class chemaxon.descriptors.pharmacophore.PMapper: Returns the ID corresponding to the given symbol.
getIDBackgroundRGBA(int) - Method in class chemaxon.marvin.common.MDocStorage: Gets the background color's RGBA value in a record.
getIdentiferCount() - Method in class chemaxon.descriptors.ECFP: Deprecated, for removal: This API element is subject to removal in a future version.
Use ECFP.getIdentifierCount() instead.
getIdentifier() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the checker identifier
getIdentifier() - Method in class chemaxon.descriptors.ECFPFeature: Gets the generated integer identifier for this ECFP feature.
getIdentifier() - Method in class chemaxon.fixers.StructureFixerDescriptor: Returns the fixer identifier
getIdentifier(MolAtom, int) - Method in class chemaxon.descriptors.ECFPFeatureLookup: Returns the corresponding integer identifier for the given atom neighborhood.
getIdentifierCount() - Method in class chemaxon.descriptors.ECFP: Gets the number of integer identifiers generated for the fingerprint.
getIDForegroundRGBA(int) - Method in class chemaxon.marvin.common.MDocStorage: Gets the foreground color's RGBA value in a record.
getIgnoreRotatableBonds() - Method in class chemaxon.descriptors.PFParameters
getImage(double) - Method in class chemaxon.marvin.beans.MSketchPane: Gets the canvas contents as an image using a scale factor.
Examples:
To get an image with a scale factor equivalent to 100% magnification: getImage(getDefaultScale());
To get an image with the actual scale factor: getImage(getScale());
getImage(Dimension) - Method in class chemaxon.marvin.beans.MSketchPane: Gets the canvas contents as an image scaled to fit in the specified rectangle.
getImageImportServiceURL() - Method in class chemaxon.marvin.common.UserSettings
getImageMolecule() - Method in class chemaxon.calculations.LogDPlugin: Returns the molecule to be used for legend image.
getImplicitH() - Method in class chemaxon.marvin.beans.MarvinPane: Query the display method of implicit hydrogens.
getImplicitH() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the display method of implicit hydrogens.
getImplicitHcount() - Method in class chemaxon.struc.MolAtom: Gets the number of implicit hydrogens attached.
getImplicitHcount() - Method in class chemaxon.struc.MoleculeGraph: Gets the total number of implicit hydrogens attached to the molecule.
getImplicitHCount(boolean) - Method in class chemaxon.struc.MolAtom: Gets the implicit Hydrogen count of the atom.
getImplicitHCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets the number of implicit hydrogens attached to the given atom.
getImplicitHMatching() - Method in class chemaxon.search.api.options.SearchOptions: Get option for matching implicit and explicit hydrogens
getImplicitizableHList(Molecule, int) - Static method in class chemaxon.core.calculations.Hydrogenizer: Gets which atom is an implicitizable hydrogen.
getImplicitizeFlag() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult: Returns the flag which can used to identify which hydrogens should be implicitize.
getIncludedIds() - Method in class chemaxon.search.RgroupDecompositionResults: Returns indexes of those targets that are matched by query.
getIndex() - Method in enum class chemaxon.calculations.PkaTrainingResult.PkaType
getIndex(String) - Method in class chemaxon.descriptors.pharmacophore.PSymbols: Gets the index associated of the specified symbol.
getIndexOfOriginalLigand() - Method in class chemaxon.calculations.CalculatorPlugin.HydrogenData
getInnerPointRef(int, Transform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
getInputCount() - Method in class chemaxon.formats.converter.MolConverter.Builder: Gets the number of input files/streams.
getInputFormat() - Method in class chemaxon.struc.MDocument: Gets the input file format.
getInputFormat() - Method in class chemaxon.struc.Molecule: Gets the input file format.
getInputMolDim() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the input molecule dimension.
getInputMolecule() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Gets the input molecule.
getInputMolecule() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor: Returns the input molecule (the molecule before standardization).
getInputPriority() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor: Priority of the MTransferable object when importing from clipboard.
getInputStreamFromClipboard() - Method in class chemaxon.marvin.datatransfer.MarvinTransferable: Gets an InputStream from the clipboard data if the format is supported by this MTransferable
getInstance() - Static method in class chemaxon.structurechecker.CheckerFixerFactory: Creates a CheckerFixerFactory based on the CheckerFixerFactory.DEFAULT_CONFIGURATION_PATH and the user defined checkers/fixers located at the default user
getInt(int) - Method in class chemaxon.descriptors.CustomDescriptor
getIntArray() - Method in class chemaxon.struc.prop.MIntegerArrayProp: Gets the integer value.
getIntegralValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the value of the NMR integral function at a given x point.
getIntensity(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the intensity of the ith line.
getInternalMetricIndex() - Method in class chemaxon.descriptors.MDParameters: Gets the MolecularDescriptor specific metric index of the current parametrized metric.
getInternalSize() - Method in class chemaxon.descriptors.MDParameters: Gets the required memory size to store the descriptor according to the specified parameters.
getInternalVersionId() - Static method in class chemaxon.common.version.VersionInfo: Returns the internal version identifier.
getIntesityPattern() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the intensity pattern of this multiplet.
getIntValue() - Method in enum class chemaxon.struc.EZConfiguration: Gets the integer value of the stereo configuration.
As the configuration represents a CIS/TRANS stereo configuration as well therefore the corresponding constants are returned: 0 for EZConfiguration.NONE StereoConstants.TRANS for EZConfiguration.E StereoConstants.CIS for EZConfiguration.Z StereoConstants.CIS | StereoConstants.TRANS for EZConfiguration.E_OR_Z StereoConstants.TRANS | StereoConstants.CTUNSPEC for EZConfiguration.E_OR_UNSPEC StereoConstants.CIS | StereoConstants.CTUNSPEC for EZConfiguration.Z_OR_UNSPEC
getIntValue() - Method in enum class chemaxon.struc.Radical: Gets the integer representation of the radical.
getInverseName() - Method in class chemaxon.formats.OptionDescriptor: Gets the inverse option name.
getInvisibleSets() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the visibility of the specified atom sets.
getIonizerErrorMessage() - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin: Returns the calculation error information message or the empty string if there is no error.
getIonizerErrorMessage() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the calculation error information message or the empty string if there is no error.
getIsoelectricPoint() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the isoelectric point.
getIsotope(int, int) - Static method in class chemaxon.struc.PeriodicTable: Retrieves an isotope of the element
getIsotopeComposition() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the molecular composition (w/w%).
getIsotopeComposition(boolean) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the molecular composition (w/w%).
getIsotopeCount() - Static method in class chemaxon.struc.PeriodicTable: Number of isotopes in the periodic table
getIsotopeCount(int) - Static method in class chemaxon.struc.PeriodicTable: Number of isotopes of the element
getIsotopeDistribution() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the isotopic distributions for the molecule.
getIsotopeFormalChargeFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular formula (isotopes are separated).
getIsotopeFormalChargeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular formula with formal charge (isotopes are separated).
getIsotopeFormula() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular formula (isotopes are separated).
getIsotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular formula (isotopes are separated).
getIsotopeMatching() - Method in class chemaxon.search.api.options.SearchOptions: Get option for matching isotopes
getIterator() - Method in class chemaxon.formats.MoleculeImporter: Returns an iterator that iterates through all molecules in the file/stream.
getItsArrow() - Method in class chemaxon.struc.RxnMolecule: Gets the reaction arrow of this reaction.
getJar() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor: Gets the jar containing the standardizer class
getJar() - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor: Gets the jar containing the checker class
getJavaVersionStr() - Static method in class chemaxon.common.version.VersionInfo: Returns the Java VM version information as string.
getKeepCounts() - Method in class chemaxon.descriptors.ECFPParameters: Gets the counts (multiplicity) parameter.
getKey(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the menu key for a plugin.
getKey(int) - Method in class chemaxon.struc.MPropertyContainer: Gets a property key.
getKey(int) - Method in class chemaxon.struc.prop.MHashProp: Gets a key.
getKeys() - Method in class chemaxon.struc.MPropertyContainer: Returns the property keys.
getKnownExtension(String) - Static method in class chemaxon.formats.MFileFormatUtil: Returns the file extension if it is a known extension.
getL(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets a label.
getL(int, int) - Method in class chemaxon.marvin.common.MDocStorage: Gets a text label in a record.
getLabel() - Method in class chemaxon.alignment.NodeColor.ExtendedAtomColoring
getLabel() - Method in class chemaxon.alignment.NodeColor: Returns a label for the coloring scheme.
getLabel() - Method in class chemaxon.struc.NoStructure: The label for the noStructure.
getLabelCenter() - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the index of the character in the label the bonds should point to.
getLabels(double[]) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns formatted array.
getLargestConjugatedSystem() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the largest conjugated system in the molecule.
getLargestConjugatedSystemSize() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the largest conjugated system size (number of pi electron pairs).
getLargestRing() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the atoms of the largest ring (number of atoms) in the molecule.
getLargestRingSize() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the largest ring size.
getLargestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the size of largest ring containing the specified atom.
getLargestRingSystem() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the atoms of the largest ring system (number of rings) in the molecule.
getLargestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the size of the largest ring system (number of rings) in the molecule.
getLastEOL() - Method in class chemaxon.formats.PositionedInputStream
getLastIndexOfAction(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Gets the last index of an action defined by the provided action string
getLastSketchFrameSize() - Method in class chemaxon.marvin.common.UserSettings
getLastViewFrameSize() - Method in class chemaxon.marvin.common.UserSettings
getLeftBracket(Transform3D) - Method in class chemaxon.struc.graphics.MBracket
getLeftMargin() - Method in class chemaxon.struc.PageSettings
getLeftName() - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the string that will be shown at the left side of the molecule.
getLegendMols() - Method in class chemaxon.calculations.gui.MChart
getLegendTexts() - Method in class chemaxon.calculations.gui.MChart
getLength() - Method in class chemaxon.descriptors.MDParameters: Returns the number of cells forming the descriptor.
getLength() - Method in class chemaxon.struc.MolBond: Gets the actual length of the bond.
getLevel() - Method in interface chemaxon.core.util.MProgressMonitor: Deprecated.

Gets the level of this progress monitor.
getLibrarySizeString() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the display string representation of the Markush library size (number of all enumerated structures).
getLicenseEnvironment() - Method in class chemaxon.standardizer.Standardizer: Gets the license environment of the standardizer
getLigand(int) - Method in class chemaxon.struc.MolAtom: Gets the i-th ligand of this atom.
getLigand(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph: Gets the n-th ligand of the given atom.
getLigandAtno(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph: Gets the atomic number of the n-th ligand of the given atom.
getLigandBondType(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph: Gets the type of the n-th ligand bond of the given atom.
getLigandCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets the number of ligands of the given atom.
getLigandIds() - Method in class chemaxon.search.Decomposition: Returns the target ligand IDs.
getLigandIndex(MolAtom) - Method in class chemaxon.struc.MolAtom: Returns the index of the specified ligand in this atom.
getLigandIndexes() - Method in class chemaxon.core.calculations.stereo.StereoActivePart: Get the indexes of the ligands of the stereo active atom which take part in the stereo description.
getLigandOrder(MolAtom) - Method in class chemaxon.struc.MolAtom: Gets the order of a specified ligand.
getLigandOrderVisibility() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the ligand order visibility setting.
getLigands() - Method in class chemaxon.core.calculations.stereo.StereoActivePart: Deprecated, for removal: This API element is subject to removal in a future version.
Use StereoActivePart.getLigandIndexes() instead.
getLigands() - Method in class chemaxon.search.Decomposition: Returns the R-ligand array.
getLigands() - Method in class chemaxon.struc.MolAtom: Returns the atoms connected to this atom by a bond.
getLigands(Integer) - Method in class chemaxon.struc.SelectionMolecule
getLigandsNumber() - Method in class chemaxon.search.RgroupDecompositionResults: Returns the number of ligands in one target structure.
getLigandTableHeader(int, int) - Method in class chemaxon.search.RgroupDecomposition: Returns ligand table header.
getLigandTableHeader(int, int, String) - Method in class chemaxon.search.RgroupDecomposition: Returns ligand table header.
getLimitedStructureCount() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the number of structures to be generated.
getLine(int) - Method in class chemaxon.struc.graphics.MTextBox: Gets a line.
getLineColor() - Method in class chemaxon.struc.MObject: Gets the line color of the object.
getLineCount() - Method in class chemaxon.formats.MolImporter: Gets the current line number.
getLineCount() - Method in class chemaxon.formats.MolImportModule: Returns the line count in the molecule input stream.
getLineCount() - Method in class chemaxon.formats.PositionedInputStream: Gets the current line number.
getLineCount() - Method in class chemaxon.struc.graphics.MTextBox: Gets the number of lines.
getLineMiddlePoint(Point3D, Point3D) - Static method in class chemaxon.struc.graphics.MPolyline
getLineNumberInFile() - Method in exception class chemaxon.formats.MolFormatException: Gets the line number relative to the first line of the file.
getLineNumberInRecord() - Method in exception class chemaxon.formats.MolFormatException: Gets the line number relative to the first line of the record.
getLineOnScreen(int) - Method in class chemaxon.struc.sgroup.DataSgroup: Returns the i-th row of the data sgroup label, as displayed on the screen (with tag, query operator, units etc.)
getLinkNodeOuterAtom(int) - Method in class chemaxon.struc.MolAtom: Gets the index of one of the link node's outer neighbor atoms.
getList() - Method in class chemaxon.checkers.AtomLabels: Gets the list of atom labels
getList() - Method in class chemaxon.struc.MolAtom: Gets the atom list.
getList() - Method in class chemaxon.struc.prop.MListProp: Gets the array.
getListeners() - Method in class chemaxon.marvin.common.MDocStorage
getLoadSaveLocation() - Method in class chemaxon.marvin.common.UserSettings: Gets the load/save filechooser working directory selection method names, based on the preferences dialog.
getLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings: Gets the filechooser's default working directory, if it is set, and the filechooser working directory selection method is saveCustomLocation.
getLocalMaximumPlaces() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the local maximum places of the multiplet in ascending order.
getLocalMaximumPlaces() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Gets the locations (elements of domain) of the local maximums of the function.
getLocalMenuName() - Method in class chemaxon.checkers.AbstractStructureChecker
getLocalMenuName() - Method in class chemaxon.checkers.InvalidChecker
getLocalMenuName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getLocalMenuName() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getLocalMenuName() - Method in interface chemaxon.checkers.StructureChecker: Gets the local menu name of the checker
getLocalMenuName() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the local menu name
getLocalParity(int) - Method in class chemaxon.struc.MoleculeGraph: Computes the local parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getLocalParity(int) - Method in class chemaxon.struc.RgMolecule: Computes the local parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getLocalParity(int) - Method in class chemaxon.struc.RxnMolecule: Computes the local parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getLocation() - Method in class chemaxon.struc.MolAtom: Gets the coordinates.
getLocation() - Method in class chemaxon.struc.MoleculeGraph: Gets the origin of the molecule.
getLocation() - Method in class chemaxon.struc.MPoint: Gets the point's location.
getLocation() - Method in class chemaxon.struc.NoStructure: Returns the clone of the location of the NoStructure.
getLocation(Point3D) - Method in class chemaxon.struc.MolAtom: Gets the coordinates.
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the location.
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Gets the location.
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MElectron
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MMidPoint: Gets the location.
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MMidPoint.Sticky: Gets the location.
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky: Gets the location.
getLocation(Point3D, Transform3D) - Method in class chemaxon.struc.MPoint: Gets the point's location.
getLocation(Transform3D) - Method in class chemaxon.struc.MPoint: Gets the point's location.
getLock() - Method in class chemaxon.struc.MolAtom: Get lock object for synchronization.
getLock() - Method in class chemaxon.struc.MoleculeGraph: Gets the lock object for synchronization.
getlogD() - Method in class chemaxon.calculations.LogDPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogDPlugin.getLogD() instead. This method will be removed in a future version.
getLogD() - Method in class chemaxon.calculations.LogDPlugin: Returns the logD value for the pH specified in LogDPlugin.setPh(double).
getLogDAtIsoelectricPoint() - Method in class chemaxon.calculations.LogPPlugin: Returns the logD value at the isoelectric point (pI).
getlogDpI() - Method in class chemaxon.calculations.LogPPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPPlugin.getLogDAtIsoelectricPoint() instead. This method will be removed in a future version.
getlogDs() - Method in class chemaxon.calculations.LogDPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogDPlugin.getLogDValues() instead. This method will be removed in a future version.
getLogDValues() - Method in class chemaxon.calculations.LogDPlugin: Returns the logD array.
getLogger() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder: Returns the dipole calculator logger.
getLogger() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder: Gets the calculator logger.
getLogicalValue(Object) - Static method in class chemaxon.chemterms.ChemTermsExpression: Returns the logical correspondent of the specified result object: ChemTermsExpression.TRUE, ChemTermsExpression.FALSE or ChemTermsExpression.UNDECIDED.
getLogPercentageLimit() - Method in class chemaxon.calculations.PkaPlugin
getlogPMicro() - Method in class chemaxon.calculations.LogPPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPPlugin.getLogPMicro() instead. This method will be removed in a future version.
getLogPMicro() - Method in class chemaxon.calculations.LogPPlugin: Returns the micro logP value.
getlogPNonionic() - Method in class chemaxon.calculations.LogPPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPPlugin.getLogPNonionic() instead. This method will be removed in a future version.
getLogPNonionic() - Method in class chemaxon.calculations.LogPPlugin: Returns the logP value for the non-ionic form.
getLogPTrainingIds() - Static method in class chemaxon.calculations.LogDPlugin: Returns the IDs of available logP trainings.
getlogPTrue() - Method in class chemaxon.calculations.LogPPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPPlugin.getLogPTrue() instead. This method will be removed in a future version.
getLogPTrue() - Method in class chemaxon.calculations.LogPPlugin: Returns the most typical logP among logD at pI, micro logP and nonionic logP.
getLonePairCount() - Method in class chemaxon.struc.MDocument: Returns the number of Lone Pair electrons.
getLonePairCount() - Method in class chemaxon.struc.MolAtom: Returns the automatically calculated lone pair count of this atom.
getLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph: Deprecated.
use MolAtom.getLonePairCount() instead
getLonePairCount(int) - Method in class chemaxon.struc.RgMolecule: Gets the number of lone pairs.
getLonePairsVisible() - Method in class chemaxon.marvin.beans.MarvinPane: Tests whether lone pairs are visible.
getLowBridgeAtomIndexes() - Method in class chemaxon.struc.BicycloStereoDescriptor: Return the atom indexes of the atoms of the bridge with the lower index.
getLowBridgeAtoms() - Method in class chemaxon.struc.BicycloStereoDescriptor: Return the atoms of the bridge with the lower index.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.MolecularDescriptor: Calculates an estimate for the minimum value of the distance using the default distance metric.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the lower bound estimate of the dissimilarity from the given fingerprint.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.ReactionFingerprint: Calculates the lower bound estimate of the dissimilarity from the given fingerprint.
getLowerBound(MolecularDescriptor) - Method in class chemaxon.descriptors.ScalarDescriptor: Calculates the lower bound estimate of the dissimilarity from the given descriptor.
getLowestEigenvalue(int, int) - Method in class chemaxon.descriptors.BCUT: Gets the specified lowest eigenvalue.
getLowestEigenvaluesCount(int) - Method in class chemaxon.descriptors.BCUTParameters: Gets the number of lowest eigenvalues calculated.
getLowestEnergyConformer() - Method in class chemaxon.calculations.ConformerPlugin: Returns the calculated lowest energy conformer.
getLowestEnergyConformer() - Method in class chemaxon.calculations.GeometryPlugin: Returns the lowest energy conformer of the molecule.
getM(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the nth molecule in memory.
getM(int, String) - Method in class chemaxon.marvin.beans.MViewPane: Gets the nth molecule in a text format.
getMacroDistributions() - Method in class chemaxon.calculations.PkaPlugin: Returns the macrospecies distribution arrays for all macro pKa values: the i-th row is the disrtibution vector of the i-th ionization state as function of the pH.
getMacroDistributions(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the i-th macrospecies distribution as function of the pH
getMacropKaValues(int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getMacroPkaValues(int) instead. This method will be removed in a future version.
getMacropKaValues(int, double[], int[]) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getMacroPkaValues(int, double[], int[]) instead. This method will be removed in a future version.
getMacroPkaValues(int) - Method in class chemaxon.calculations.PkaPlugin: Calculates the acidic pKa values in ascending order or the basic pKa values in descending order.
getMacroPkaValues(int, double[], int[]) - Method in class chemaxon.calculations.PkaPlugin: Calculates the least acidic pKa values in ascending order or the biggest basic pKa values in descending order.
getMacrospeciesCharge(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the formal charges of a given macrospecies.
getMacroSpeciesCharge(int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getMacrospeciesCharge(int) instead. This method will be removed in a future version.
getMacroSpeciesCount() - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
No replacement. This method will be removed in a future version.
getMainDoc(int) - Method in class chemaxon.marvin.common.MDocStorage: Gets the document at the specified position.
getMainDoc(int, ProgressMonitor) - Method in class chemaxon.marvin.common.MDocStorage: Gets the document at the specified position.
getMainMoleculeGraph() - Method in class chemaxon.struc.MDocument: Gets the main molecule graph.
getMainMolFieldness() - Method in class chemaxon.marvin.common.TableOptions: Tests whether the main molecule is a field.
getMajorMicrospecies() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the major microspecies at the pH set in MajorMicrospeciesPlugin.setPh(double).
getMap() - Method in class chemaxon.struc.prop.MHashProp: Gets the map.
getMap(MoleculeGraph) - Method in class chemaxon.struc.prop.MHCoords3DProp: Gets a map containing MolAtom objects as keys and DPoint3 arrays as values.
getMappingStyle() - Method in class chemaxon.reaction.mapper.AutoMapper: Returns the mapping style of the mapper.
getMappingStyle() - Method in class chemaxon.reaction.mapper.AutoMapper.Options
getMappingStyle() - Method in class chemaxon.standardizer.actions.MapAction: Returns the mapping style of the underlying mapper.
getMappingStyle() - Method in class chemaxon.standardizer.actions.MapReactionAction: Returns the mapping style of the underlying mapper.
getMarginSize() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the documents margin size.
getMarginSize() - Method in class chemaxon.marvin.common.UserSettings: Gets the documents margin size.
getMarkushAromHandling() - Method in class chemaxon.search.api.options.SearchOptions: Gets the Markush aromatic search behavior.
getMarkushDisplayMode() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the Markush display mode.
getMass() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.MolAtom: Gets the atomic weight.
getMass() - Method in class chemaxon.struc.MoleculeGraph: Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.RgMolecule: Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.RxnMolecule: Calculates the molecular weight of the molecule.
getMass(int) - Static method in class chemaxon.struc.PeriodicTable: Atomic weight of the element based on the natural abundance of its isotopes
getMass(int, int) - Static method in class chemaxon.struc.PeriodicTable: Atomic weight of an isotope
getMassno() - Method in class chemaxon.struc.MolAtom: Gets the mass number.
getMassPrecision(int) - Static method in class chemaxon.struc.PeriodicTable: The precision of an elemental mass is the number of measured digits after the decimal separator.
getMassPrecision(int, int) - Static method in class chemaxon.struc.PeriodicTable: The precision of an isotopic mass is the number of measured digits after the decimal separator.
getMatchCount() - Method in class chemaxon.search.AbstractSearch: The number of times the query molecule appears in the target molecule.
getMatchedQueryAtoms() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the indices of the query atoms that are part of the found common substructure.
getMatchedQueryBonds() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the indices of the query bonds that are part of the found common substructure.
getMatchedTargetAtoms() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the indices of the target atoms that are part of the found common substructure.
getMatchedTargetBonds() - Method in class chemaxon.search.mcs.McsSearchResult: Gets the indices of the target bonds that are part of the found common substructure.
getMaxAttachmentPointOrder(int) - Method in class chemaxon.struc.RgMolecule: Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.
getMaxCols() - Method in class chemaxon.marvin.common.TableOptions: Get maximum value of columns in the table.
getMaxConsideredRingSize() - Method in class chemaxon.search.mcs.McsSearchOptions: Returns the maximum size of rings considered during search for the specified ring handling mode.
getMaxDimCached() - Method in class chemaxon.marvin.common.MDocStorage: Gets the maximum molecule dimension.
getMaxDist() - Method in class chemaxon.descriptors.PFParameters: Gets the miximum distance of pharmacophore points that is considered.
getMaxDist() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getMaxEnergy() - Method in class chemaxon.alignment.DihedralScanResult: Observed largest energy.
getMaxGradLimit() - Method in class chemaxon.alignment.AlignmentBase: Returns the maximum gradient component limit used for the optimization.
getMaximalProjectionArea() - Method in class chemaxon.calculations.GeometryPlugin: Returns the maximal projection area in Angstrom^2.
getMaximalProjectionRadius() - Method in class chemaxon.calculations.GeometryPlugin: Returns the radius of the circle surrounding the maximal projection in Angstrom.
getMaximum() - Method in interface chemaxon.core.util.MProgressMonitor: Deprecated.

Gets the maximum progress value.
getMaximum() - Method in interface chemaxon.core.util.ProgressMonitor: Gets the maximum progress value.
getMaximumBitRatio() - Method in class chemaxon.descriptors.MDGenerator: Gets the maximum percentage of non-zero cells in descriptors generated.
getMaxRepetitions() - Method in class chemaxon.struc.MolAtom: Gets the maximum number of repetitions for a link atom.
getMaxRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MoleculeGraph: Returns the maximal attachment point order of R-group attachment point atoms in this molecule graph.
getMaxRows() - Method in class chemaxon.marvin.common.TableOptions: Get maximum value of rows in the table
getMaxs() - Method in class chemaxon.alignment.ShapeData
getMaxSize() - Method in class chemaxon.marvin.common.TableOptions: Get the maximum number of molecules displayed in the table.
getMaxThreadCount() - Method in class chemaxon.reaction.mapper.AutoMapper.Options
getMaxZ() - Method in class chemaxon.calculations.GeometryPlugin
getMChemicalStruct() - Method in class chemaxon.struc.MDocument
getMcsSimilarityLimit() - Method in class chemaxon.alignment.MMPAlignmentProperties
getMDocumentStream() - Method in class chemaxon.formats.MDocSource: Creates an MDocument stream with the iterator of the importer.
getMDocumentStream() - Method in class chemaxon.formats.MolImporter: Creates an MDocument stream with the iterator of the importer.
getMDocumentStream() - Method in interface chemaxon.formats.MolImporterInterface: Creates an MDocument stream with the iterator of the importer.
getMeaningfulFrequencies() - Static method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the array of meaningful NMR measurement frequencies in MHz.
getMeasure() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction: Gets the measure of the action
getMediumReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint: Returns the tanimoto distance of the reaction centers and their neighbouring atoms and bonds.
getMElectron() - Method in class chemaxon.struc.graphics.MEFlow
getMElectronContainer() - Method in class chemaxon.struc.graphics.MEFlow
getMElectronContainerIndexInAtom(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
getMElectronRef() - Method in class chemaxon.struc.graphics.MEFlow
getMenu(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the menu string for a plugin.
getMergedst() - Method in class chemaxon.marvin.beans.MSketchPane: Gets the merge distance.
getMessage() - Method in interface chemaxon.calculations.api.CalculatorError: Returns the message that describes this error.
getMessage() - Method in class chemaxon.calculations.stereo.ErrorReport: Returns an error message.
getMessage() - Method in exception class chemaxon.reaction.ReactionException: Returns the detailed message string of this exception, plus all the causes concatenated.
getMessage() - Method in exception class chemaxon.search.api.SearchException: Returns the detailed message string of this exception, plus all the causes concatenated.
getMetalAtoms() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult: This method returns the metallocene relevant metal atoms represented by a List of MolAtom.
getMethod() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction: Gets the method of the action
getMethod() - Method in class chemaxon.standardizer.actions.TautomerizeAction
getMethodName() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the method name to call
getMetricIndex(String) - Method in class chemaxon.descriptors.MDParameters: Gets the index of the given parametrized metric.
getMetricIndex(String) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the index of the given parameterized metric.
getMetricName() - Method in class chemaxon.descriptors.MDParameters: Gets the user defined symbolic name of the current parametrized metric.
getMetricName() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the name of the current parameterized metric.
getMetricName(int) - Method in class chemaxon.descriptors.MDParameters: Gets the user defined symbolic name of the specified parametrized metric.
getMetricName(int) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the name of a metric specified parameterized metric by its index.
getMicrospecies(int) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the microspecies molecule.
getMicrospeciesCount() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the number of microspecies
getMidPointLocation(int, Transform3D) - Method in class chemaxon.struc.graphics.MPolyline: Gets the middle point of the arc.
getMinDist() - Method in class chemaxon.descriptors.PFParameters: Gets the minimum distance of pharmacophore points that is considered.
getMinDist() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getMinEnergy() - Method in class chemaxon.alignment.DihedralScanResult: Observed lowest energy.
getMinFragmentSize() - Method in class chemaxon.search.mcs.McsSearchOptions: Returns the minimum required size of the fragments of the common substructures.
getMinimalProjectionArea() - Method in class chemaxon.calculations.GeometryPlugin: Returns the minimal projection area in Angstrom^2.
getMinimalProjectionRadius() - Method in class chemaxon.calculations.GeometryPlugin: Returns the radius of the circle surrounding the minimal projection in Angstrom.
getMinimumBitRatio() - Method in class chemaxon.descriptors.MDGenerator: Gets the minimum percentage of non-zero cells in descriptors generated.
getMinimumHeight() - Method in class chemaxon.struc.graphics.MTextBox: Gets the minimum height of the text.
getMinRepetitions() - Method in class chemaxon.struc.MolAtom: Gets the minimum number of repetitions for a link node.
getMins() - Method in class chemaxon.alignment.ShapeData
getMinZ() - Method in class chemaxon.calculations.GeometryPlugin
getMirroredArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline: Mirror transformation for arrow heads.
getMMFF94Energy() - Method in class chemaxon.calculations.GeometryPlugin: Returns the MMFF94 energy of the structure (default: kcal/mol).
getMnemonic() - Method in class chemaxon.marvin.common.MAction: Gets the mnemonic.
getMnemonic(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the menu mnemonic for a plugin.
getModifiedAtoms() - Method in class chemaxon.standardizer.Changes: Gets the list of modified atoms during the standardization procedure
getMol() - Method in class chemaxon.marvin.beans.MSketchPane: Returns the clone of the current molecule being on the canvas.
getMol(String) - Method in class chemaxon.marvin.beans.MSketchPane: Gets the molecule in a text format.
getMolbg() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the molecule background color.
getMolCenter(int, String) - Method in class chemaxon.marvin.common.MDocStorage: Gets a molecule center.
getMolConstant(String) - Method in class chemaxon.descriptors.pharmacophore.PMapper: Returns the molecule constant corresponding to the given ID.
getMolCrd() - Method in class chemaxon.alignment.AlignmentMolecule
getMolecule() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the input molecule of the dipole moment computation.
getMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the molecule under examination.
getMolecule() - Method in class chemaxon.calculations.solubility.SolubilityResult: Returns the input molecule.
getMolecule() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getMolecule() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getMolecule() - Method in class chemaxon.chemterms.MolContext: Returns the input molecule.
getMolecule() - Method in class chemaxon.core.calculations.Ring: Retrieves the input molecule
getMolecule() - Method in class chemaxon.core.calculations.stereo.Stereochemistry: Retrieves the input molecule
getMolecule() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Retrieves the input molecule
getMolecule() - Method in class chemaxon.struc.graphics.MAnalysisBox: Returns the molecule associated with this analysis box.
getMolecule() - Method in class chemaxon.struc.prop.MMoleculeProp: Gets the molecule.
getMolecule() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

Returns the molecule
getMolecule(int) - Method in class chemaxon.standardizer.actions.CreateGroupAction: Gets the molecule at the provided index
getMolecule(int) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Gets the molecule at the provided index
getMolecule(int) - Method in class chemaxon.standardizer.actions.StripSaltsAction: Gets the molecule at the provided index
getMolecule(int) - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets the specified frame.
getMolecule1Aligned() - Method in interface chemaxon.alignment.AlignmentResult: The molecule with coordinates changed to fulfill the alignment requested by the input parameters.
getMolecule1Aligned() - Method in class chemaxon.alignment.MMPAlignmentResult
getMolecule2Aligned() - Method in interface chemaxon.alignment.AlignmentResult: The molecule with coordinates changed to fulfill the alignment requested by the input parameters.
getMolecule2Aligned() - Method in class chemaxon.alignment.MMPAlignmentResult
getMoleculeCount() - Method in class chemaxon.descriptors.MDGenerator: Gets the number of molecules processed (that is, the number of descriptors generated) since the initialization of the object.
getMoleculeCount() - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets the number of frames.
getMoleculeGraph() - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets the stored molecule graph.
getMoleculeIndex() - Method in class chemaxon.reaction.AtomIdentifier: Gets the index of the molecule - in the input molecules of the reaction - containing the atom
getMoleculeIterator() - Method in class chemaxon.formats.MDocSource: Gets a molecule iterator for this document source.
getMoleculeIterator(MolImporter) - Static method in class chemaxon.formats.MoleculeIteratorFactory: Returns a molecule iterator for the given MolImporter.
getMoleculeIterators(MolImporter[]) - Static method in class chemaxon.formats.MoleculeIteratorFactory: Gets molecule iterators from the importers in an array.
getMoleculeIterators(List<MolImporter>) - Static method in class chemaxon.formats.MoleculeIteratorFactory: Returns molecule iterators fof the given list of MolImporter objects.
getMoleculeMovie() - Method in class chemaxon.struc.MDocument: Gets the molecule movie.
getMoleculeOrig() - Method in class chemaxon.alignment.AlignmentMolecule: Gets back a clone of the unmodified input structure.
getMolecules() - Method in class chemaxon.alignment.AlignmentBase: Returns the collection of alignment molecules.
getMolecules() - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets all molecules.
getMoleculeWithAlignedCoordinates(int) - Method in class chemaxon.alignment.Alignment: After the alignment result molecule can be obtained.
getMolfileExtensions() - Static method in class chemaxon.formats.MFileFormatUtil: Gets the array of known molecule file extensions.
getMolfileFormats() - Static method in class chemaxon.formats.MFileFormatUtil: Gets the array of known molecule file formats.
getMolID() - Method in class chemaxon.alignment.AlignmentMolecule
getMolImportModule() - Method in class chemaxon.formats.MolImporter
getMolIndex() - Method in exception class chemaxon.formats.MolExportException: Returns the molecule index.
getMolNameFontSize() - Method in class chemaxon.marvin.common.TableOptions: Gets the molecule name font size.
getMolObject(int) - Method in class chemaxon.struc.graphics.MEFlow: Gets the electron source or sink.
getMolPainter(int, String) - Method in class chemaxon.marvin.common.MDocStorage: Gets a molecule painter.
getMolPanel() - Method in class chemaxon.marvin.beans.MarvinPane: Returns the underlying panel.
getMolPanel() - Method in class chemaxon.marvin.beans.MSketchPane
getMolPanel() - Method in class chemaxon.marvin.beans.MViewPane
getMolPolarizability() - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the molecular polarizability value.
getMolStream() - Method in class chemaxon.formats.MDocSource: Creates a Molecule stream with the iterator of the importer.
getMolStream() - Method in class chemaxon.formats.MolImporter: Creates a Molecule stream with the iterator of the importer.
getMolStream() - Method in interface chemaxon.formats.MolImporterInterface: Creates a Molecule stream with the iterator of the importer.
getMonitor() - Method in class chemaxon.structurechecker.AdvancedCheckerRunner: Returns the current monitor.
getMoreErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the more error message
getMostFrequentNaturalIsotope(int) - Static method in class chemaxon.struc.PeriodicTable: Returns the mass number of the most frequent natural isotope of the element
getMostLikelyMolFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil: Gets the most likey molecule file format from the file name extension.
getMostSimplifiedMolecule() - Method in class chemaxon.struc.Molecule: Gets the simplified molecule object even if there is a parent document with other objects.
getMostSimplifiedMolecule() - Method in class chemaxon.struc.RgMolecule: Gets the simplified molecule object even if there is a parent document with other objects.
getMProp() - Method in class chemaxon.struc.MDocument: Gets the document as a property.
getMsAcceptorCounts() - Method in class chemaxon.calculations.HBDAPlugin: Returns the average acceptor counts over the microspecies distribution for different pH-s.
getMsCount() - Method in class chemaxon.calculations.PkaPlugin: Returns the number of microspecies and/or distributions.
getMsDistribution(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the microspecies distribution array.
getMsDistributions() - Method in class chemaxon.calculations.PkaPlugin: Returns the microspecies distribution arrays for all microspecies: the i-th element is the disrtibution array of the i-th microspecies.
getMsDonorCounts() - Method in class chemaxon.calculations.HBDAPlugin: Returns the average donor counts over the microspecies distribution for different pH-s.
getMSketchPane() - Method in class chemaxon.marvin.beans.MSketch
getMsMolecule(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the microspecies molecule.
getMultiplets() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Gets the multiplets of the function.
getMultiplicities(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the multiplicities of the ith atom of the multiplet.
getMultiplier() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the multiplier.
getMViewPane() - Method in class chemaxon.marvin.beans.MView
getMViewParam() - Method in class chemaxon.marvin.beans.MViewParams: Generates the parameter string that can be set to MViewPane.
getName() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the name of the NMR spectrum.
getName() - Method in class chemaxon.calculations.PkaTrainingResult
getName() - Method in class chemaxon.calculations.services.ServiceArgument: Returns the name of the argument
getName() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the name of the service
getName() - Method in class chemaxon.calculations.stereo.stereocenters.AttachedData: Gets the name.
getName() - Method in class chemaxon.checkers.AbstractStructureChecker
getName() - Method in class chemaxon.checkers.InvalidChecker
getName() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getName() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getName() - Method in interface chemaxon.checkers.StructureChecker: Gets the name of the checker
getName() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the checker name
getName() - Method in class chemaxon.descriptors.BCUT: Gets the name of the BCUT descriptor object.
getName() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the name of the ChemicalFingerprint object.
getName() - Method in class chemaxon.descriptors.CustomDescriptor: Gets the name of the CustomDescriptor object.
getName() - Method in class chemaxon.descriptors.ECFP: Gets the name of the ECFP fingerprint object.
getName() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the name of the descriptor.
getName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the name of the PharmacophoreFingerprint object.
getName() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the nice name of the ReactionFingerprint descriptor object.
getName() - Method in class chemaxon.descriptors.ScalarDescriptor: Gets the name of the ScalarDescriptor object.
getName() - Method in class chemaxon.descriptors.scalars.HAcc: Gets the name of the HAcc descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.HDon: Gets the name of the HDon descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.Heavy: Gets the name of the HeavyAtomCount descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.LogD: Gets the name of the LogD descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.LogP: Gets the name of the LogP descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.Mass: Gets the name of the Mass descriptor object.
getName() - Method in class chemaxon.descriptors.scalars.TPSA: Gets the name of the TPSA descriptor object.
getName() - Method in class chemaxon.descriptors.ShapeDescriptor: Gets the name of the ShapeDescriptor fingerprint object.
getName() - Method in class chemaxon.fixers.StructureFixerDescriptor: Returns the fixer name
getName() - Method in class chemaxon.formats.MFileFormat: Gets the codename of the format.
getName() - Method in class chemaxon.formats.OptionDescriptor: Gets the option name.
getName() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor: Gets the name of the represented MTransferable.
getName() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the name of the action
getName() - Method in class chemaxon.struc.Molecule: Gets the molecule name/title that was set by Molecule.setName(String).
getName() - Method in class chemaxon.struc.MoleculeGraph: Gets the molecule title/name.
getName() - Method in class chemaxon.struc.RgMolecule: Gets the name of the root molecule.
getName(int) - Static method in class chemaxon.struc.PeriodicTable: Name of the element
getNameIOServiceURL() - Method in class chemaxon.marvin.common.UserSettings
getNameList() - Method in class chemaxon.formats.MFileFormat: Gets all the codenames of the format.
getNavmode() - Method in class chemaxon.marvin.beans.MViewPane: Gets the mouse drag action.
getNDists() - Method in class chemaxon.descriptors.PFParameters: Gets the number of histograms bars, that is that number of distance values disguished.
getNetIntensity() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the net intensity of this multiplet which corresponds to the number of atoms in the multiplet.
getNewOldIndexMap() - Method in class chemaxon.calculations.TautomerPlugin
getNewToOld() - Method in class chemaxon.standardizer.Standardizer: Returns the new to old atom index mapping.
getNextAromatizedStructure() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the next enumerated structure.
getNextHit() - Method in class chemaxon.search.hitdisplay.HitDisplayTool: Gets the next hit.
getNextStructure() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the next enumerated structure, or null if no more structures.
getNodeColor() - Method in class chemaxon.alignment.AlignmentBase: Returns the node color used for the alignment.
getNodeCount() - Method in class chemaxon.alignment.AlignmentMolecule
getNodeType() - Method in class chemaxon.alignment.AlignmentBase: Returns the node type used for the alignment.
getNoErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the no error message of the concerning checker
getNominalMass() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
getNonHitColor() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the color to be used when coloring the part of the target which is not matching to the query.
getNonHitColor3D() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the color to be used when coloring the part of the 3D target which is not matching to the query.
getNonQueryImplicitHcount() - Method in class chemaxon.struc.MolAtom: Gets the number of implicit hydrogens attached.
getNotSpec() - Method in enum class chemaxon.alignment.AlignmentProperties
getNucleophilicEnergy(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
getNucleophilicOrder(int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Deprecated.
Use HuckelAnalysisPlugin.getHMONucleophilicOrder(int)
getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder: Gets the nucleus type.
getNucleus() - Method in class chemaxon.calculations.nmr.NMRCalculator: Returns the NMR active nucleus.
getNucleusString() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the nucleus type string.
getNucleusType() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the type of the nucleus under examination.
getNumber() - Method in class chemaxon.calculations.stereo.stereocenters.EnhancedStereo: Number of type.
getNumberFormat() - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
getNumberOfFeatures() - Method in class chemaxon.descriptors.PFParameters: The number of pharmacophore features (aka types, properties) used in the fingerprints.
getNumberOfFeatures() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getNumberOfLines() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the number of NMR lines in this multiplet.
getNumberOfMetrics() - Method in class chemaxon.descriptors.MDParameters: Gets the total number of parametrized metrics available in the present configuration.
getNumberOfMetrics() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the number of parameterized metrics available for the particular descriptor.
getNumberOfMetrics() - Method in class chemaxon.descriptors.SDParameters: Gets the total number of parametrized metrics available in the present configuration.
getNumberOfNMRActiveNuclei() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns number of the NMR active nuclei.
getNumberOfWeights() - Method in class chemaxon.descriptors.MDParameters: Gets the number of weights the current parametrized metric takes.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.BCUTParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.CDParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.CFParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.ECFPParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.MDParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.PFParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(int) - Method in class chemaxon.descriptors.RFParameters: Gets the number of weight factors used by the specified metric.
getNumberOfWeights(String) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the number of weight factors used by the specified metric.
getNumElectrons() - Method in class chemaxon.struc.graphics.MEFlow: Gets the number of electrons the arrow represents.
getObject(int) - Method in class chemaxon.struc.MDocument: Gets an object from the document.
getObject(String) - Method in class chemaxon.struc.MPropertyContainer: Gets a property object.
getObjectAtPointer() - Method in class chemaxon.marvin.beans.MSketchPane: Get the object at the mouse pointer.
getObjectContainingSelection() - Method in class chemaxon.struc.MDocument: Gets the object that contains the selection.
getObjectCount() - Method in class chemaxon.struc.MDocument: Gets the number of objects in this document.
getObjectCount() - Method in class chemaxon.struc.Molecule: Returns the count of the MObjects that belong to this molecule.
getObjectCount() - Method in class chemaxon.struc.RgMolecule
getObjectCount() - Method in class chemaxon.struc.RxnMolecule
getObjectsMiddle() - Method in class chemaxon.struc.sgroup.DataSgroup
getObjectsMiddle(Point3D) - Method in class chemaxon.struc.sgroup.DataSgroup: Calculates the middle point of the coordinates of objects this sgroup is associated to.
getOffset() - Method in class chemaxon.marvin.common.MDocStorage: Gets the offset in the document source.
getOldNewIndexMap() - Method in class chemaxon.calculations.TautomerPlugin
getOldToNew() - Method in class chemaxon.standardizer.Standardizer: Returns the old to new atom index mapping.
getOneErrorMessage() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the one error message
getOneLetterName() - Method in class chemaxon.struc.sgroup.AminoAcidSgroup: Returns the one letter name of the amino acid.
getOption(String) - Method in class chemaxon.search.api.options.SearchOptions: Returns option value in string format.
getOptionDescriptors(String) - Method in class chemaxon.formats.MolExportModule: Gets an array of option descriptors for the specified format.
getOptionDescriptors(String, String, List<OptionDescriptor>) - Method in class chemaxon.formats.MolExportModule: Gets an array of option descriptors.
getOptionDescriptors(ResourceBundle, String, String, List<OptionDescriptor>) - Static method in class chemaxon.formats.MolExportModule: Gets an array of option descriptors.
getOptionNames() - Method in class chemaxon.search.api.options.SearchOptions: Returns the name of all available options which can be used to set/get option values with SearchOptions.setOption(String, String) and SearchOptions.getOption(String) methods.
getOptions() - Method in class chemaxon.formats.MolExportModule: Returns the output options.
getOptions() - Method in class chemaxon.formats.MolImporter: Gets the import options.
getOptionSign() - Method in class chemaxon.formats.MolExportModule: Gets the sign of the options.
getOptionsPane() - Method in class chemaxon.calculations.gui.PluginFactory.PluginRecord
getOptionsPane(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the options pane for a plugin, loads it if needed.
getOptionsToDeselect() - Method in class chemaxon.formats.OptionDescriptor: Gets the options that must be deselected if this option is selected.
getOptionsToDisable() - Method in class chemaxon.formats.OptionDescriptor: Gets the options that must be switched off if this option is selected.
getOptionsToEnable() - Method in class chemaxon.formats.OptionDescriptor: Gets the options that must be switched off if this option is selected.
getOptionString() - Method in enum class chemaxon.search.api.options.HaltOnErrorOption
getOptionString() - Method in enum class chemaxon.search.api.options.HomologyTranslationOption
getOptionString() - Method in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption
getOptionString() - Method in interface chemaxon.search.api.options.OptionStringProvider
getOptionString() - Method in enum class chemaxon.search.api.options.SetOfSmallestRingsOption
getOptionString() - Method in enum class chemaxon.search.api.options.TargetHomologyMatchingMode
getOptionString() - Method in enum class chemaxon.search.api.options.TautomerEqualityMode
getOptionString() - Method in enum class chemaxon.search.api.options.TautomerSubstructureMode
getOrder() - Method in class chemaxon.struc.graphics.MAssigner: Gets the order of an assigner.
getOrder() - Method in class chemaxon.struc.sgroup.AttachmentPoint: Gets the order of the attachment point.
getOrientation() - Method in enum class chemaxon.alignment.AlignmentProperties
getOrientationType() - Method in class chemaxon.alignment.Alignment
getOriginal() - Method in class chemaxon.standardizer.actions.GroupDefinition: Gets the original molecule of the group.
getOriginal() - Method in class chemaxon.standardizer.Changes: Gets the original molecule of the standardization process.
getOriginalMolecule() - Method in class chemaxon.calculations.CalculatorPlugin
getOrigQueryAtom(int) - Method in class chemaxon.search.api.MolComparator: Converts search internal atom index (in the query) to the original atom index in the query molecule.
getOrigQueryAtom1(int) - Method in class chemaxon.search.api.MolComparator: Returns the index of the first atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).
getOrigQueryAtom2(int) - Method in class chemaxon.search.api.MolComparator: Returns the index of the second atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).
getOrigQueryBond(int) - Method in class chemaxon.search.api.MolComparator: Returns bond index in the query molecule for the given query bond (search internal bond index in the query).
getOrigQueryNeighbour(int) - Method in class chemaxon.search.api.MolComparator: For a search internal atom index (in the query), returns a neighbour atom index (original atom index in the query molecule).
getOrigTargetAtom(int) - Method in class chemaxon.search.api.MolComparator: Converts search internal atom index (in the target) to the original atom index in the target molecule.
getOrigTargetAtom1(int) - Method in class chemaxon.search.api.MolComparator: Returns the index of the first atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).
getOrigTargetAtom2(int) - Method in class chemaxon.search.api.MolComparator: Returns the index of the second atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).
getOrigTargetBond(int) - Method in class chemaxon.search.api.MolComparator: Returns bond index in the target molecule for the given target bond (search internal bond index in the target).
getOrigTargetNeighbour(int) - Method in class chemaxon.search.api.MolComparator: For a search internal atom index (in the target), returns a neighbour atom index (original atom index in the target molecule).
getOsVersionStr() - Static method in class chemaxon.common.version.VersionInfo: Returns the OS version information as string.
getOtherAtom(MolAtom) - Method in class chemaxon.struc.MolBond: Gets the other end of the bond.
getOtherCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Gets the other bond if a bond is a crossing bond in a ladder-type polymer bracket.
getOtherEnd() - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Gets the atom at the other end point.
getOwnerCount() - Method in class chemaxon.marvin.common.UserSettings: Gets the current number of owners.
getP0() - Method in class chemaxon.struc.graphics.MTextBoxTransformation
getPageFormat(String) - Method in class chemaxon.marvin.common.UserSettings: Gets the specified PageFormat
getPageSettings() - Method in class chemaxon.struc.MDocument: Gets the page settings of multipage molecular document.
getParameter(String) - Method in class chemaxon.marvin.beans.MarvinPane: Gets a parameter.
getParameterPanel() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns the parameter panel.
getParameterPanel() - Method in class chemaxon.calculations.gui.PluginFactory.PluginRecord
getParameterPanel(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets the parameter panel for a plugin, loads it if needed.
getParameters() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the parameters associated with the object.
getParameters() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction: Gets the parameter map of the action
getParameters(Properties) - Method in interface chemaxon.calculations.gui.ParameterPanelHandler: Returns the plugin parameters.
getParametersClassName() - Method in class chemaxon.descriptors.BCUT: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.CustomDescriptor: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ECFP: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the name of the parameters class corresponding to the descriptor (prefixed with the package name as getClass().getName() would return).
getParametersClassName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ScalarDescriptor: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.HAcc: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.HDon: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.scalars.LogD: Gets the name of the parameters class corresponding to the descriptor.
getParametersClassName() - Method in class chemaxon.descriptors.ShapeDescriptor: Gets the name of the parameters class corresponding to the descriptor.
getParametersOf(PkaTrainingResult.PkaType) - Method in class chemaxon.calculations.PkaTrainingResult
getParams() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the parameter string.
getParent() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Gets the parent component.
getParent() - Method in class chemaxon.struc.MolAtom: Return the molecule graph that contains this atom.
getParent() - Method in class chemaxon.struc.MolBond: Gets the parent graph.
getParent() - Method in class chemaxon.struc.MoleculeGraph: Gets the parent graph that contains this substructure.
getParentDocument() - Method in class chemaxon.struc.MoleculeGraph: Gets the document or the document of the parent graph.
getParentLine() - Method in class chemaxon.struc.graphics.MMidPoint: Gets the parent line.
getParentMolecule() - Method in class chemaxon.struc.Sgroup: Gets the parent molecule.
getParentRect() - Method in class chemaxon.struc.graphics.MRectanglePoint: Gets the parent rectangle.
getParentSgroup() - Method in class chemaxon.struc.Sgroup: Gets the parent S-group.
getParentSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Deprecated.
as of Marvin 6.2, intended for internal use, similar functionality can be reached by SuperatomSgroup.getSgroupGraph()
getParity(int) - Method in class chemaxon.struc.MoleculeGraph: Computes the parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getParity(int) - Method in class chemaxon.struc.RgMolecule: Computes the parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getParity(int) - Method in class chemaxon.struc.RxnMolecule: Computes the parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
getParityType(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the parity type.
getPath() - Method in class chemaxon.formats.MolInputStream: Gets the path or URL of the file.
getPeakDomainMax() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the array of peak upper ends.
getPeakDomainMax(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the upper end of the ith peak.
getPeakDomainMin() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the array of peak lower ends.
getPeakDomainMin(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the lower end of the ith peak.
getPeptideDisplayType() - Method in class chemaxon.marvin.common.UserSettings: Gets the current peptide display type
getpH() - Method in class chemaxon.calculations.CalculatorPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use CalculatorPlugin.getPh() instead. This method will be removed in a future version.
getpH() - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use MajorMicrospeciesAccessorPlugin.getPh() instead. This method will be removed in a future version.
getpH() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use MajorMicrospeciesPlugin.getPh() instead. This method will be removed in a future version.
getPh() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the pH where the major microspecies should be taken.
getPh() - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin: Returns the pH where the major microspecies should be taken.
getPh() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the pH where the major microspecies should be taken.
getPharmacophore() - Method in class chemaxon.alignment.Pharmacophore3D
getpHs() - Method in class chemaxon.calculations.HBDAPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use HBDAPlugin.getPhValues() instead. This method will be removed in a future version.
getpHs() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use IsoelectricPointPlugin.getPhValues() instead. This method will be removed in a future version.
getpHs() - Method in class chemaxon.calculations.LogDPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogDPlugin.getPhValues() instead. This method will be removed in a future version.
getpHs() - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPhValues() instead. This method will be removed in a future version.
getPhValues() - Method in class chemaxon.calculations.HBDAPlugin: Returns the pH array.
getPhValues() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the pH array.
getPhValues() - Method in class chemaxon.calculations.LogDPlugin: Returns the pH array.
getPhValues() - Method in class chemaxon.calculations.PkaPlugin: Returns the pH array.
getpI() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use IsoelectricPointPlugin.getIsoelectricPoint() instead. This method will be removed in a future version.
getPiCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the pi charge of a specified atom.
getPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane: Gets the current molecule piece in the specified format.
getPiOEN(int) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the pi orbital electronegativity of a specified atom.
getpKa(int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPka(int) instead. This method will be removed in a future version.
getPka(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the most significant pKa value for the given atom index.
getPka(int, int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated.
Use PkaPlugin.getPkaValues(int, int)
getpKaConc(int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPkaConcentration(int) instead. This method will be removed in a future version.
getPkaConcentration(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the so-called concentration ionization constant.
getpKaMixed(int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPkaMixed(int) instead. This method will be removed in a future version.
getPkaMixed(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the so-called mixed ionization constant.
getPkaOfIsoelectricPoint() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the pKa values of the calculated isoelectric point.
getpKaOfpI() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use IsoelectricPointPlugin.getPkaOfIsoelectricPoint() instead. This method will be removed in a future version.
getpKaPrefixType() - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPkaPrefixType() instead. This method will be removed in a future version.
getPkaPrefixType() - Method in class chemaxon.calculations.PkaPlugin: Returns the pKa prefix type.
getpKaType(int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPkaType(int) instead. This method will be removed in a future version.
getPkaType(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the pKa type: PkaPlugin.ACIDIC, PkaPlugin.BASIC or 0 if there is no pKa value for the given atom.
getpKaValues(int, int) - Method in class chemaxon.calculations.PkaPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use PkaPlugin.getPkaValues(int, int) instead. This method will be removed in a future version.
getPkaValues(int, int) - Method in class chemaxon.calculations.PkaPlugin: Returns the pKa values for the given atom index and pKa type.
getPlaceholderText() - Method in class chemaxon.calculations.services.DynamicArgument: Returns the value placeholder text.
getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument: Gets the document as plain text, with no formatting and escaping.
getPlainText() - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the selected text as a plain text string.
getPlattIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
getPlugin() - Method in class chemaxon.calculations.CalculatorPluginService: Returns the calculator plugin object.
getPlugin() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay
getPlugin() - Method in class chemaxon.calculations.gui.PluginFactory.PluginRecord
getPlugin() - Method in class chemaxon.calculations.output.CalculatorPluginOutput
getPlugin(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets a plugin, loads it if needed.
getPluginIndex(String) - Method in class chemaxon.calculations.gui.PluginFactory: Gets a plugin index from record key.
getPluginParameters() - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the plugin parameter table (this should be set in the plugin).
getPMap(Molecule, PSymbols) - Method in class chemaxon.descriptors.PFGenerator: Gets pharmacophore map of the input molecule.
getPMAPTagName() - Method in class chemaxon.descriptors.PFGenerator: Gets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.
getPoint(int) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the point.
getPoint(int) - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.graphics.MEFlow: Gets a point of the line.
getPoint(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Gets the point.
getPoint(int) - Method in class chemaxon.struc.graphics.MElectron
getPoint(int) - Method in class chemaxon.struc.graphics.MElectronContainer
getPoint(int) - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the clone of a point of the line.
getPoint(int) - Method in class chemaxon.struc.MObject: Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.MPoint: Gets the point.
getPointCount() - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets the number of points (atoms).
getPointCount() - Method in class chemaxon.struc.graphics.MElectronContainer
getPointCount() - Method in class chemaxon.struc.graphics.MMoleculeMovie: Gets the number of points (atoms).
getPointCount() - Method in class chemaxon.struc.graphics.MPolyline: Gets the number of points.
getPointCount() - Method in class chemaxon.struc.MObject: Gets the number of points.
getPointCount() - Method in class chemaxon.struc.MPoint: Gets the number of points.
getPointRef(int, Transform3D) - Method in class chemaxon.struc.graphics.MElectron
getPointRef(int, Transform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
getPointRef(int, Transform3D) - Method in class chemaxon.struc.graphics.MPolyline: Gets a reference to a point or midpoint in the polyline.
getPointRef(int, Transform3D) - Method in class chemaxon.struc.graphics.MRectangle: Gets an internal selectable point of the rectangle.
getPointRef(int, Transform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle: Gets an internal selectable point of the rectangle.
getPointRef(int, Transform3D) - Method in class chemaxon.struc.MObject: Gets a reference to a point of the object.
getPointRef(int, Transform3D) - Method in class chemaxon.struc.MPoint: Gets a point of the line.
getPointRefCount() - Method in class chemaxon.struc.graphics.MEFlow: Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MElectronContainer
getPointRefCount() - Method in class chemaxon.struc.graphics.MPolyline: Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MReactionSign
getPointRefCount() - Method in class chemaxon.struc.graphics.MRectangle: Gets the number of internal selectable point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MRoundedRectangle: Gets the number of internal selectable point references.
getPointRefCount() - Method in class chemaxon.struc.MObject: Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.MPoint: Gets the number of point references.
getPoints() - Method in class chemaxon.struc.graphics.MPolyline: Gets the points.
getPoints() - Method in class chemaxon.struc.MoleculeGraph: Gets an array containing the atom coordinates.
getPoints(int) - Method in class chemaxon.struc.prop.MHCoords3DProp: Gets the Hydrogen locations for an atom.
getPolarizability(int) - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the atom polarizability value.
getPopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane: Are popup menus enabled?
getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument: Gets a portion of the document.
getPortion(int, int) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets a portion of the text relative to this portion.
getPos() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the data display DASP position (0...9).
getPosition() - Method in class chemaxon.struc.graphics.MTextDocument.Section: Gets the position in the document.
getPosition(int) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the position of the ith NMR line.
getPositionInPolyline() - Method in class chemaxon.struc.graphics.MMidPoint: Gets the position in the polyline.
getPositionInRect() - Method in class chemaxon.struc.graphics.MRectanglePoint: Gets the position in the rectangle.
getPossibleRotatableBondCount() - Method in class chemaxon.alignment.AtropIsomerDetector: Rotatable bond count before the atrop isomer calculation.
getPreBreakingChars() - Method in class chemaxon.struc.graphics.MNameTextBox: Gets the breaking characters before that the text in the text box can be broken if it doesn't fit into the text box.
getPreBreakingChars() - Method in class chemaxon.struc.graphics.MTextBox: Gets the breaking characters before that the text in the text box can be broken if it doesn't fit into the text box.
getPrecision() - Method in interface chemaxon.struc.graphics.MAnalysisBoxTerm.Formatter
getPreferredIUPACName() - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns the preferred IUPAC name.
getPreferredLabelDir(Transform3D, int) - Method in class chemaxon.struc.MolAtom: Gets the preferred direction for an additional label.
getPreferredWidth() - Method in class chemaxon.struc.graphics.MNameTextBox: Gets the preferred width of the text-box.
getPrefix() - Method in exception class chemaxon.naming.NameFormatException: The part of the input name that was recognized, or null.
getPreviousNormalTextSectionIndex() - Method in class chemaxon.struc.graphics.MTextBox: Gets the index of the last `normal' text section before the current subscript/superscript section.
getPrimaryIndexes() - Method in class chemaxon.calculations.stereo.stereocenters.AtomSelection: Gets the primary indexes.
getPrimaryMolecule() - Method in class chemaxon.struc.MDocument: Gets the primary molecule object.
getPrimaryMolecules() - Method in class chemaxon.struc.MDocument: Gets an array containing the primary molecule objects.
getPrincipalPolarizabilityComponents() - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the principal components a(xx), a(yy), a(zz) of polarizability tensor (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
getPriority() - Method in class chemaxon.fixers.StructureFixerDescriptor: Returns the fixer priority.
getPriority() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor: Gets the priority of the MTransferable object by exporting to clipboard.
getProduct() - Method in exception class chemaxon.license.api.LicenseException
getProduct(int) - Method in class chemaxon.struc.RxnMolecule: Gets a product.
getProductCount() - Method in class chemaxon.reaction.Reactor: Returns the number of products.
getProductCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of products.
getProductName() - Method in class chemaxon.calculations.AlignmentPlugin
getProductName() - Method in class chemaxon.calculations.api.ProgressableCalculator: Returns the product identifier of the plugin.
getProductName() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the product identifier of the plugin.
getProductName() - Method in class chemaxon.calculations.ChargePlugin
getProductName() - Method in class chemaxon.calculations.ChemicalNamePlugin
getProductName() - Method in class chemaxon.calculations.ConformerPlugin
getProductName() - Method in class chemaxon.calculations.dipole.DipoleCalculator
getProductName() - Method in class chemaxon.calculations.ElementalAnalysisPlugin
getProductName() - Method in class chemaxon.calculations.GeometryPlugin
getProductName() - Method in class chemaxon.calculations.HBDAPlugin
getProductName() - Method in class chemaxon.calculations.HLBPlugin
getProductName() - Method in class chemaxon.calculations.HuckelAnalysisPlugin
getProductName() - Method in class chemaxon.calculations.IonChargePlugin
getProductName() - Method in class chemaxon.calculations.IsoelectricPointPlugin
getProductName() - Method in class chemaxon.calculations.LogDPlugin
getProductName() - Method in class chemaxon.calculations.LogPPlugin
getProductName() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin
getProductName() - Method in class chemaxon.calculations.MarkushEnumerationPlugin
getProductName() - Method in class chemaxon.calculations.MolecularDynamicsPlugin
getProductName() - Method in class chemaxon.calculations.MSAPlugin
getProductName() - Method in class chemaxon.calculations.nmr.NMRCalculator
getProductName() - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin
getProductName() - Method in class chemaxon.calculations.PkaPlugin
getProductName() - Method in class chemaxon.calculations.PolarizabilityPlugin
getProductName() - Method in class chemaxon.calculations.RefractivityPlugin
getProductName() - Method in class chemaxon.calculations.ResonancePlugin
getProductName() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the product identifier of the plugin as given by LicenseGlobals.
getProductName() - Method in class chemaxon.calculations.StructuralFrameworksPlugin
getProductName() - Method in class chemaxon.calculations.TautomerPlugin
getProductName() - Method in class chemaxon.calculations.TopologyAnalysisPlugin
getProductName() - Method in class chemaxon.calculations.TPSAPlugin
getProducts() - Method in class chemaxon.struc.RxnMolecule: Gets all products in an array.
getProductTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint: Returns the tanimoto distance of the product sides.
getProgessLength() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
getProgessLength() - Method in interface chemaxon.structurechecker.CheckerRunner
getProgress() - Method in class chemaxon.reaction.ConcurrentReactorProcessor: Estimates the progress.
getProgress() - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor: Estimates the progress.
getProgressBar() - Method in class chemaxon.alignment.AlignmentMoleculeFactory
getProgressMonitor(Component) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Creates a progress observer object to be used in CalculatorPlugin.setProgressMonitor(ProgressMonitor).
getPropArraySize() - Method in class chemaxon.struc.MDocument.Prop: Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.MProp: Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MByteArrayProp: Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MDoubleArrayProp: Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MHashProp: Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MIntegerArrayProp: Gets the array size.
getPropArraySize() - Method in class chemaxon.struc.prop.MListProp: Gets the array size.
getProperties() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult: Returns the flag which can used to identify which properties should be fixed.
getProperty(String) - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns a descriptor property
getProperty(String) - Method in class chemaxon.marvin.common.UserSettings: Returns the value for the given key.
getProperty(String) - Method in class chemaxon.struc.MObject: Returns the property value to which the specified property key is mapped at this MObject, or null if this MObject has no mapping for this property key.
getProperty(String) - Method in class chemaxon.struc.MolAtom: Returns the property value to which the specified property key is mapped at this atom, or null if this atom has no mapping for this property key.
getProperty(String) - Method in class chemaxon.struc.MolBond: Returns the property value to which the specified property key is mapped at this bond, or null if this bond has no mapping for this property key.
getPropertyChangeSupport() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the property change support for this object
getPropertyCount() - Method in class chemaxon.struc.Molecule: Gets the total number of RDfile/SDfile properties.
getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo: Returns the property descriptor array.
getPropertyDescriptors() - Method in class chemaxon.marvin.beans.MViewPaneBeanInfo: Returns the property descriptor array.
getPropertyDescriptors(Class<?>, Vector<PropertyDescriptor>) - Method in class chemaxon.marvin.beans.MarvinPaneBeanInfo: Puts the descriptors of the common Marvin bean properties into the specified Vector.
getPropertyKey(int) - Method in class chemaxon.struc.Molecule: Gets an RDfile/SDfile property key.
getPropertyKeys() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the array of property keys
getPropertyMap() - Method in class chemaxon.marvin.common.UserSettings: Shortcut to getPropertyMap(UserSettings.PROPERTY_TYPE_ALL)
getPropertyMap(String) - Method in class chemaxon.marvin.common.UserSettings: Returns a map of properties from the given type.
getPropertyName(CalculatorLogger.Level, int) - Method in class chemaxon.calculations.api.CalculatorLogger
getPropertyObject(MoleculeGraph, String) - Static method in class chemaxon.formats.MPropHandler: Returns the property object associated with the given key in the given molecule.
getPropertyObject(String) - Method in class chemaxon.struc.Molecule: Gets an RDfile/SDfile property object.
getPropertyString(MoleculeGraph, String) - Static method in class chemaxon.formats.MPropHandler: Converts the property object associated with the given key in the given molecule to string.
getPropertyText(Molecule) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns molecule properties in text form.
getPropList() - Method in class chemaxon.struc.MPropertyContainer: Gets the list of basic properties.
getPropType() - Method in class chemaxon.struc.MDocument.Prop: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.MProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MBooleanProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MByteArrayProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MDoubleArrayProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MDoubleProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MFontProp
getPropType() - Method in class chemaxon.struc.prop.MHashProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MHCoords3DProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MIntegerArrayProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MIntegerProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MListProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MMoleculeProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MObjectProp: Gets the type name of the property.
getPropType() - Method in class chemaxon.struc.prop.MStringProp: Gets the type name of the property.
getPropValue() - Method in class chemaxon.struc.MDocument.Prop: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.MProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MBooleanProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MByteArrayProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MDoubleArrayProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MDoubleProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MFontProp
getPropValue() - Method in class chemaxon.struc.prop.MHashProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MHCoords3DProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MIntegerArrayProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MIntegerProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MListProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MMoleculeProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MObjectProp: Gets the property value as an object.
getPropValue() - Method in class chemaxon.struc.prop.MStringProp: Gets the property value as an object.
getPropXSDType() - Method in class chemaxon.struc.MDocument.Prop: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.MProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MBooleanProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MByteArrayProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MCollectionProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleArrayProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MDoubleProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MFontProp
getPropXSDType() - Method in class chemaxon.struc.prop.MHCoords3DProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerArrayProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MIntegerProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MMoleculeProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MObjectProp: Gets the XSD type name of the property.
getPropXSDType() - Method in class chemaxon.struc.prop.MStringProp: Gets the XSD type name of the property.
getPSymbols() - Method in class chemaxon.descriptors.PFParameters: Gets the pharmacophore type symbols used in the current configuration.
getQProp(String) - Method in class chemaxon.struc.MolAtom: Gets a query property.
getQPropAsInt(String) - Method in class chemaxon.struc.MolAtom: Gets a query property as an integer.
getQPropMinMax(String) - Method in class chemaxon.struc.MolAtom: Gets the minimum and maximum possible values of a query property.
getQPropNames() - Method in class chemaxon.struc.MolAtom: Gets the names of query properties with non-null values.
getQPropNameSet() - Method in class chemaxon.struc.MolAtom: Gets the names of query properties with non-null values, or null if no query properties are set.
getQuery() - Method in class chemaxon.chemterms.SearchContext: Returns the query molecule.
getQuery() - Method in class chemaxon.search.AbstractSearch: Retrieves the query structure.
getQuery() - Method in class chemaxon.search.Decomposition: Returns the R-grouped query used in the R-group decomposition.
getQuery() - Method in class chemaxon.search.FormulaSearch: Gets the chemical formula query string used for searching
getQuery() - Method in class chemaxon.search.MarkushGenerator: Returns the query.
getQuery() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Gets the query structure.
getQuery() - Method in class chemaxon.search.MolSearch
getQuery() - Method in class chemaxon.search.RgroupDecomposition: Retrieves the original query structure.
getQueryAromaticity() - Method in class chemaxon.struc.MolAtom: Gets the aromatic/aliphatic query property.
getQueryAtom() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction: Gets the atom to be searched for by the action (the query atom)
getQueryCode() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the program code of the query option.
getQueryFingerprint() - Method in class chemaxon.chemterms.SearchContext: Returns the query molecule fingerprint.
getQueryFingerprint(Object) - Method in class chemaxon.chemterms.SearchContext: Returns the query molecule fingerprint if argument is the query molecule, null otherwise.
getQueryLabel() - Method in class chemaxon.struc.MolAtom: Gets the string representation of the query atom
getQueryMode() - Method in class chemaxon.formats.MolImporter: Gets query mode.
getQueryMoleculeErrorMessage(Molecule) - Static method in class chemaxon.calculations.CalculatorPlugin
getQueryOp() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the data query operator.
getQuerystr() - Method in class chemaxon.struc.MolBond: Gets the query properties.
getQuerystr() - Method in class chemaxon.struc.QueryBond: Gets the query properties.
getQueryString() - Method in class chemaxon.struc.MolAtom: Returns the query string assigned to this atom.
getQueryToPrint() - Method in class chemaxon.search.AbstractSearch: For internal purposes only.
getRadicalCount() - Method in class chemaxon.struc.MDocument: Returns the number of Radical electrons.
getRadicalCount() - Method in class chemaxon.struc.MolAtom: Gets the number of free electrons.
getRadicalCount(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets the number of free electrons of the given atom.
getRadicalMatching() - Method in class chemaxon.search.api.options.SearchOptions: Get option for radical matching behavior.
getRadicalValue() - Method in class chemaxon.struc.MolAtom: Gets the radical value of the atom.
getRadius() - Method in class chemaxon.struc.graphics.MElectron
getRadius() - Method in class chemaxon.struc.graphics.MElectronContainer: Returns the radius of MElectrons.
getRandicIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
getRandomSeed() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Gets the random seed value.
getRangeMax() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Maximal y value of the NMR spectrum function.
getRangeMin() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Minimal y value of the NMR spectrum function.
getRawValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the value of the unscaled NMR spectrum function at a given x point.
getReactant(int) - Method in class chemaxon.struc.RxnMolecule: Gets a reactant.
getReactantCount() - Method in class chemaxon.reaction.Reactor: Returns the number of reactants.
getReactantCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of reactants.
getReactants() - Method in class chemaxon.reaction.ConcurrentReactorProcessor: Returns the input reactants of the last processed reaction.
getReactants() - Method in class chemaxon.reaction.Reactor: Returns the input reactants.
getReactants() - Method in class chemaxon.struc.RxnMolecule: Gets all reactants in an array.
getReactantTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint: Returns the tanimoto distance of the reactant sides.
getReaction() - Method in class chemaxon.chemterms.ReactionContext: Returns the reaction.
getReaction() - Method in class chemaxon.reaction.Reactor: Returns the reaction.
getReaction(MoleculeGraph) - Static method in class chemaxon.struc.RxnMolecule: Returns the reaction represented by the given molecule if exists, otherwise null.
getReactionArrow() - Method in class chemaxon.struc.RxnMolecule: Gets a two-element array containing the endpoints of the reaction arrow.
getReactionArrow(boolean) - Method in class chemaxon.struc.RxnMolecule: Gets the reaction arrow of this reaction with the possibility to generate an arrow if the arrow is not yet set.
getReactionArrowList() - Method in class chemaxon.struc.RxnMolecule: Gets the list of the reaction arrows of this reaction.
getReactionArrowType() - Method in class chemaxon.struc.RxnMolecule: Gets the reaction arrow type.
getReactionArrowTypeName() - Method in class chemaxon.struc.RxnMolecule: Gets the reaction arrow type name.
getReactionID() - Method in class chemaxon.reaction.Reactor: Returns the reaction ID.
getReactionIDPropertyName() - Method in class chemaxon.reaction.Reactor: Returns the reaction ID property (RDF/MRV tag) name.
getReactionMap() - Method in class chemaxon.reaction.Reactor: Gets the mapping for the last performed reaction.
getReactionProduct(int) - Method in class chemaxon.reaction.Reactor: Returns a reaction product.
getReactionReactant(int) - Method in class chemaxon.reaction.Reactor: Returns a reaction reactant.
getReactionSchemaMap() - Method in class chemaxon.reaction.AtomIdentifier: Gets the mapping of the target atom in the reaction schema
getReactionSmarts() - Method in class chemaxon.checkers.result.SubstructureCheckerResult: Returns the reactionSmarts
getReactionSmarts() - Method in class chemaxon.checkers.SubstructureChecker: Returns the reactionSmarts
getReactionStereo() - Method in class chemaxon.struc.MolAtom: Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
getReactionSupport() - Method in class chemaxon.marvin.beans.MSketchPane: Is reaction drawing supported?
getRealBondCount() - Method in class chemaxon.struc.MolAtom: Gets the number of bonds connected to "real" atoms.
getRealEigenValue() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Deprecated.
Use HuckelAnalysisPlugin.getHMORealEigenValue()
getRealRotatableBondCount() - Method in class chemaxon.alignment.AtropIsomerDetector: Rotatable bond count (atrop bonds excluded)
getRecordCount() - Method in class chemaxon.calculations.CalculatorPluginMDocSource: Gets the current record number.
getRecordCount() - Method in class chemaxon.formats.MDocSource: Gets the current record number.
getRecordCount() - Method in class chemaxon.formats.MolImporter: Gets the current record number.
getRecordCountMax() - Method in class chemaxon.calculations.CalculatorPluginMDocSource: Gets the total number of records.
getRecordCountMax() - Method in class chemaxon.formats.MDocSource: Gets the total number of records.
getRecordCountMax() - Method in class chemaxon.formats.MolImporter: Gets the total number of records read.
getRecordIDBackground(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the highlight color of a record.
getRecordIDForeground(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the foreground color of a record.
getRecordIndex() - Method in exception class chemaxon.marvin.common.MDocStorage.RecordUnavailableException: Gets the requested, unavailable record index.
getRecordIndexMax() - Method in exception class chemaxon.marvin.common.MDocStorage.RecordUnavailableException: Gets the maximum available record index.
getRecordIndexMin() - Method in exception class chemaxon.marvin.common.MDocStorage.RecordUnavailableException: Gets the minimum available record index.
getReferenceAndRotatedFused() - Method in class chemaxon.alignment.AlignRigidEasy: before getRotatedMolecule the AlignRigidEasy.align() method must be called
getReferenceLogDValues() - Method in class chemaxon.calculations.LogDPlugin: Returns the reference logD values.
getReferenceMolecule() - Method in interface chemaxon.alignment.MCSAlignment: Reference molecule.
getReferencePhValues() - Method in class chemaxon.calculations.LogDPlugin: Returns the reference pH values.
getReferenceWithNewCoordinates() - Method in class chemaxon.alignment.AlignOnPairedAtoms
getReflogDs() - Method in class chemaxon.calculations.LogDPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogDPlugin.getReferenceLogDValues() instead. This method will be removed in a future version.
getRefpHs() - Method in class chemaxon.calculations.LogDPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogDPlugin.getReferencePhValues() instead. This method will be removed in a future version.
getRefractivity() - Method in class chemaxon.calculations.RefractivityPlugin: Returns the refractivity value.
getRefractivityHIncrement(int) - Method in class chemaxon.calculations.RefractivityPlugin: Returns the refractivity increment on the H atoms attached to a given atom.
getRefractivityIncrement(int) - Method in class chemaxon.calculations.RefractivityPlugin: Returns the refractivity increment for a given atom.
getRegNo() - Method in class chemaxon.struc.prop.MMoleculeStringProp
getRelativeNegativity() - Method in class chemaxon.struc.MolAtom: Check negativity compared to the neighbors.
getRemark() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the calculation remark.
getRemark() - Method in class chemaxon.calculations.GeometryPlugin: Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.
getRemark() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns the calculation remark.
getRemark() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns a warning message in case of arithmetical overflow (the number of enumerated structures exceeds Long.MAX_VALUE), null otherwise.
getRemark() - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the calculation remark.
getRemark() - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the calculation remark.
getRemark() - Method in class chemaxon.calculations.ResonancePlugin: Returns a warning message if there are no resonants, null otherwise.
getRemark() - Method in class chemaxon.calculations.TautomerPlugin: Returns a warning message if there are no tautomers, null otherwise.
getRemark() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.
getRemovedAtoms() - Method in class chemaxon.standardizer.Changes: Gets the list of atoms removed during the standardization procedure
getRendering() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the rendering style.
getRendering() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the rendering style of atoms and bonds.
getRepeatingUnitAtom(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets a paradigmatic repeating unit atom.
getRepeatingUnitAtomCount() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the number of atoms in the pararadigmatic repeating unit.
getRepeatingUnitAtoms() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the repeating unit atoms.
getReplaceAtom() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction: Gets the atom to replaced with by the action
getRepresentation() - Method in class chemaxon.checkers.AttachedDataChecker.DataExclusionList
getRepresentationClass() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor: Gets the name of the representation class of the MTransferable.
getRequestMethod() - Method in class chemaxon.calculations.services.JsonServiceDescriptor: Gets the HTTP method of the request.
getRequiredHlbValue() - Method in class chemaxon.calculations.HLBPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, use HLBPlugin.getRequiredHLBValue() instead.
getRequiredHLBValue() - Method in class chemaxon.calculations.HLBPlugin: Returns the Required HLB value calculated by Chemaxon method.
getResidueAtomId() - Method in class chemaxon.struc.MolAtom: Gets the residue atom identifier.
getResidueSeq() - Method in class chemaxon.struc.MolAtom: Gets the residue sequence number.
getResidueType() - Method in class chemaxon.struc.MolAtom: Gets the residue type.
getResolution() - Method in class chemaxon.descriptors.PFParameters: Gets the resolution of histograms.
getResolution() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getResourceBundle(String) - Static method in class chemaxon.marvin.beans.MarvinPane: Utility method to get a resource bundle.
getResult() - Method in class chemaxon.calculations.StructuralFrameworksPlugin
getResult() - Method in class chemaxon.standardizer.Changes: Gets the result molecule of the standardization process
getResult(int) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the result item for the specified type and index.
getResult(Molecule) - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the result string for the given molecule.
getResult(Molecule) - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the result string for the given molecule.
getResult(Object, int) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.ChargePlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.ConformerPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.GeometryPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.HBDAPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.HLBPlugin
getResult(Object, int) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.IonChargePlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.LogDPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.LogPPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the microsepcies if pH is different from Double.NaN, otherwise returns the input molecule itself.
getResult(Object, int) - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.MSAPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.PkaPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.calculations.RefractivityPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.ResonancePlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.StructuralFrameworksPlugin
getResult(Object, int) - Method in class chemaxon.calculations.TautomerPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.calculations.TPSAPlugin: Returns the result item for the specified key and index.
getResultantImplicitHCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the implicit H charge around a central atom
getResultAsRGB(int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result color as int format (alphainvalid input: '<'invalid input: '<'24 + redinvalid input: '<'invalid input: '<'16 + greeninvalid input: '<'invalid input: '<'8 + blue).
getResultAsRGB(Object, int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsRGB(Object, int, Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsRGB(Object, int, Object) - Method in class chemaxon.calculations.PkaPlugin: Returns the specified result color as int format (alphainvalid input: '<'invalid input: '<'24 + redinvalid input: '<'invalid input: '<'16 + greeninvalid input: '<'invalid input: '<'8 + blue): RED for acidic pKa, BLUE for basic pKa.
getResultAsString(int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result in String format for the first result type.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.ChargePlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.ConformerPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.GeometryPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.HLBPlugin
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.IonChargePlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.LogDPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.LogPPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the specified result molecule in SMILES format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.MSAPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.PkaPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.RefractivityPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.ResonancePlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.StructuralFrameworksPlugin: Get a calculation result (returned by StructuralFrameworksPlugin.getResultMolecule() after a StructuralFrameworksPlugin.run() call in the given format StructuralFrameworksPlugin.setFormat(String)
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.TautomerPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.calculations.TPSAPlugin: Returns the specified result in String format.
getResultComponent() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns the result component for display.
getResultCount() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the number of result items for the first result type.
getResultCount() - Method in class chemaxon.calculations.StructuralFrameworksPlugin
getResultCount(Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.ChargePlugin: Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.calculations.ConformerPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.GeometryPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.IonChargePlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.LogDPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.LogPPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the number of result items: 1.
getResultCount(Object) - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.MSAPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.calculations.PkaPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.RefractivityPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.ResonancePlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.TautomerPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.calculations.TPSAPlugin: Returns the number of result items for the given result key.
getResultDomain() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
getResultDomain() - Method in class chemaxon.calculations.HLBPlugin
getResultDomain() - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the domain for the first result type.
getResultDomain(Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
getResultDomain(Object) - Method in class chemaxon.calculations.ChargePlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.ConformerPlugin: Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.GeometryPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.IonChargePlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.LogDPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.LogPPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the calculation domain CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.MSAPlugin: Returns the calculation domain CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULE in case of increments .
getResultDomain(Object) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.PkaPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.RefractivityPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.ResonancePlugin: Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.StructuralFrameworksPlugin
getResultDomain(Object) - Method in class chemaxon.calculations.TautomerPlugin: Returns the calculation domain.
getResultDomain(Object) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.calculations.TPSAPlugin: Returns the calculation domain CalculatorPlugin.MOLECULE.
getResultList() - Method in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.
getResultList() - Method in interface chemaxon.structurechecker.CheckerRunner
getResultMessage() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the plugin calculation error message, error or warning.
getResultMessage() - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the plugin calculation error message, error or warning.
getResultMessage() - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the plugin calculation error message, error or warning.
getResultMolecule() - Method in class chemaxon.alignment.AlignmentMoleculeFactory
getResultMolecule() - Method in class chemaxon.alignment.AtropIsomerDetector: The result molecule will be 3D and aromatized version of the input molecules.
getResultMolecule() - Method in class chemaxon.calculations.AlignmentPlugin
getResultMolecule() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.ChargePlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.ChemicalNamePlugin
getResultMolecule() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.GeometryPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.HBDAPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.HLBPlugin
getResultMolecule() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.LogPPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the major microspecies for display.
getResultMolecule() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.MSAPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.PkaPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.RefractivityPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.StructuralFrameworksPlugin: Get result structure
getResultMolecule() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the result molecule for display.
getResultMolecule() - Method in class chemaxon.calculations.TPSAPlugin: Returns the result molecule for display.
getResultMolecule(Molecule) - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the decorated result molecule for the given target molecule.
getResultMolecule(Molecule) - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the decorated result molecule for the given target molecule.
getResultMolecules() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the result molecule array for display.
getResultMolecules() - Method in class chemaxon.calculations.GeometryPlugin: Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
getResultMolecules() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
getResultMolecules(Molecule) - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the result molecules for the given target molecule.
getResultMolecules(Molecule) - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the result molecules for the given target molecule.
getResults(Object) - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns result items for the given result type.
getResultsAsRGB(int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.calculations.PkaPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsString(int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result with possible subresults.
getResultsAsString(Object, int, Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns the specified result with possible subresults.
getResultsAsString(Object, int, Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns the specified result in GUI-specific String format: A for acceptor, D for donor.
getResultsAsString(Object, int, Object) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the specified results in String format.
getResultsAsString(Object, int, Object) - Method in class chemaxon.calculations.PkaPlugin: Returns the specified result with possible subresults (both pKa values instead of the most significant pKa) in String format.
getResultSource() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the result as a document source object.
getResultSource() - Method in class chemaxon.calculations.ConformerPlugin: Returns the result as a document source object.
getResultSource() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the result as a document source object.
getResultSource() - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the result as a document source object.
getResultSource() - Method in class chemaxon.calculations.ResonancePlugin: Returns the result as a document source object.
getResultSource() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the result as a document source object.
getResultSource() - Method in class chemaxon.calculations.TautomerPlugin: Returns the result as a document source object.
getResultTypeList() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.AlignmentPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.ChargePlugin: Returns the result types (possible types: "sigma", "pi", "total").
getResultTypes() - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.ConformerPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns the string IDs of the result types.
getResultTypes() - Method in class chemaxon.calculations.GeometryPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.HBDAPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.HLBPlugin
getResultTypes() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.IonChargePlugin: Returns the result types (possible type: "charge").
getResultTypes() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.LogDPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.LogPPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the result types (possible types: "majority-ms").
getResultTypes() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.MSAPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the result types (possible types: "sigma", "pi").
getResultTypes() - Method in class chemaxon.calculations.PkaPlugin: Returns the result types (possible types: pKa, acidic, basic, msdistr).
getResultTypes() - Method in class chemaxon.calculations.PolarizabilityPlugin: Returns the result types (possible types: sigma, pi, total).
getResultTypes() - Method in class chemaxon.calculations.RefractivityPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.ResonancePlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.StructuralFrameworksPlugin
getResultTypes() - Method in class chemaxon.calculations.TautomerPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.calculations.TPSAPlugin: Returns the result types.
getRgroup() - Method in class chemaxon.struc.MolAtom: Gets the R-group ID.
getRgroupAttachmentPointOrder() - Method in class chemaxon.struc.MolAtom: Gets the attachment point order of an R-group attachment point.
getRgroupBridgeCount() - Method in class chemaxon.struc.RgMolecule: Returns the number of R-group bridges defined in this structure.
getRgroupBridgeIds() - Method in class chemaxon.struc.RgMolecule: Returns the list of R-group bridge IDs defined in this structure.
getRgroupBridgeMember(RgroupBridgeId, int) - Method in class chemaxon.struc.RgMolecule: Returns a definition member of the given R-group bridge.
getRgroupBridgeMemberCount(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule: Returns the number of definition members of the given R-group bridge.
getRgroupCount() - Method in class chemaxon.struc.RgMolecule: Gets the number of R-groups.
getRgroupCount() - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the number of R-groups.
getRgroupDisplayLabel(int) - Method in class chemaxon.struc.RgMolecule
getRgroupDisplayLabel(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Returns the display label of an R-group.
getRGroupedQuery() - Method in class chemaxon.search.RgroupDecomposition: Returns the R-grouped query.
getRgroupId(int) - Method in class chemaxon.struc.RgMolecule: Gets the ID of an R-group.
getRgroupId(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the ID of an R-group.
getRgroupId(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule
getRgroupId(RgroupBridgeId) - Method in interface chemaxon.struc.RgMoleculeGraph: Returns the ID of the ordinary R-group that actually represents the given R-group bridge.
getRgroupId1() - Method in class chemaxon.struc.RgroupBridgeId: Returns the ID of the first bridged R-group.
getRgroupId2() - Method in class chemaxon.struc.RgroupBridgeId: Returns the ID of the second bridged R-group.
getRgroupIds() - Method in class chemaxon.checkers.result.RgroupCheckerResult: Returns the list of affected R-group IDs.
getRgroupIndex(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Finds R-group R#.
getRgroupIndex(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule: Returns the index of the ordinary R-group that actually represents the given R-group bridge.
getRgroupIndexFromMemberId(long) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the R-group index from the R-group member ID.
getRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule: Gets an R-group member.
getRgroupMemberCount(int) - Method in class chemaxon.struc.RgMolecule: Gets the number of R-group members.
getRgroupMemberCount(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the number of R-group members.
getRgroupMemberG(int, int) - Method in class chemaxon.struc.RgMolecule: Gets an R-group member.
getRgroupMemberG(int, int) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets an R-group member.
getRgroupMemberId(MolAtom) - Method in class chemaxon.struc.RgMolecule: Gets the unique identifier of the R-group member that contains the specified atom.
getRgroupMemberId(MolAtom) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the unique indentifier of the R-group member that contains the specified atom.
getRgroupMemberIndexFromMemberId(long) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the R-group member index from the R-group member ID.
getRightBracket(Transform3D) - Method in class chemaxon.struc.graphics.MBracket
getRightMargin() - Method in class chemaxon.struc.PageSettings
getRightName() - Method in class chemaxon.struc.sgroup.SgroupAtom: Set the string that will be shown at the right side of the molecule.
getRingAtomCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the ring atom count.
getRingBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the ring bond count.
getRingCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the ring count.
getRingCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
getRingCountOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
getRingHandlingMode() - Method in class chemaxon.search.mcs.McsSearchOptions: Returns the ring handling mode.
getRings() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the rings in the molecule.
getRings(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies rings in the molecule having a given size.
getRingSystemCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of ring systems.
getRingSystemCount(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the number of ring systems having a given size (number of rings) in the molecule.
getRingSystems() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the ring systems in the molecule.
getRingSystems(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Indentifies the ring systems in the molecule having a given size (number of rings).
getRLigandCount() - Method in class chemaxon.search.RgroupDecomposition: Returns the number of R-atoms in the R-grouped query (see RgroupDecomposition.getRGroupedQuery()).
getRLigandEqualityCheck() - Method in class chemaxon.search.api.options.SearchOptions: Returns true if undefined R-atoms with the same R-group ID should match the same structure.
getRlogic(int) - Method in class chemaxon.struc.RgMolecule: Gets R-logic flags.
getRlogic(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets R-logic flags.
getRlogicRange(int) - Method in class chemaxon.struc.RgMolecule: Gets R-logic occurrence range.
getRlogicRange(int) - Method in interface chemaxon.struc.RgMoleculeGraph: Gets R-logic occurrence range.
getRLogicVisible() - Method in class chemaxon.marvin.common.UserSettings: Tells whether the R-logic is visible if exists
getRmsd() - Method in class chemaxon.alignment.Alignment
getRmsd() - Method in class chemaxon.alignment.AlignOnPairedAtoms
getRmsd() - Method in class chemaxon.alignment.MMPAlignmentResult
getRoot() - Method in class chemaxon.struc.RgMolecule: Gets the root structure.
getRootG() - Method in class chemaxon.struc.RgMolecule: Gets the root structure.
getRootG() - Method in interface chemaxon.struc.RgMoleculeGraph: Gets the root structure.
getRootSgroups() - Method in class chemaxon.struc.Molecule: Gets root S-groups (groups that are not embedded into another S-group).
getRotatableBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the rotatable bond count.
getRotatedCoordinates() - Method in class chemaxon.alignment.AlignRigidEasy: before getRotatedCoordinates the AlignRigidEasy.align() method must be called
getRotatedMolecule() - Method in class chemaxon.alignment.AlignRigidEasy: before getRotatedMolecule the AlignRigidEasy.align() method must be called
getRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the rotation part of the transformation matrix.
getRotBondCount() - Method in class chemaxon.alignment.AlignmentMolecule
getRow(int) - Static method in class chemaxon.struc.MolAtom: The row or or period of an element in the periodic table.
getRow(int) - Static method in class chemaxon.struc.PeriodicTable: The row or or period of an element in the periodic table.
getRowCount() - Method in class chemaxon.struc.PageSettings
getRowHeight() - Method in class chemaxon.marvin.common.TableOptions: Gets the row height.
getSaltCount() - Method in class chemaxon.standardizer.actions.StripSaltsAction: Gets the count of the salts of the action
getSaltID(int) - Method in class chemaxon.standardizer.actions.StripSaltsAction: Gets the salt ID at the provided index
getSaltList() - Method in class chemaxon.standardizer.actions.StripSaltsAction: Gets the custom salt list of the action
getSaveGlobalGUIProperties() - Method in class chemaxon.marvin.beans.MarvinPane: Checks whether we have to read GUI properties from a .MRV file
getSaveGUIPropertiesInMRV() - Method in class chemaxon.marvin.common.UserSettings
getSaveLoadZoomFactorToMRV() - Method in class chemaxon.marvin.common.UserSettings: Tells if marvin save the zoom factor to mrv or not.
getScaffold() - Method in class chemaxon.search.Decomposition: Returns the scaffold in target.
getScaffold() - Method in class chemaxon.search.RgroupDecompositionResults: Returns scaffold of the query (r-groups are added automatically if needed).
getScale() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the scale factor in units of regular bond length.
getScale() - Method in class chemaxon.marvin.beans.MSketchPane: Returns the scale factor of the current magnification.
getScale() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the relative size of the font compared to the base font.
getScale() - Method in class chemaxon.struc.graphics.MTextBoxTransformation
getScale() - Method in class chemaxon.struc.Transform3D: Gets the scale factor.
getScaledAWTFont(Float) - Method in class chemaxon.struc.graphics.MFont: Gets an AWT font instance after scaling.
getScaledTanimoto(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Gets the Tanimoto dissimilarity coefficient.
getScaledTanimoto(PharmacophoreFingerprint, PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the scaled Tanimoto metric (adapted to hystograms).
getScaleFactor() - Method in class chemaxon.descriptors.MDParameters: Gets the scale factor used in the current parametrized scalable metrics.
getScalingHypothesis() - Method in class chemaxon.descriptors.MDParameters: Gets the scaling hypothesis used in scaled metrics.
getScheme() - Method in class chemaxon.alignment.NodeColor: Returns the ColoringScheme associated with this NodeColor.
getScreeningConfigurationString(String, String, String) - Method in class chemaxon.descriptors.MDParameters: Returns parts of the parameter values in string.
getScriptCount(int, int) - Method in class chemaxon.struc.graphics.MTextDocument: Gets the number of subscripts or superscripts on the last normal character.
getSearchMode() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Gets the current search mode.
getSearchOptions() - Method in class chemaxon.search.AbstractSearch: Returns the SearchOptions object associated with this Search object.
getSearchOptions() - Method in class chemaxon.search.MarkushGenerator: Returns the search options.
getSearchOptions() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Returns the search options used by this instance.
getSearchOptions() - Method in class chemaxon.standardizer.actions.TransformAction: Gets the search options of the action
getSearchType() - Method in class chemaxon.search.api.options.SearchOptions: Returns the currently set global search operation mode.
getSearchType() - Method in class chemaxon.search.FormulaSearch: Gets the formula search type.
getSearchType(String) - Static method in class chemaxon.search.api.options.SearchOptions: Decodes the string representation of the search type and returns the predefined constant value defined in SearchConstants.
getSecondaryIndexes() - Method in class chemaxon.calculations.stereo.stereocenters.AtomSelection: Gets the secondary indexes.
getSection(int) - Method in class chemaxon.struc.graphics.MTextDocument: Gets a section of the document.
getSectionCount() - Method in class chemaxon.struc.graphics.MTextDocument: Gets the number of sections in the document.
getSectionIndexOfCharAt(int) - Method in class chemaxon.struc.graphics.MTextDocument: Gets the section index of a character.
getSectionShiftY(int) - Method in class chemaxon.struc.graphics.MTextDocument: Gets the y shift of a section.
getSelectedAtoms(int, String) - Method in class chemaxon.marvin.common.MDocStorage: Gets the selected atom indices.
getSelectedDocument() - Method in class chemaxon.struc.graphics.MTextBox
getSelectedFieldCount() - Method in class chemaxon.marvin.common.TableOptions: Gets the number of selected fields.
getSelectedFields() - Method in class chemaxon.marvin.common.TableOptions: Get selected fields array which are selected in Table Options dialog box
getSelectedFieldTypes() - Method in class chemaxon.marvin.common.TableOptions: Get type array of selected field types.
getSelectedIndex() - Method in class chemaxon.marvin.beans.MViewPane: Gets the index of the molecule that is selected by the user.
getSelectedPage() - Method in class chemaxon.struc.PageSettings
getSelectedString() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selected substring.
getSelection() - Method in class chemaxon.calculations.stereo.ErrorReport: Returns the selection of atoms.
getSelection() - Method in class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter
getSelection() - Method in class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter
getSelection() - Method in class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter
getSelection() - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenter: Gets a selection which contains index of center atom and indexes of ligands.
getSelection() - Method in class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter
getSelection() - Method in class chemaxon.marvin.beans.MSketchPane: Gets a clone of the selection.
getSelectionEndColumn() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's end column number.
getSelectionEndPos() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's end position.
getSelectionEndRow() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's end row number.
getSelectionStartColumn() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's start column number.
getSelectionStartPos() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's start position.
getSelectionStartRow() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's start row number.
getSeparator(int) - Method in class chemaxon.calculations.gui.PluginFactory: Gets if a separator is required after the plugin menuitem in the Tools menu.
getSeries(ChartSample) - Method in class chemaxon.calculations.gui.MChart
getServiceDescriptorConfigurationAsStream() - Static method in class chemaxon.calculations.services.ServiceDescriptorTools: Returns an InputStream with service configuration.
getServiceDescriptorConfigurationAsStream(String) - Static method in class chemaxon.calculations.services.ServiceDescriptorTools: Returns the service descriptor configuration stream from path, or null.
getServiceDescriptorConfigurationAsStream(Supplier<String>) - Static method in class chemaxon.calculations.services.ServiceDescriptorTools: Returns an InputStream with service configuration.
getServiceHandler() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the default service handler instance for this descriptor.
getServicesConfigurationPath() - Method in class chemaxon.chemterms.ChemTermsEvaluator: Returns the custom services configuration path.
getServicesConfigURL() - Method in class chemaxon.marvin.common.UserSettings: Returns the URL of configuration for Services in marvin sketch
getSet() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the set of attributes used.
getSetSeq() - Method in class chemaxon.struc.MolAtom: Gets the atom set sequence number.
getSetSeq() - Method in class chemaxon.struc.MolBond: Gets the bond set.
getSeverity() - Method in class chemaxon.checkers.StructureCheckerDescriptor: Returns the severity
getSgroup() - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the S-group corresponding to this superatom.
getSgroup(int) - Method in class chemaxon.struc.Molecule: Gets an S-group.
getSgroupArray() - Method in class chemaxon.struc.Molecule: Gets the array of S-groups.
getSgroupCount() - Method in class chemaxon.struc.Molecule: Gets the number of S-groups in the molecule.
getSgroupGraph() - Method in class chemaxon.struc.Sgroup: Gets a COPY of the molecule graph.
getSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the molecule graph as a selection.
getSgroupIterator() - Method in class chemaxon.struc.Molecule: Deprecated, for removal: This API element is subject to removal in a future version.
use Molecule.getSgroupArray() instead.
getSgroups() - Method in class chemaxon.checkers.result.SgroupCheckerResult: Returns a List which contains the affected groups of the problem
getSgroupType() - Method in class chemaxon.struc.sgroup.AminoAcidSgroup
getSgroupType() - Method in class chemaxon.struc.Sgroup: Gets the S-group type.
getShapes(Transform3D) - Method in class chemaxon.struc.graphics.MBracket
getShapeScore() - Method in class chemaxon.alignment.MMPAlignmentResult
getShapeSimilarity(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeDescriptor
getShapeTanimoto() - Method in class chemaxon.alignment.MMPAlignmentResult
getShapeTanimoto() - Method in class chemaxon.alignment.PairwiseAlignment
getShapeTanimoto() - Method in interface chemaxon.alignment.PairwiseComparison
getShapeTanimoto() - Method in class chemaxon.alignment.PairwiseSimilarity3D
getShift() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the chemical shift.
getShift() - Method in class chemaxon.calculations.nmr.NMRShift: Returns the chemical shift.
getShiftError() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the estimated error of the chemical shift.
getShiftError() - Method in class chemaxon.calculations.nmr.NMRShift: Returns the error (confidence interval radius) of the shift.
getShiftErrorClassification() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns error classification of the chemical shift.
getShiftErrorClassification() - Method in class chemaxon.calculations.nmr.NMRShift: Returns the error classification of the stored chemical shift.
getShifts() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns chemical shifts.
getShortestPath(int, int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the shortest topological path (number of bonds) between two atoms.
getShortName() - Method in class chemaxon.descriptors.BCUT: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ChemicalFingerprint: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.CustomDescriptor: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ECFP: Gets the short name of the fingerprint.
getShortName() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ReactionFingerprint: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ScalarDescriptor: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.HAcc: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.HDon: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.Heavy: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.LogD: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.LogP: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.Mass: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.scalars.TPSA: Gets the short name of the descriptor.
getShortName() - Method in class chemaxon.descriptors.ShapeDescriptor: Gets the short name of the fingerprint.
getShortName() - Method in enum class chemaxon.struc.SgroupType
getShowLogPercentage() - Method in class chemaxon.calculations.PkaPlugin
getSigmaCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the sigma charge of a specified atom.
getSigmaOEN(int) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns the sigma orbital electronegativity of a specified atom.
getSimilarity() - Method in class chemaxon.search.mcs.McsSearchResult: Returns a Tanimoto-like similarity score of the input molecules based on the found maximum common substructure.
getSimilarity(T) - Method in class chemaxon.descriptors.SimilarityCalculator: Gets the similarity value according to previously defined metric and its parameters.
getSimilarityScoreDisplay() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns the mode of similarity score display.
getSimpleName() - Method in class chemaxon.calculations.services.HttpServiceDescriptor
getSimpleName() - Method in class chemaxon.calculations.services.JsonServiceDescriptor
getSimpleName() - Method in class chemaxon.calculations.services.LocalServiceDescriptor
getSimpleName() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the simple name of the service type
getSimpleParamString() - Method in enum class chemaxon.descriptors.MetricsType
getSimplifiedMolecule() - Method in class chemaxon.struc.Molecule: Gets the simplified molecule object.
getSingleHit() - Method in class chemaxon.search.api.SearchHit: Returns the single hit view of the hit object.
getSingleMsDistribution(int) - Method in class chemaxon.calculations.PkaPlugin: Returns the microspecies distribution at the specified pH value set in PkaPlugin.setPh(double).
getSink() - Method in class chemaxon.struc.graphics.MEFlow: Gets the destination of the electron-flow arrow (MolAtom, MolBond, or MolAtom[2] for incipient bond).
getSinkAtom() - Method in class chemaxon.struc.graphics.MEFlow: Gets the atom at the sink of this arrow.
getSinkAtoms() - Method in class chemaxon.struc.graphics.MEFlow: Gets the atom or atoms at the arrow sink.
getSinkBond() - Method in class chemaxon.struc.graphics.MEFlow: Gets the bond at the sink of this arrow.
getSize() - Method in class chemaxon.marvin.common.MDocStorage: Gets the total number of entries.
getSizeDouble() - Method in class chemaxon.struc.graphics.MFont: Gets the font size.
getSketchAnyBond() - Method in class chemaxon.marvin.common.UserSettings: Gets the default any bond drawing style in the sketcher.
getSketchArrowHeadLength() - Method in class chemaxon.marvin.common.UserSettings: Gets the current arrow head length.
getSketchArrowHeadWidth() - Method in class chemaxon.marvin.common.UserSettings: Gets the current arrow head width.
getSketchArrowTailLength() - Method in class chemaxon.marvin.common.UserSettings: Gets the current arrow tail length.
getSketchArrowTailWidth() - Method in class chemaxon.marvin.common.UserSettings: Gets the current arrow tail width.
getSketchCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings: Gets the default carbon displaying style in the sketcher.
getSketchColorScheme() - Method in class chemaxon.marvin.common.UserSettings: Gets the sketcher's default color scheme.
getSketchImplicitH() - Method in class chemaxon.marvin.common.UserSettings: Gets the display method of implicit hydrogens for the sketcher.
getSketchLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings: Gets the default ligand order displaying style in the sketcher.
getSketchLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings: Based on the preferences this funtion returns the proper working directory for the MarvinSketch application's load filechooser.
getSketchMode() - Method in class chemaxon.marvin.beans.MSketchPane: Gets the sketching mode.
getSketchMolbg2d() - Method in class chemaxon.marvin.common.UserSettings: Gets the sketcher's default 2D molecule background color.
getSketchMolbg3d() - Method in class chemaxon.marvin.common.UserSettings: Gets the sketcher's default 3D molecule background color.
getSketchRecentFileList() - Method in class chemaxon.marvin.common.UserSettings: Gets the recent files' list at marvinsketch, the last item is the most recent.
getSketchRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings: Gets the recent file list requested size, based on a preferences setting
getSketchRendering2d() - Method in class chemaxon.marvin.common.UserSettings: Gets the rendering style for the 2D sketcher.
getSketchRendering3d() - Method in class chemaxon.marvin.common.UserSettings: Gets the rendering style for the 3D sketcher.
getSketchSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings: Not implemented yet don't use it.
getSkip(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the distance of the (visible) head or tail from the corresponding line end point.
getSkippedIds() - Method in class chemaxon.search.RgroupDecompositionResults: Returns indexes of those targets that are not matched by query.
getSkippedTargetIndexes() - Method in class chemaxon.search.MarkushGenerator: Returns the target array indexes of targets that have been skipped in the last RgMolecule generation in MarkushGenerator.generate().
getSmallestRing() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the smallest ring (number of stoms) in the molecule.
getSmallestRingSize() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the smallest ring size.
getSmallestRingSizeForIdx() - Method in class chemaxon.struc.MoleculeGraph: Get the smallest ring size in which the atom (specified with its index) can be located.
getSmallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the size of smallest ring containing the specified atom.
getSmallestRingSystem() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Identifies the smallest ring system (number of rings) in the molecule.
getSmallestRingSystemSize() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns the size of the smallest ring system (number of rings) in the molecule.
getSMILESFontSize() - Method in class chemaxon.marvin.common.TableOptions: Gets the SMILES font size.
getSolubility() - Method in class chemaxon.calculations.solubility.SolubilityResult: Returns the solubility value.
getSolubility(SolubilityUnit) - Method in class chemaxon.calculations.solubility.SolubilityResult: Returns the solubility value.
getSolubilityCategory() - Method in class chemaxon.calculations.solubility.SolubilityResult: Returns the solubility category.
getSolubilityCategory(SolubilityCategories) - Method in class chemaxon.calculations.solubility.SolubilityResult: Returns the solubility category.
getSolventCount() - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Gets the count of the solvents of the action
getSolventID(int) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Gets the solvent ID at the provided index
getSolventList() - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Gets the custom solvent list of the action
getSortedMicrospecies(int) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the microspecies molecule, sorted by descreasing distribution at the given pH.
getSortedMsDistribution(int) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns the microspecies distribution, sorted by descreasing distribution at the given pH.
getSortedSgroups() - Method in class chemaxon.struc.Molecule: Gets the sorted S-groups in parent-child order.
getSource() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
getSource() - Method in interface chemaxon.checkers.result.StructureCheckerResult
getSource() - Method in class chemaxon.struc.graphics.MEFlow: Gets the origin of the electron-flow arrow (MolAtom or MolBond).
getSourceAtom() - Method in class chemaxon.struc.graphics.MEFlow: Gets the atom at the source of this arrow.
getSourceAtoms() - Method in class chemaxon.struc.graphics.MEFlow: Gets the atom or atoms at the arrow source.
getSourceBond() - Method in class chemaxon.struc.graphics.MEFlow: Gets the bond at the source of this arrow.
getSSRType() - Method in class chemaxon.search.api.options.SearchOptions: Gets the type of the set of smallest rings to use
getSSSR() - Method in class chemaxon.struc.MoleculeGraph: Gets the Smallest Set of Smallest Ring atom indexes array.
getSSSRBonds() - Method in class chemaxon.struc.MoleculeGraph: Gets the Smallest Set of Smallest Ring bond indexes array.
getSSSRBondsAsBitSet() - Method in class chemaxon.struc.MoleculeGraph: Gets the Smallest Set of Smallest Ring edges as an array of BitSets, one BitSet for each ring.
getSSSRBondSet() - Method in class chemaxon.struc.MoleculeGraph: Get SSSR bond index bitset.
getSSSRIdxesForAtoms() - Method in class chemaxon.struc.MoleculeGraph: Get the sssr ring indexes in which the atom (specified with its index) can be located.
getStandardError(Object, int) - Method in class chemaxon.calculations.LogPPlugin
getStandardizer() - Method in class chemaxon.reaction.Reactor: Returns the reactant standardizer object.
getStandardizerAction(String, Map<String, String>) - Method in class chemaxon.standardizer.StandardizerActionFactory: This method creates a requested (type represented in actionId) StandardizerAction instance with the give parameters
getStartAt() - Method in class chemaxon.marvin.common.TableOptions: Get the index number of the molecule that is the first to be displayed.
getStartPos() - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the position of the first character.
getStartPosition() - Method in class chemaxon.struc.MDocument: Gets the starting position of this document in the input file.
getStartPosition() - Method in class chemaxon.struc.Molecule: Gets the starting position of this molecule in the input file.
getStepLimit() - Method in class chemaxon.alignment.AlignmentBase
getSteps() - Method in enum class chemaxon.alignment.AtropIsomerDetector.Accuracy
getSteps() - Method in class chemaxon.alignment.DihedralScanResult: Represented scan steps.
getStereo(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates absolute stereo configuration of the given atom.
getStereo(int, int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates absolute stereo configuration of the given double bond.
getStereo1(MolAtom) - Method in class chemaxon.struc.MolBond: Gets wedge bond type relative to the specified chiral atom.
getStereo2(int, int, int, int) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans (Z/E) stereo information for the given bond.
getStereo2(MolBond, MolAtom, int, int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, int, int, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, MolAtom, MolAtom, boolean) - Method in class chemaxon.struc.RgMolecule
getStereoActiveAtom() - Method in class chemaxon.core.calculations.stereo.StereoActivePart: Deprecated, for removal: This API element is subject to removal in a future version.
Use StereoActivePart.getActiveAtomIndex() instead.
getStereoActiveParts() - Method in class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor
getStereoActiveParts() - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor
getStereoActiveParts() - Method in class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor
getStereoActiveParts() - Method in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
getStereoActiveParts() - Method in interface chemaxon.core.calculations.stereo.CIPStereoDescriptor: Returns the stereo active parts.
getStereoCare() - Method in class chemaxon.struc.MolAtom: Reports double bond stereo care information on the connected bonds.
getStereoCenter() - Method in class chemaxon.calculations.stereo.ErrorReport: Returns an optional of stereo centers.
getStereoCenters() - Method in class chemaxon.calculations.stereo.stereocenters.EnhancedStereoGroup
getStereoDoubleBondCount() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the number of stereo double bonds.
getStereoFontRatio() - Method in class chemaxon.marvin.beans.MolPrinter: Returns the current ratio of the font size of the stereo label compared to the normal atom label size.
getStereoGroupNumber() - Method in class chemaxon.struc.MolAtom: Gets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
getStereoGroupType() - Method in class chemaxon.struc.MolAtom: Gets the stereochemical group type for the enhanced stereo representation.
getStereoisomer(int) - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns a stereoisomer.
getStereoisomerCount() - Method in class chemaxon.calculations.stereo.StereoisomerEnumeration: Returns the number of stereoisomers.
getStereoisomerCount() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the number of different stereoisomers.
getStereoisomers() - Method in class chemaxon.calculations.stereo.StereoisomerEnumeration: Returns the list of generated stereoisomers.
getStereoisomers() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns the stereoisomers in a Molecule[] array.
getStereoModel() - Method in class chemaxon.search.api.options.SearchOptions: Get the stereo model option.
getStereoSearchType() - Method in class chemaxon.search.api.options.SearchOptions: Get the stereo search type option.
getStereoValue() - Method in class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor
getStereoValue() - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor
getStereoValue() - Method in class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor
getStereoValue() - Method in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
getStereoValue() - Method in interface chemaxon.core.calculations.stereo.CIPStereoDescriptor: Returns the CIP stereo value.
getStereoValue() - Method in class chemaxon.struc.BicycloStereoDescriptor: Return the bicyclo stereo value.
getStericEffectIndex(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.
getStericHindrance(int) - Method in class chemaxon.calculations.GeometryPlugin: Calculates hindrance of an atom from covalent radii values and distances.
getStickdst() - Method in class chemaxon.marvin.beans.MSketchPane: Gets the sticking distance.
getStickThickness() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the stick thickness.
getStickThickness() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the 3D stick's diameter.
getStickThickness() - Method in class chemaxon.marvin.common.UserSettings: Gets the stick diameter for ball and stick mode.
getStoichiometry() - Method in class chemaxon.standardizer.actions.ExpandAction: Gets the stoichiometry value of the action
getStoredParameters(Properties) - Method in interface chemaxon.calculations.gui.ParameterPanelHandler: Returns the stored parameters.
getStrictMolecule() - Method in class chemaxon.calculations.nmr.NMRSpectrum
getStrictReactionTanimoto(ReactionFingerprint) - Method in class chemaxon.descriptors.ReactionFingerprint: Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms and bonds, and the neighbours' neighbouring atoms and bonds.
getString() - Method in class chemaxon.struc.graphics.MFont: Gets the string representation.
getString() - Method in class chemaxon.struc.graphics.MTextDocument.Section: Gets the text string.
getStructurallogPIncrement() - Method in class chemaxon.calculations.LogPPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Use LogPPlugin.getStructuralLogPIncrement() instead. This method will be removed in a future version.
getStructuralLogPIncrement() - Method in class chemaxon.calculations.LogPPlugin: Returns the structural logP increment.
getStructure(int) - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns a structure.
getStructure(int) - Method in class chemaxon.calculations.ResonancePlugin: Returns a resonant structure.
getStructure(int) - Method in class chemaxon.calculations.TautomerPlugin: Returns a tautomer.
getStructureCount() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the number of all enumerated structures, -1 in case of arithmetical overflow (if the number would exceed Long.MAX_VALUE).
getStructureCount() - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns the number of different structures.
getStructureCount() - Method in class chemaxon.calculations.ResonancePlugin: Returns the number of different resonant structures.
getStructureCount() - Method in class chemaxon.calculations.TautomerPlugin: Returns the number of different tautomers.
getStructureID() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the structure ID used in Markush code (enumeration ID) generation.
getStructures() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns the enumerated structures.
getStructures() - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns all structures.
getStructures() - Method in class chemaxon.calculations.ResonancePlugin: Returns resonant structures in Molecule[] array.
getStructures() - Method in class chemaxon.checkers.result.SubstructureCheckerResult: Returns the structures
getStyle() - Method in class chemaxon.struc.graphics.MFont: Gets the font style.
getStyleFromPropertiesOf(MolBond) - Static method in enum class chemaxon.rendering.constants.AnyBondStyle
getSubDocument(int, int) - Method in class chemaxon.struc.graphics.MTextDocument
getSubFormatPriority(String) - Static method in class chemaxon.formats.MFileFormat: Gets the priority of the specified subformat name.
getSubGraphCount() - Method in class chemaxon.struc.MoleculeGraph: Gets the number of all "submolecules".
getSubGraphCount() - Method in class chemaxon.struc.RgMolecule: Gets the number of all "submolecules".
getSubGraphCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of all "submolecules".
getSubGraphs() - Method in class chemaxon.struc.MoleculeGraph: Gets all "submolecules".
getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.MoleculeGraph: Gets all "submolecules".
getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RgMolecule: Gets all "submolecules".
getSubGraphs(MoleculeGraph[], int) - Method in class chemaxon.struc.RxnMolecule: Gets all "submolecules".
getSubLevel() - Method in class chemaxon.struc.graphics.MTextAttributes: Gets the subscript/superscript level.
getSubscript() - Method in class chemaxon.struc.sgroup.AminoAcidSgroup: Gets the three letter name if it isn't empty, otherwise the one letter name (or empty String if both of them are empty).
getSubscript() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the subscript for non-superatom S-groups.
getSubscript() - Method in class chemaxon.struc.Sgroup: Gets the subscript for non-superatom S-groups.
getSubscript() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the subscript.
getSubstructure() - Method in class chemaxon.descriptors.ECFPFeature: Gets the corresponding substructure as a Molecule object.
getSubType() - Method in class chemaxon.struc.Sgroup: Gets polymer S-group subtype.
getSuperAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the superatom.
getSuperscript() - Method in class chemaxon.struc.Sgroup: Gets the superscript for non-superatom S-groups.
getSuperscript() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Gets the superscript for SRU S-groups.
getSurfaceArea() - Method in class chemaxon.calculations.MSAPlugin: Returns the surface area, calculation type is previously set in MSAPlugin.setSurfaceAreaType(int).
getSurfaceArea() - Method in class chemaxon.calculations.TPSAPlugin: Returns the surface area.
getSymbol() - Method in class chemaxon.struc.MolAtom: Gets the element symbol.
getSymbol() - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the abbreviated group symbol.
getSymbol(int) - Method in class chemaxon.descriptors.PFParameters: Gets the symbol associated with the specified Pharmacophore.
getSymbol(int) - Method in class chemaxon.descriptors.pharmacophore.PSymbols: Gets the symbol at the given index.
getSymbol(int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
getSymbol(int) - Static method in class chemaxon.struc.PeriodicTable: Symbol of the element
getSymbolCount() - Method in class chemaxon.descriptors.pharmacophore.PSymbols: returns the number of symbols
getSymbolIndex(String) - Method in class chemaxon.descriptors.PFParameters: Gets the index associated with the specified Pharmacophore symbol.
getSymbols() - Method in class chemaxon.descriptors.pharmacophore.PMapper: Returns the symbol storing object.
getSymmetricFBPA(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the symmetric FBPA convolution product based distasnce of the fingerprint from an other (given as parameter).
getSzegedIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Szeged index of the molecule.
getT(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets a text field value in a GridBagView table.
getT(int, int) - Method in class chemaxon.marvin.common.MDocStorage: Gets a text field in a record.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewCellEditor: Sets up the editor component.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer: The implementation of this method sets up the rendering component to display the passed-in molecule, and then returns the component.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewCellRenderer: The implementation of this method sets up the rendering component to display the passed-in molecule, and then returns the component.
getTableOptions() - Method in class chemaxon.marvin.common.TableSupport: Gets the table options component.
getTableSupport() - Method in class chemaxon.marvin.beans.MViewPane: Gets an object that helps to build and use a viewer table.
getTableText(String, String[], double[][]) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns table in string form.
getTabScale() - Method in class chemaxon.marvin.beans.MViewPane: Gets the magnification in the molecule cells.
getTabScale(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the magnification for a molecule cell.
getTag() - Method in class chemaxon.struc.MolAtom: Gets the tag of the atom.
getTag() - Method in class chemaxon.struc.MolBond: Gets the tag of the bond.
getTag() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the tag character for footnote display (or space if blank).
getTags() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the tags associated to the action
getTailCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Gets the tail crossing bonds of a ladder-type polymer.
getTanimoto(byte[], byte[]) - Static method in class chemaxon.search.util.SimilarityUtil: Calculates the Tanimoto coefficient of the two bit strings.
getTanimoto(byte[], byte[], int) - Static method in class chemaxon.search.util.SimilarityUtil: Calculates the Tanimoto coefficient of the two bit strings.
getTanimoto(int[], int[]) - Static method in class chemaxon.search.util.SimilarityUtil: Calculates the Tanimoto coefficient of the two bit strings.
getTanimoto(int[], int[], int) - Static method in class chemaxon.search.util.SimilarityUtil: Calculates the Tanimoto coefficient of the two bit strings.
getTanimoto(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the Tanimoto metric.
getTanimoto(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Gets the Tanimoto dissimilarity coefficient.
getTanimoto(ECFP) - Method in class chemaxon.descriptors.ECFP: Calculates the Tanimoto distance.
getTanimoto(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the Tanimoto metric (adapted to hystograms)
getTarget() - Method in class chemaxon.chemterms.SearchContext: Returns the target molecule.
getTarget() - Method in class chemaxon.search.AbstractSearch: Retrieves the target molecule.
getTarget() - Method in class chemaxon.search.Decomposition: Returns the target.
getTarget() - Method in class chemaxon.search.FormulaSearch: Gets the chemical formula of the target used to search in
getTarget() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Gets the target structure.
getTarget() - Method in class chemaxon.search.MolSearch
getTargetFingerprint() - Method in class chemaxon.chemterms.SearchContext: Returns the target molecule fingerprint.
getTargetHomologyMatchingMode() - Method in class chemaxon.search.api.options.SearchOptions: Returns the target homology matching mode.
getTargets() - Method in class chemaxon.search.MarkushGenerator: Returns the targets.
getTargetToPrint() - Method in class chemaxon.search.AbstractSearch: For internal purposes only.
getTautomerEqualityMode() - Method in class chemaxon.search.api.options.MolSearchOptions: Internal use only.
getTautomerizationSgroupName() - Method in enum class chemaxon.search.api.options.TautomerTransformationMode
getTautomerSearch() - Method in class chemaxon.search.api.options.SearchOptions: Indicates if tautomers of the query should be enumerated for search.
getTautomerSubstructureMode() - Method in class chemaxon.search.api.options.MolSearchOptions: Internal use only.
getTautomerTransformationMode() - Method in enum class chemaxon.search.api.options.TautomerEqualityMode
getTCenter() - Method in class chemaxon.struc.graphics.MRectangle: Gets the transformed point.
getTemplates() - Method in class chemaxon.standardizer.actions.Clean2DAction: Gets the template molecules of the clean action
getTemporaryObject(String) - Method in class chemaxon.struc.MolAtom: Gets a temporary object.
getTerm() - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm: Returns the term string, which is used to calculate the value of this term.
getTerminalBondDeletionStyle() - Method in class chemaxon.marvin.common.UserSettings: Gets the terminal bon deletion style.
getTerms() - Method in class chemaxon.struc.graphics.MAnalysisBox: Returns the terms of this analysis box.
getText() - Method in class chemaxon.struc.graphics.MTextBox: Gets the text stored.
getTextAttributesAtCursor() - Method in class chemaxon.struc.graphics.MTextBox: Gets the common attributes of the text on the cursor.
getTextDocument() - Method in class chemaxon.struc.graphics.MTextBox: Gets the text document.
getThickness() - Method in class chemaxon.struc.graphics.MPolyline: Gets the line thickness.
getThreeLetterName() - Method in class chemaxon.struc.sgroup.AminoAcidSgroup: Returns the three letter name of the amino acid.
getThreshold() - Method in class chemaxon.descriptors.MDParameters: Gets the threshold value being set for the current parametrized version.
getThreshold() - Method in class chemaxon.descriptors.MolecularDescriptor: Gets threshold value of the current parameterized metric.
getThreshold(int) - Method in class chemaxon.descriptors.MDParameters: Gets a metric dependent threshold value.
getThreshold(int) - Method in class chemaxon.descriptors.MolecularDescriptor: Gets a metric dependent default threshold value.
getThrowable() - Method in class chemaxon.calculations.output.CalculatorPluginOutput: Returns the throwable object.
getThrowable() - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess: Returns the throwable object.
getTimeLimit() - Method in class chemaxon.alignment.AlignmentBase
getTimeLimit() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Gets the maximum allowed MCS search time in milliseconds.
getTimeoutLimitMilliseconds() - Method in class chemaxon.search.api.options.SearchOptions: The search on a single target timeouts reaching this amount of time.
getTitle() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Returns the frame title.
getTitle() - Method in class chemaxon.calculations.TautomerPlugin: Returns the frame title.
getTitle() - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm: Returns the title of this term, which is shown in the analysis box.
getTopLeftIndex() - Method in class chemaxon.marvin.beans.MViewPane: Gets the index of the top left cell.
getTopLevelContainer() - Method in class chemaxon.marvin.beans.MarvinPane
getTopMargin() - Method in class chemaxon.struc.PageSettings
getTopologyConstraint() - Method in class chemaxon.search.mcs.BuildupMcs: Gets the maximum difference in topology the mapped part of the molecules can have.
getTOption() - Method in class chemaxon.struc.graphics.MRectangle: Gets the transformation options.
getTotalCharge() - Method in class chemaxon.struc.MoleculeGraph: Gets the total (formal) charge of the molecule.
getTotalCharge() - Method in class chemaxon.struc.Sgroup: Calculates the sum of the charge values on the atoms in this S-group.
getTotalCharge(int) - Method in class chemaxon.calculations.ChargePlugin: Returns the total charge of a specified atom.
getTotalPiEnergy() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Deprecated.
Use HuckelAnalysisPlugin.getHMOTotalPiEnergy()
getTraditionalName() - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns the traditional IUPAC name.
getTrainingIds() - Static method in class chemaxon.calculations.LogPPlugin: Returns the id's of available logP trainings.
getTransferData(DataFlavor) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable: Returns the result of the transfer operation.
getTransferDataFlavors() - Method in class chemaxon.marvin.datatransfer.MarvinTransferable: Returns the DataFlavors supported by the actual implementation.
getTransform() - Method in class chemaxon.standardizer.actions.TransformAction: Gets the transformation molecule of the action
getTransformedGraphics() - Method in class chemaxon.struc.graphics.MTextBoxTransformation
getTversky(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the Tversky !!DISSIMILARITY!! index: (1-(commonly used tversky))
getTversky(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the Tversky !!DISSIMILARITY!! index
getTverskyAlpha() - Method in class chemaxon.descriptors.MDParameters: Gets Tversky alpha value for the given parametrized metric.
getTverskyBeta() - Method in class chemaxon.descriptors.MDParameters: Gets Tversky beta value for the given parametrized metric.
getType() - Method in class chemaxon.calculations.services.ServiceArgument: Returns the argument type
getType() - Method in class chemaxon.calculations.stereo.stereocenters.EnhancedStereo: Gets the type of enhanced stereo flag.
getType() - Method in class chemaxon.checkers.AromaticityErrorChecker: Returns the type of the aromatization
getType() - Method in class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor
getType() - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor
getType() - Method in class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor
getType() - Method in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
getType() - Method in interface chemaxon.core.calculations.stereo.CIPStereoDescriptor: Returns the CIP stereo type.
getType() - Method in class chemaxon.descriptors.SDParameters
getType() - Method in class chemaxon.formats.OptionDescriptor: Gets the option type.
getType() - Method in class chemaxon.standardizer.actions.AromatizeAction: Gets the type of aromatization
getType() - Method in class chemaxon.standardizer.actions.Clean2DAction: Gets the type of action
getType() - Method in class chemaxon.standardizer.actions.ClearStereoAction: Gets the type of the action as string.
getType() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction: Gets the type of action
getType() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction: Gets the type value of the action
getType() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction: Gets the type of action
getType() - Method in class chemaxon.standardizer.actions.TransformAction: Gets the type of transformation
getType() - Method in class chemaxon.struc.graphics.MBracket: Gets the bracket type.
getType() - Method in class chemaxon.struc.graphics.MRArrow: Returns the type of this arrow.
getType() - Method in class chemaxon.struc.MolBond: Gets the bond type.
getType() - Method in class chemaxon.struc.Sgroup: Gets S-group type.
getType(int) - Method in class chemaxon.descriptors.BCUTParameters: Gets the type of the BCUT descriptor.
getType(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule: Checks whether the atoms in the selection are all in reactants, products or agents.
getType(String) - Static method in enum class chemaxon.search.api.options.TautomerEqualityMode
getType(String) - Static method in enum class chemaxon.struc.SgroupType: Returns an SgroupType for the given short name.
getTypeCount() - Method in class chemaxon.descriptors.BCUTParameters: Gets the count of descriptor types.
getTypes() - Method in class chemaxon.checkers.AtomTypeChecker: Returns the checked atom types
getTypeString(Object) - Method in class chemaxon.calculations.CalculatorPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.ChargePlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.ChemicalNamePlugin
getTypeString(Object) - Method in class chemaxon.calculations.ConformerPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.GeometryPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.HBDAPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.LogPPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.MSAPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.RefractivityPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.StructuralFrameworksPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.calculations.TPSAPlugin: Returns a string representation of the given type.
getUndefinedRAtom() - Method in class chemaxon.search.api.options.SearchOptions: Returns undefined R atom matching behavior mode.
getUndo() - Method in class chemaxon.marvin.beans.MSketchPane: Gets the maximum undo depth.
getUnguessableFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil: Gets the file format from the file name extension for formats that are not guessable from the file content.
getUnit() - Method in class chemaxon.calculations.dipole.DipoleResult: Returns the dipole moment unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder: Gets the NMR unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRCalculator: Returns NMR spectrum unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRMultiplet: Return the unit.
getUnit() - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the unit type.
getUnits() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the unit of this data field.
getUpperLeftPoint() - Method in class chemaxon.struc.PageSettings
getUpperLimit() - Method in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory
getUpperLimit() - Method in class chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
getUpperLimit() - Method in interface chemaxon.calculations.solubility.SolubilityCategory: The upper limit of category.
getURL() - Method in class chemaxon.calculations.services.ServiceDescriptor: Returns the service URL
getUserComparators() - Method in class chemaxon.search.api.options.SearchOptions: Returns the user defined comparators.
getUserSettings() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the user settings object.
getUserTypes() - Method in class chemaxon.calculations.LogPPlugin: Returns the user defined result types.
getVagueBondLevel() - Method in class chemaxon.search.api.options.SearchOptions: Getter for vague bond level.
getValence() - Method in class chemaxon.struc.MolAtom: Gets the valence.
getValenceCheckOptions() - Method in class chemaxon.struc.MoleculeGraph: Returns the options for valence checking.
getValenceCheckOptions() - Method in class chemaxon.struc.RgMolecule
getValenceProp() - Method in class chemaxon.struc.MolAtom: Gets the valence property.
getValenceProperty(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Gets the valence property of the given atom.
getValencePropMinMax() - Method in class chemaxon.struc.MolAtom: Gets the minimum and maximum possible values of the valence property.
getValue() - Method in class chemaxon.calculations.services.ServiceArgument: Returns the argument value
getValueAt(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet: Returns the value of the multiplet function at a given point.
getValueAt(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum: Returns the value of the NMR spectrum function at a given x point.
getValueCount() - Static method in enum class chemaxon.rendering.constants.AnyBondStyle
getValueCount() - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
getValueCount() - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle
getVanDerWaalsRadius(int) - Static method in class chemaxon.struc.PeriodicTable: Van der Waals radius of the element in Angstroms.
getVariable(String) - Method in interface chemaxon.chemterms.ChemTermsContext: Returns the value of a variable.
getVDWSA() - Method in class chemaxon.calculations.MSAPlugin: Returns van der Waals surface area.
getVersion() - Static method in class chemaxon.common.version.VersionInfo: Returns the product version.
getVerticalAlignment() - Method in class chemaxon.struc.graphics.MTextBox: Gets the vertical alignment.
getViewAnyBond() - Method in class chemaxon.marvin.common.UserSettings: Gets the default any bond drawing style in the viewer.
getViewCarbonVisibility() - Method in class chemaxon.marvin.common.UserSettings: Gets the default carbon displaying style in the viewer.
getViewColorScheme() - Method in class chemaxon.marvin.common.UserSettings: Gets the viewer's default color scheme.
getViewHandlerType() - Method in class chemaxon.marvin.common.TableOptions: Gets the view handler type.
getViewImplicitH() - Method in class chemaxon.marvin.common.UserSettings: Gets the display method of implicit hydrogens for the viewer.
getViewLayout() - Method in class chemaxon.marvin.common.UserSettings: Gets the table layout of the Viewer.
getViewLigandOrderVisibility() - Method in class chemaxon.marvin.common.UserSettings: Gets the default ligand order displaying style in the viewer.
getViewLoadWorkingDir() - Method in class chemaxon.marvin.common.UserSettings: Based on the preferences this funtion returns the proper working directory for the MarvinView application's load filechooser.
getViewMolbg2d() - Method in class chemaxon.marvin.common.UserSettings: Gets the viewer's default molecule background color for 2D.
getViewMolbg3d() - Method in class chemaxon.marvin.common.UserSettings: Gets the viewer's default molecule background color for 3D.
getViewNavmode2d() - Method in class chemaxon.marvin.common.UserSettings: Gets the navigation mode for the 2D viewer.
getViewNavmode3d() - Method in class chemaxon.marvin.common.UserSettings: Gets the navigation mode for the 3D viewer.
getViewRecentFileList() - Method in class chemaxon.marvin.common.UserSettings: Gets the recent files' list in MarvinView, the last item is the most recent.
getViewRecentFileListSize() - Method in class chemaxon.marvin.common.UserSettings: Gets the recent file list requested size, based on a preferences setting
getViewRendering2d() - Method in class chemaxon.marvin.common.UserSettings: Gets the rendering style for the 2D viewer.
getViewRendering3d() - Method in class chemaxon.marvin.common.UserSettings: Gets the rendering style for the 3D viewer.
getViewSaveWorkingDir() - Method in class chemaxon.marvin.common.UserSettings: Not implemented yet, don't use it.
getVisibleButtonB(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the i-th button in the visible area of the viewer.
getVisibleButtonC(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the i-th checkbox in the visible area of the viewer.
getVisibleCellComponent(int) - Method in class chemaxon.marvin.beans.MViewPane: Gets the canvas of the specified cell in a GridBag layout based table.
getVisibleCellCount() - Method in class chemaxon.marvin.beans.MViewPane: Gets the number of the visible cells in a GridBag layout based table.
getVisibleCellIndex(int) - Method in class chemaxon.marvin.beans.MViewPane: Determines the visible cell index of a cell
getVisibleCoords(MolAtom) - Method in class chemaxon.struc.Molecule: Returns the coordinates of the given atom (contained in the molecule).
getVisibleCoords(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Returns the coordinates of the given atom (contained in the molecule).
getVolume() - Method in class chemaxon.alignment.AlignmentMolecule
getVolume() - Method in class chemaxon.calculations.GeometryPlugin
getVolumeScore() - Method in class chemaxon.alignment.Alignment: Calculates the volume score between the current orientation and conformation of the two molecules.
getVolumeTanimoto() - Method in class chemaxon.calculations.AlignmentPlugin
getWarningMessage() - Method in class chemaxon.calculations.AlignmentPlugin: Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.calculations.CalculatorPlugin: Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.calculations.ConformerPlugin: Returns a warning message if there are no conformers, null otherwise.
getWarningMessage() - Method in class chemaxon.calculations.GeometryPlugin: Returns a warning message if lowest energy conformer calculation was unsuccessful or aborted by user, null otherwise.
getWarningMessage() - Method in class chemaxon.calculations.HBDAPlugin: Returns the calculation warning information message if no H-bond donor/acceptor atoms found, returns the empty string otherwise.
getWarningMessage() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Returns the calculation warning information message if no isoelectric point exists, returns the empty string otherwise.
getWarningMessage() - Method in class chemaxon.calculations.LogDPlugin: Returns the calculation warning message.
getWarningMessage() - Method in class chemaxon.calculations.LogPPlugin: Returns the calculation warning message.
getWarningMessage() - Method in class chemaxon.calculations.PkaPlugin: Returns the calculation warning information message.
getWarningMessage() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns a warning message if there are no stereoisomers, null otherwise.
getWarningMessage() - Method in class chemaxon.calculations.TautomerPlugin
getWeight(int, int) - Method in class chemaxon.alignment.NodeColor: Returns the weight of aligning two types based on the coloring scheme and user-defined weights.
getWeightedAsymmetricEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the weighted asymmetric Euclidean distance.
getWeightedAsymmetricEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Calculates the weighted asymmetric Euclidean distance.
getWeightedAsymmetricEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP: Calculates the weighted asymmetric Euclidean distance.
getWeightedAsymmetricEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the weighted asymmetric Euclidean distance.
getWeightedEuclidean(BCUT) - Method in class chemaxon.descriptors.BCUT: Calculates the weighted Euclidean distance.
getWeightedEuclidean(ChemicalFingerprint) - Method in class chemaxon.descriptors.ChemicalFingerprint: Calculates the weighted Euclidean distance.
getWeightedEuclidean(CustomDescriptor) - Method in class chemaxon.descriptors.CustomDescriptor: Calculates the weighted Euclidean distance.
getWeightedEuclidean(ECFP) - Method in class chemaxon.descriptors.ECFP: Calculates the weighted Euclidean distance.
getWeightedEuclidean(PharmacophoreFingerprint) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Calculates the weighted Euclidean distance.
getWeights() - Method in class chemaxon.descriptors.MDParameters: Gets all weights for the given parametrized metric.
getWeights() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the atom weights used in average location calculation.
getWidth() - Method in class chemaxon.struc.PageSettings
getWienerIndex() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
getWienerPolarity() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.
getWinScale() - Method in class chemaxon.marvin.beans.MViewPane: Gets the magnification in the zoom windows.
getWireThickness() - Method in class chemaxon.marvin.beans.MarvinPane: Gets the line thickness for wireframe mode.
getWireThickness() - Method in class chemaxon.marvin.beans.MolPrinter: Gets the line thickness for wireframe mode.
getWireThickness() - Method in class chemaxon.marvin.common.UserSettings: Gets the bond thickness in wireframe mode.
getWord(ByteBuffer, int) - Method in class chemaxon.formats.PositionedInputStream
getX() - Method in class chemaxon.struc.MolAtom: Gets the X coordinate.
getX() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the X coordinate.
getXMLTokens() - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Gets the XML tokens of the action
getXState() - Method in class chemaxon.struc.Sgroup: Gets the expanded/contracted state.
getY() - Method in class chemaxon.struc.MolAtom: Gets the Y coordinate.
getY() - Method in class chemaxon.struc.sgroup.DataSgroup: Gets the Y coordinate.
getZ() - Method in class chemaxon.struc.MolAtom: Gets the Z coordinate.
GLOBAL - Static variable in class chemaxon.struc.ValenceCheckOptions: An options object with ValenceCheckOptions.isLocalAromatic() returning false and ValenceCheckOptions.isTraditionalNitrogensAllowed() returning true.
GOOD - Enum constant in enum class chemaxon.calculations.nmr.NMRErrorClassification: Good quality
GRAFT - Enum constant in enum class chemaxon.struc.SgroupType
GRAPH_INVARIANTS - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "grinv".
GRAPH_INVARIANTS_VISIBLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "grinvVisible".
graphInvariant() - Method in class chemaxon.core.calculations.TopologyAnalyzer
GRID_VISIBLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: sketchGridVisible property.
GRINV_DONT_STORE - Static variable in class chemaxon.struc.MoleculeGraph: Graph invariant option to instruct that the graph invariant should not be stored in MoleculeGraph.
GRINV_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Show graph invariants flag.
GRINV_NOHYDROGEN - Static variable in class chemaxon.struc.MoleculeGraph: Graph invariant option for ignoring explicit hydrogens.
GRINV_OLDSTEREO - Static variable in class chemaxon.struc.MoleculeGraph: Graph invariant option for calculating graph invariants using the old stereo method.
GRINV_STEREO - Static variable in class chemaxon.struc.MoleculeGraph: Graph invariant option for calculating graph invariants using stereo information.
GRINV_USEMAPS - Static variable in class chemaxon.struc.MoleculeGraph: Graph invariant option for calculating graph invariants considering atom maps also.
GRINV_VALUE_OPTIONS - Static variable in class chemaxon.struc.MoleculeGraph: Unified mask of graph invariant options affecting grinv value.
grinvCC - Variable in class chemaxon.struc.MoleculeGraph: Graph invariant change count.
GROUP_END_TOKEN - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringReader: End of group list token of the action string
GROUP_END_TOKEN - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: End of group list token of the action string
GROUP_END_TOKEN - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: End of group list token of the action string
GROUP_LIST_KEY - Static variable in class chemaxon.standardizer.actions.CreateGroupAction: Property key for group list modification
GROUP_SCHEME - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Group color scheme in display option flags.
GROUP_SCHEME_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Group color scheme.
GROUP_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringReader: Group entry separator token of the action string
GROUP_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: Group entry separator token of the action string
GROUP_SEPARATOR - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: Group entry separator token of the action string
GROUP_START_TOKEN - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringReader: Start of group list token of the action string
GROUP_START_TOKEN - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: Start of group list token of the action string
GROUP_START_TOKEN - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: Start of group list token of the action string
GroupDefinition - Class in chemaxon.standardizer.actions: Pattern of a group.
GroupDefinition() - Constructor for class chemaxon.standardizer.actions.GroupDefinition: Creates an empty group pattern.
GroupDefinition(String, Molecule) - Constructor for class chemaxon.standardizer.actions.GroupDefinition: Creates a new group pattern.
GROUPED_DOTDISCONNECTED_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "groupeddotdisconnectedformula".
GROUPTYPE_ALTERNATING_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_ANYPOLYMER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_BLOCK_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_COMPONENT_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_CROSSLINK_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_GENERIC_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_GRAFT_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_MER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_MODIFICATION_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_MONOMER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_MULTIPLE_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_ORDERED_MIXTURE_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_RANDOM_COPOLYMER_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_RANGE_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_SRU_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_SUPERATOM_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
GROUPTYPE_UNORDERED_MIXTURE_GROUP - Static variable in class chemaxon.marvin.common.SketchParameterConstants
guessFormat(String) - Method in class chemaxon.formats.Recognizer: Tries to guess the format of the given line.
GZIP - Static variable in class chemaxon.formats.MFileFormat: GZIP compressed file.

H

H - Static variable in class chemaxon.alignment.Pharmacophore3D
H - Static variable in class chemaxon.chemterms.SearchContext
H - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element H.
H_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator: Name of the 1H chemical shift atom property.
H1 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus: 1H NMR
HA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction: Number of heavy atoms.
HAcc - Class in chemaxon.descriptors.scalars: Implements hydrogen bond acceptor atom count as a scalar descriptor.
HAcc() - Constructor for class chemaxon.descriptors.scalars.HAcc: Creates a new, empty HAcc descriptor.
HAcc(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.HAcc: Copy constructor.
HAcc(HBParameters) - Constructor for class chemaxon.descriptors.scalars.HAcc: Creates a new instance according to the parameters given.
HAcc(String) - Constructor for class chemaxon.descriptors.scalars.HAcc: Creates a new instance according to the parameters given.
HALOAc - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType
HaltOnErrorOption - Enum Class in chemaxon.search.api.options: Option type describing the error handling behaviour.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.AlignmentPlugin
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.CalculatorPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.ChargePlugin
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.ChemicalNamePlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.ConformerPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.GeometryPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.ResonancePlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.StructuralFrameworksPlugin: This plugin handles multifrag molecules.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.TautomerPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
hararyIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
hasAcceptedFormats() - Method in record class chemaxon.formats.Recognizer.RecognizerResult: Returns true if the recognition was successful and at least one format was accepted, false otherwise.
hasAlternativeName() - Method in class chemaxon.struc.sgroup.SgroupAtom: Checks whether there is an alternative name at all.
hasAromaticBond() - Method in class chemaxon.struc.MolAtom: Tests whether the atom has aromatic bonds.
hasAtom() - Method in class chemaxon.struc.graphics.MElectron
hasAtom(MolAtom) - Method in class chemaxon.struc.Sgroup: Is the specified atom an element of this group?
hasAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Is the specified atom an element of this group?
hasAtomSet() - Method in class chemaxon.struc.Molecule
hasAtomSet() - Method in class chemaxon.struc.MoleculeGraph: Tests whether the molecule graph has atom sets.
hasAtomSet() - Method in class chemaxon.struc.RgMolecule: Tests whether the molecule graph has atom sets.
hasAtomSet() - Method in class chemaxon.struc.RxnMolecule: Tests whether the molecule graph has atom sets.
hasBackground() - Method in class chemaxon.struc.graphics.MBracket: A bracket has no background.
hasBackground() - Method in class chemaxon.struc.graphics.MPolyline: A polyline has a background only if it is closed.
hasBackground() - Method in class chemaxon.struc.graphics.MTextBox: A text box has a background always.
hasBackground() - Method in class chemaxon.struc.MObject: Can the object have a background?
hasBondSet() - Method in class chemaxon.struc.MoleculeGraph: Tests whether the molecule graph has atom sets.
hasBondSet() - Method in class chemaxon.struc.RgMolecule: Tests whether the molecule graph has atom sets.
hasBondSet() - Method in class chemaxon.struc.RxnMolecule: Tests whether the molecule graph has atom sets.
hasBrackets() - Method in class chemaxon.struc.sgroup.DataSgroup: Brackets are painted if mouse runs over sgroup atoms.
hasBrackets() - Method in class chemaxon.struc.Sgroup: Checks if brackets should be painted or not.
hasBrackets() - Method in class chemaxon.struc.sgroup.MulticenterSgroup: Does a bracket belong to this sgroup?
hasBrackets() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Checks if brackets should be painted or not.
hasChangesInUserComparators() - Method in class chemaxon.search.api.options.SearchOptions: Used in initializing searches.
hasCharge() - Method in class chemaxon.struc.MolAtom: Returns true if this atom has a non-zero formal charge.
hasColor() - Method in class chemaxon.struc.graphics.MPolyline: A polyline does not have a non-line, non-background color.
hasColor() - Method in class chemaxon.struc.graphics.MTextBox: A text box has a text color.
hasColor() - Method in class chemaxon.struc.MObject: Can the object have a color (non-line and non-background)?
hasContainerFreeMElectron() - Method in class chemaxon.struc.graphics.MElectronContainer
hasContractedSgroup() - Method in class chemaxon.struc.Molecule: Tests if the molecule has contracted S-groups or not.
hasDistanceRanges() - Method in class chemaxon.alignment.ShapeData
hasElectronContainer(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
hasElectrons() - Method in class chemaxon.struc.MDocument: Returns whether MDocument contains any electrons.
hasExplicitLonePairs() - Method in class chemaxon.struc.MDocument: Returns true if the MDocument has any electrons drawn by the user.
hasExtraLabelSet() - Method in class chemaxon.struc.MoleculeGraph
hasFace() - Method in class chemaxon.struc.graphics.MPolyline: Is it 2 dimensional?
hasFace() - Method in class chemaxon.struc.graphics.MTextBox: Is it 2 dimensional?
hasFeature(int) - Method in class chemaxon.descriptors.pharmacophore.PMap: Tells weather a given atom has any pharmacophore property.
hasFeature(int, int) - Method in class chemaxon.descriptors.pharmacophore.PMap: Tells weather a given atom has a given pharmacophore property.
hashCode() - Method in record class chemaxon.calculations.admet.HergActivityPrediction: Returns a hash code value for this object.
hashCode() - Method in record class chemaxon.calculations.admet.HergClassPrediction: Returns a hash code value for this object.
hashCode() - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Returns a hash code value for this object.
hashCode() - Method in record class chemaxon.calculations.elemental.FormulaAtom: Returns a hash code value for this object.
hashCode() - Method in class chemaxon.calculations.PkaTrainingResult
hashCode() - Method in class chemaxon.checkers.AbbreviatedGroupChecker
hashCode() - Method in class chemaxon.checkers.AbstractStructureChecker
hashCode() - Method in class chemaxon.checkers.AromaticityErrorChecker
hashCode() - Method in class chemaxon.checkers.AtomLabels
hashCode() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
hashCode() - Method in class chemaxon.checkers.AttachedDataChecker.DataExclusionList
hashCode() - Method in class chemaxon.checkers.AttachedDataChecker
hashCode() - Method in class chemaxon.checkers.ExplicitHydrogenChecker
hashCode() - Method in class chemaxon.checkers.result.AromaticityCheckerResult
hashCode() - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
hashCode() - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
hashCode() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
hashCode() - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
hashCode() - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
hashCode() - Method in class chemaxon.checkers.result.RgroupCheckerResult
hashCode() - Method in class chemaxon.checkers.result.SgroupCheckerResult
hashCode() - Method in class chemaxon.checkers.result.SubstructureCheckerResult
hashCode() - Method in class chemaxon.checkers.StructureCheckerDescriptor
hashCode() - Method in class chemaxon.checkers.ValencePropertyChecker
hashCode() - Method in class chemaxon.core.calculations.stereo.AtropStereoDescriptor
hashCode() - Method in class chemaxon.core.calculations.stereo.AtropStereoIUPACDescriptor
hashCode() - Method in class chemaxon.core.calculations.stereo.AxialStereoDescriptor
hashCode() - Method in class chemaxon.core.calculations.stereo.AxialStereoIUPACDescriptor
hashCode() - Method in record class chemaxon.core.calculations.stereo.CIPStereoCalculator.CIPStereoCalculatorResult: Returns a hash code value for this object.
hashCode() - Method in class chemaxon.core.calculations.stereo.CisTransStereoDescriptor
hashCode() - Method in class chemaxon.core.calculations.stereo.CisTransStereoIUPACDescriptor
hashCode() - Method in class chemaxon.core.calculations.stereo.StereoActivePart
hashCode() - Method in class chemaxon.core.calculations.stereo.TetrahedralStereoDescriptor
hashCode() - Method in class chemaxon.core.calculations.stereo.TetrahedralStereoIUPACDescriptor
hashCode() - Method in class chemaxon.fixers.StructureFixerDescriptor
hashCode() - Method in class chemaxon.formats.Encoding
hashCode() - Method in record class chemaxon.formats.Recognizer.RecognizerResult: Returns a hash code value for this object.
hashCode() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor
hashCode() - Method in class chemaxon.reaction.AtomIdentifier
hashCode() - Method in class chemaxon.search.api.SearchHit
hashCode() - Method in class chemaxon.search.Decomposition
hashCode() - Method in class chemaxon.standardizer.actions.GroupDefinition
hashCode() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
hashCode() - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm
hashCode() - Method in class chemaxon.struc.graphics.MAtomSetPoint
hashCode() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
hashCode() - Method in class chemaxon.struc.graphics.MElectron
hashCode() - Method in class chemaxon.struc.graphics.MElectronContainer
hashCode() - Method in class chemaxon.struc.graphics.MFont
hashCode() - Method in class chemaxon.struc.graphics.MMidPoint
hashCode() - Method in class chemaxon.struc.graphics.MRectanglePoint
hashCode() - Method in class chemaxon.struc.graphics.MTextAttributes
hashCode() - Method in class chemaxon.struc.MPoint
hashCode() - Method in class chemaxon.struc.Point3D
hashCode() - Method in class chemaxon.struc.prop.MBooleanProp
hashCode() - Method in class chemaxon.struc.prop.MByteArrayProp
hashCode() - Method in class chemaxon.struc.prop.MCollectionProp
hashCode() - Method in class chemaxon.struc.prop.MDoubleArrayProp
hashCode() - Method in class chemaxon.struc.prop.MDoubleProp
hashCode() - Method in class chemaxon.struc.prop.MFontProp
hashCode() - Method in class chemaxon.struc.prop.MHashProp
hashCode() - Method in class chemaxon.struc.prop.MHCoords3DProp
hashCode() - Method in class chemaxon.struc.prop.MIntegerArrayProp
hashCode() - Method in class chemaxon.struc.prop.MIntegerProp
hashCode() - Method in class chemaxon.struc.prop.MListProp
hashCode() - Method in class chemaxon.struc.prop.MMoleculeProp
hashCode() - Method in class chemaxon.struc.prop.MMoleculeStringProp
hashCode() - Method in class chemaxon.struc.prop.MObjectProp
hashCode() - Method in class chemaxon.struc.prop.MStringProp
hashCode() - Method in class chemaxon.struc.RgroupBridgeId
hashCode() - Method in class chemaxon.struc.Transform3D
hashCode() - Method in class chemaxon.struc.ValenceCheckOptions
HashCode - Class in chemaxon.search.util: Hash code generator for molecules.
HashCode() - Constructor for class chemaxon.search.util.HashCode: Creates a new instance of HashCode
HASHED - Enum constant in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle: Hashed bond is used when rendering Coordinate bonds.
HASHED - Static variable in class chemaxon.struc.MolBond: "Hashed" attribute of the bond.
hasId(String) - Method in class chemaxon.struc.Molecule
hasImplicitH() - Method in class chemaxon.struc.MoleculeGraph: Tests whether the molecule has implicit hydrogen atoms.
hasLineColor() - Method in class chemaxon.struc.graphics.MPolyline: A polyline have a line color always.
hasLineColor() - Method in class chemaxon.struc.MObject: Can the object have a line color?
hasMoreStructures() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Returns true if there are more structures.
hasNext() - Method in class chemaxon.calculations.stereo.StereoisomerEnumeration
hasNext() - Method in interface chemaxon.formats.MoleculeIterator: Tests whether the iteration has more elements.
hasNext() - Method in class chemaxon.struc.IteratorFactory.AtomIterator: Deprecated.

Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.struc.IteratorFactory.BondIterator: Deprecated.

Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.struc.IteratorFactory.NeighbourIterator: Deprecated.

Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.struc.IteratorFactory.RgComponentIterator: Deprecated.

Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.struc.IteratorFactory.RxnComponentIterator: Deprecated.

Decides whether the iteration has more element.
hasNext() - Method in class chemaxon.struc.IteratorFactory.SgroupIterator: Deprecated.

Decides whether the iteration has more element.
hasNextResult() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Returns whether there are more results available.
hasNonCoordinateBond() - Method in class chemaxon.struc.sgroup.MulticenterSgroup: Decides whether the central atom of the sgroup has a non-coordinate bond.
hasOrder(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
hasOutline() - Method in class chemaxon.struc.graphics.MPolyline: Does it have an outline?
hasParameters(int) - Method in class chemaxon.calculations.gui.PluginFactory: Returns true if plugin has parameter panel, false otherwise.
hasPrecision() - Method in interface chemaxon.struc.graphics.MAnalysisBoxTerm.Formatter
hasQProps() - Method in class chemaxon.struc.MolAtom: Returns true if this atom has query properties.
hasQueryBonds() - Method in class chemaxon.struc.MolAtom: Tests whether the atom has query bonds (e.g.
hasRadicals() - Method in class chemaxon.struc.MDocument: Returns true if the MDocument has any Radical Electrons.
hasResults() - Method in class chemaxon.search.RgroupDecompositionResults
hasRgroupContainedBy(Set<?>) - Method in class chemaxon.struc.RgMolecule: Tests whether the molecule has an R-group that is a subset of the specified set of atoms.
hasRichText() - Method in class chemaxon.struc.graphics.MTextBox: Tests whether the document is rich text.
hasSelection() - Method in class chemaxon.struc.graphics.MChemicalStruct: Checks the existence of the selection.
hasSelection() - Method in class chemaxon.struc.graphics.MTextBox: Checks the existence of the selection.
hasSelection(MoleculeGraph) - Static method in class chemaxon.struc.graphics.MChemicalStruct: Checks the existence of the selection.
hasSelfReferringProperty() - Method in class chemaxon.struc.MoleculeGraph: Tests whether the property list contains the molecule.
hasTautomers(Molecule) - Static method in class chemaxon.calculations.TautomerPlugin: Returns if a molecule has tautomers.
hasTimeout() - Method in record class chemaxon.core.calculations.stereo.CIPStereoCalculator.CIPStereoCalculatorResult: Returns the value of the hasTimeout record component.
hasUserComparators() - Method in class chemaxon.search.api.options.SearchOptions: Gets whether searcher has user defined comparators.
hasValenceError() - Method in class chemaxon.struc.MolAtom: Returns previously set valence error.
hasValenceError() - Method in class chemaxon.struc.MoleculeGraph: Determines if this molecule has a valence error on any of its atoms.
hasValenceError() - Method in class chemaxon.struc.sgroup.SgroupAtom: Checks if any atom of the Sgroup has a valence error.
hasValidConformer() - Method in class chemaxon.calculations.ConformerPlugin: Returns true if the input molecule has a valid conformer (has a valid structure in 3D space).
hasWedgedBond() - Method in class chemaxon.struc.MolAtom: Tests whether the atom has a wedged bond.
hasWiggly(MolAtom) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Check if at least one wiggly bond starts from this atom.
haveEqualProperties(MolAtom) - Method in class chemaxon.struc.MolAtom: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated for removal, no replacement.
haveEqualProperties(MolBond) - Method in class chemaxon.struc.MolBond: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated for removal, no replacement.
haveEqualProperties(MolBond) - Method in class chemaxon.struc.QueryBond: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated for removal, no replacement.
haveSimilarBonds(MolAtom) - Method in class chemaxon.struc.MolAtom: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated for removal, no replacement.
HBD - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Number of hydrogen-bond donors.
HBDA - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
HBDA_MICROSPECIES - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
HBDAPlugin - Class in chemaxon.calculations: Plugin class for H bond acceptor/donor calculation.
HBDAPlugin() - Constructor for class chemaxon.calculations.HBDAPlugin: Constructor.
HBONDED_H - Static variable in class chemaxon.struc.MolAtom: Hydrogen atom wtih a MolBond.HYDROGEN bond on it.
HBParameters - Class in chemaxon.descriptors.scalars: Manages parameters for the HDon and HAcc scalar descriptor classes.
HBParameters() - Constructor for class chemaxon.descriptors.scalars.HBParameters: Creates an empty object.
HBParameters(File) - Constructor for class chemaxon.descriptors.scalars.HBParameters: Creates a new object based on a given configuration file.
HBParameters(String) - Constructor for class chemaxon.descriptors.scalars.HBParameters: Creates a new object based on a given configuration string.
HCONNECTED_H - Static variable in class chemaxon.struc.MolAtom: Hydrogen atom(s) connected to another hydrogen only.
HCOUNT_MATCHING_AUTO - Static variable in interface chemaxon.search.api.SearchConstants: Default option for H count matching (setHCountMatching).
HCOUNT_MATCHING_EQUAL - Static variable in interface chemaxon.search.api.SearchConstants: Option for H count matching.
HCOUNT_MATCHING_GREATER_OR_EQUAL - Static variable in interface chemaxon.search.api.SearchConstants: Option for H count matching.
HDon - Class in chemaxon.descriptors.scalars: Implements hidrogen bond donor atom count as a scalar descriptor.
HDon() - Constructor for class chemaxon.descriptors.scalars.HDon: Creates a new, empty HDon descriptor.
HDon(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.HDon: Copy constructor.
HDon(HBParameters) - Constructor for class chemaxon.descriptors.scalars.HDon: Creates a new instance according to the parameters given.
HDon(String) - Constructor for class chemaxon.descriptors.scalars.HDon: Creates a new instance according to the parameters given.
He - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element He.
HEAD - Static variable in class chemaxon.struc.graphics.MPolyline: Arrow head.
HEADER_MAP - Static variable in class chemaxon.search.RgroupDecomposition: Constant for header type: header with any atoms mapped by Rgroup indexes.
HEADER_NONE - Static variable in class chemaxon.search.RgroupDecomposition: Constant for header type: no header.
HEADER_RGROUP - Static variable in class chemaxon.search.RgroupDecomposition: Constant for header type: header with Rgroup atoms (cannot be exported to SMILES).
Heavy - Class in chemaxon.descriptors.scalars: Implements HeavyAtomCount (number of non-hydrogen atoms) as a scalar descriptor.
Heavy() - Constructor for class chemaxon.descriptors.scalars.Heavy: Creates a new, empty logD descriptor.
Heavy(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.Heavy: Copy constructor.
Heavy(SDParameters) - Constructor for class chemaxon.descriptors.scalars.Heavy: Creates a new instance according to the parameters given.
Heavy(String) - Constructor for class chemaxon.descriptors.scalars.Heavy: Creates a new instance according to the parameters given.
HEAVYATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement: Heavy atom count of the molecule
heavyAtomLimit(int) - Static method in interface chemaxon.calculations.api.CalculatorInputChecker: Creates a new input checker that only accepts molecules with at most the given number of heavy atoms.
HeavyAtomLimitChecker - Record Class in chemaxon.calculations.api: An input checker that only accepts molecules with at most a certain number of heavy atoms.
HeavyAtomLimitChecker(int, Map<CalculatorTag, Integer>) - Constructor for record class chemaxon.calculations.api.HeavyAtomLimitChecker: Creates an instance of a HeavyAtomLimitChecker record class.
HELP_TEXT - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: help text for checker
HELP_TEXT - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: help text for action
helpText() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the help text of the checker
helpText() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the help text of the action
HergActivityPrediction - Record Class in chemaxon.calculations.admet: The results of a hERG activity prediction.
HergActivityPrediction(double, double) - Constructor for record class chemaxon.calculations.admet.HergActivityPrediction: Creates an instance of a HergActivityPrediction record class.
HergActivityPredictor - Class in chemaxon.calculations.admet: hERG activity predictor.
HergClass - Enum Class in chemaxon.calculations.admet: The possible values of hERG class prediction.
HergClassPrediction - Record Class in chemaxon.calculations.admet: The results of a hERG class prediction.
HergClassPrediction(HergClass, List<HergClass>, Map<HergClass, Integer>) - Constructor for record class chemaxon.calculations.admet.HergClassPrediction: Creates an instance of a HergClassPrediction record class.
HergClassPredictor - Class in chemaxon.calculations.admet: hERG class predictor.
HETERO - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the hetero any atom Q.
heteroaliphaticRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
heteroaliphaticRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaliphaticRings() - Method in class chemaxon.core.calculations.Ring: Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
heteroaliphaticRings(int) - Method in class chemaxon.core.calculations.Ring: Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaromaticRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing non-carbon atoms).
heteroaromaticRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroaromaticRings() - Method in class chemaxon.core.calculations.Ring: Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).
heteroaromaticRings(int) - Method in class chemaxon.core.calculations.Ring: Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
heteroRingCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
heteroRingCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
heteroRings() - Method in class chemaxon.core.calculations.Ring: Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
heteroRings(int) - Method in class chemaxon.core.calculations.Ring: Indentifies hetero rings in the molecule having a given size (number of atoms).
Hf - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Hf.
Hg - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Hg.
HIDDEN - Static variable in class chemaxon.struc.sgroup.DataSgroup: Specifies that the data sgroup is hidden.
hierarchize() - Method in class chemaxon.struc.MPropertyContainer: Converts hierarchically specified RDF properties to MListProp and MHashProp objects.
HIGH - Enum constant in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory: High solubility.
HIGH_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor: high priority value
HIGHEST_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor: the highest priority value
highestEigenvalues - Variable in class chemaxon.descriptors.BCUT
highlight(MObject) - Method in class chemaxon.struc.MDocument: Highlight an object.
HIT - Static variable in class chemaxon.chemterms.SearchContext
HIT_ATOM_SET - Static variable in class chemaxon.search.hitdisplay.HitDisplayTool: Set identifier for hit atoms
HIT_BOND_SET - Static variable in class chemaxon.search.hitdisplay.HitDisplayTool: Set identifier for hit bonds
HIT_EXCLUDEDQ - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting excluded query atom.
HIT_LP - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting isolated lone-pair match.
HIT_MULTICENTER - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting multicenter atoms in query.
HIT_NON_R - Static variable in interface chemaxon.search.api.SearchConstants: Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.
HIT_ORDERING_NONE - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
HIT_R - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting R-node matches in case of R-group search.
HIT_R_EMPTY_MATCH - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting R-node empty match.
HIT_UNMAPABLE - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting unmapable atoms in query (e.g.
HitDisplayOptions - Class in chemaxon.search.hitdisplay: Class for specifying coloring and alignment options.
HitDisplayOptions() - Constructor for class chemaxon.search.hitdisplay.HitDisplayOptions
HitDisplayTool - Class in chemaxon.search.hitdisplay: Class for displaying hit results with hit coloring, alignment, partial clean, etc.
HitDisplayTool(HitDisplayOptions, MolSearchOptions, Molecule) - Constructor for class chemaxon.search.hitdisplay.HitDisplayTool: Creates a new instance with the specified parameters, with using a default standardization method which applies only aromatization during the search process.
HitDisplayTool(HitDisplayOptions, MolSearchOptions, Molecule, Standardizer) - Constructor for class chemaxon.search.hitdisplay.HitDisplayTool: Constructor.
HitDisplayUtil - Class in chemaxon.search.hitdisplay: Class providing some utility tools for displaying hit results with hit coloring, alignment, partial clean, etc.
HitDisplayUtil() - Constructor for class chemaxon.search.hitdisplay.HitDisplayUtil
HITMAP - Static variable in class chemaxon.chemterms.SearchContext
HLBPlugin - Class in chemaxon.calculations: Calculates hydrophilic-lipophilic balance (HLB) of a molecule.
HLBPlugin() - Constructor for class chemaxon.calculations.HLBPlugin
HLBPlugin.Builder - Class in chemaxon.calculations: Deprecated, for removal: This API element is subject to removal in a future version.
Deprecated, use the constructor of HLBPlugin class directly instead.
HM - Static variable in class chemaxon.chemterms.SearchContext
Ho - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ho.
HomologyTranslationOption - Enum Class in chemaxon.search.api.options: Option type describing the scope of homology matching.
Hs - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Hs.
HS_S - Static variable in interface chemaxon.struc.HybridizationStateConsts: S hybridization state.
HS_S - Static variable in class chemaxon.struc.MolAtom: S hybridization state.
HS_SP - Static variable in interface chemaxon.struc.HybridizationStateConsts: SP hybridization state.
HS_SP - Static variable in class chemaxon.struc.MolAtom: SP hybridization state.
HS_SP2 - Static variable in interface chemaxon.struc.HybridizationStateConsts: SP2 hybridization state.
HS_SP2 - Static variable in class chemaxon.struc.MolAtom: SP2 hybridization state.
HS_SP3 - Static variable in interface chemaxon.struc.HybridizationStateConsts: SP3 hybridization state.
HS_SP3 - Static variable in class chemaxon.struc.MolAtom: SP3 hybridization state.
HS_UNKNOWN - Static variable in interface chemaxon.struc.HybridizationStateConsts: Unknown hybridization state.
HS_UNKNOWN - Static variable in class chemaxon.struc.MolAtom: Unknown hybridization state.
HTML - Enum constant in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType
HTML - Static variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: Property display type: display in html text.
HttpServiceDescriptor - Class in chemaxon.calculations.services: HTTP Request based ServiceDescriptor implementation for HTTP POST/GET based services
HttpServiceDescriptor() - Constructor for class chemaxon.calculations.services.HttpServiceDescriptor: Constructs a HttpServiceDescriptor
HttpServiceHandler - Class in chemaxon.calculations.services: ServiceHandler implementation that invokes remote services over HTTP.
HttpServiceHandler() - Constructor for class chemaxon.calculations.services.HttpServiceHandler
HuckelAnalysisPlugin - Class in chemaxon.calculations: Plugin class for Huckel Analysis calculation.
HuckelAnalysisPlugin() - Constructor for class chemaxon.calculations.HuckelAnalysisPlugin: Constructor.
HybridizationStateConsts - Interface in chemaxon.struc: Hybridization state constants.
HYDR - Static variable in class chemaxon.alignment.Pharmacophore3D
HYDROGEN - Enum constant in enum class chemaxon.struc.BondType: Hydrogen bond type.
HYDROGEN - Static variable in record class chemaxon.calculations.elemental.FormulaAtom
HYDROGEN - Static variable in class chemaxon.struc.MolBond: Hydrogen bond type.
HydrogenData(MolAtom, int, int, int) - Constructor for class chemaxon.calculations.CalculatorPlugin.HydrogenData
hydrogenize - Variable in class chemaxon.formats.MolExportModule: Add Hydrogen atoms if 1, remove if -1, do nothing if 0.
hydrogenize(int, String, boolean, String[]) - Method in class chemaxon.marvin.common.MDocStorage: Hydrogenize molecule in the specified cell.
hydrogenizeAll(boolean, String[]) - Method in class chemaxon.marvin.common.MDocStorage: Hydrogenize molecules in all cells.
Hydrogenizer - Class in chemaxon.core.calculations: Addition and removal of explicit hydrogens or lone pairs.
Hydrogenizer() - Constructor for class chemaxon.core.calculations.Hydrogenizer
hyperWienerIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the hyper Wiener index of the molecule.
Hz - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit: Hz unit

I

I - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element I.

icell - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay

The viewer cell index (0 for sketcher).

ICON_PATH - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

icon path of checker

ICON_PATH - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

icon path of action

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

Returns the path of the icon for the checker

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

Returns the path of the icon for the action

id - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

id - Variable in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor

id() - Method in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType

Returns the ID of this result type.

ID - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor

id property of action

ID_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction

The key of the ID parameter of the abstract action.

IDENTIFIER - Static variable in class chemaxon.naming.document.DocumentToStructure

ids - Variable in class chemaxon.descriptors.ECFP

Identifier list storage of the fingerprint

IGNORE - Enum constant in enum class chemaxon.search.mcs.RingHandlingMode

This option ignores the ring/chain topology of bonds, which is the default behavior.

IGNORE_CHARGE - Enum constant in enum class chemaxon.calculations.elemental.FormulaGenerationRule

Ignore charges in the generated molecular formula.
For example: [O-]N[O+] -> NO2

IGNORE_MASS_NUMBERS - Enum constant in enum class chemaxon.calculations.elemental.FormulaGenerationRule

The generated molecular formula will not contain isotopic information.
For example: C5[13C]H6 -> C6H6

IGNORE_REACTIVITY - Static variable in class chemaxon.reaction.Reactor

No-rule type: ignore reactivity rule.

IGNORE_SELECTIVITY - Static variable in class chemaxon.reaction.Reactor

No-rule type: ignore selectivity rule.

IGNORE_TOLERANCE - Static variable in class chemaxon.reaction.Reactor

No-rule type: ignore selectivity tolerance.

ignoreAtomCharges(Set<FormulaGenerationRule>) - Static method in enum class chemaxon.calculations.elemental.FormulaGenerationRule

Returns true if the charge of each atom should be ignored in the formula based on the given rules.

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

Identifier for parameter: "imageImportServiceURL" See Parameters and Events documentation.

IMAGE_SAVE_FORMAT - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "imageSaveFormat".

IMAGE_SAVE_URL - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "imageSaveURL".

IMAGE_SHOW_URL - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "imageShowURL".

ImageExportUtil - Class in chemaxon.marvin.util

Extends ImageExportBaseUtil with additional methods.

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

Identifier of parameter: "implicitH".

IMPLICIT_H_MATCHING_DEFAULT - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for default mode.

IMPLICIT_H_MATCHING_DISABLED - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen.

IMPLICIT_H_MATCHING_ENABLED - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for indicate matching between implicit and explicit hydrogens.

IMPLICIT_H_MATCHING_IGNORE - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching.

IMPLICITH_ALL - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Display implicit hydrogens on all atoms.

IMPLICITH_ALL_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Display implicit hydrogens on all atoms.

IMPLICITH_HETERO - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Display implicit hydrogens only on heteroatoms.

IMPLICITH_HETERO_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Display implicit hydrogens only on heteroatoms.

IMPLICITH_HETEROTERM - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Display implicit hydrogens only on hetero and terminal atoms.

IMPLICITH_HETEROTERM_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Display implicit hydrogens only on hetero and terminal atoms.

IMPLICITH_LEVELS - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Array of implicit Hydrogen visibility levels.

IMPLICITH_MASK - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Implicit hydrogen visibility mask.

IMPLICITH_OFF - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Do not display any implicit hydrogens.

IMPLICITH_OFF_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Do not display any implicit hydrogens.

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

Identifier of parameter: "importConv".

IMPORT_ENABLED - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "importEnabled".

importDoc(byte[]) - Static method in class chemaxon.formats.MolImporter

Reads a document from a byte array.

importDoc(byte[], String, String) - Static method in class chemaxon.formats.MolImporter

Reads a document from a byte array.

importMol(byte[]) - Static method in class chemaxon.formats.MolImporter

Reads a molecule from a byte array.

importMol(byte[], String, String) - Static method in class chemaxon.formats.MolImporter

Reads a molecule from a byte array.

importMol(InputStream, String, String) - Static method in class chemaxon.formats.MolImporter

Reads a molecule from an input stream.

importMol(String) - Static method in class chemaxon.formats.MolImporter

Reads a molecule from a string.

importMol(String, Object) - Static method in class chemaxon.formats.MolImporter

Deprecated.

Use MolImporter.importMol(String, String) instead and pass the options as a string (call toString() on the object). This method will be removed in a future release.

importMol(String, String) - Static method in class chemaxon.formats.MolImporter

Reads a molecule from a string.

importNodes(Document, boolean) - Method in class chemaxon.descriptors.MDParameters

Imports nodes from the specified Document into the current (main) Document.

importNodes(Document, boolean) - Method in class chemaxon.descriptors.PFParameters

In - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element In.

IN_POPUP - Static variable in class chemaxon.marvin.common.MAction

Popup menu item.

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

Increments the content of the specified hitogram bin by one.

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

Increments the histogram corresponding to two features ('fa'-'fb') and a distance, 'dist'.

inc(int, int, int, float[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

The fuzzy version of inc( int fa, int fb, int dist ).

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

The fuzzy version of inc( int fa, int fb, int dist ).

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

Increases the graph invariant change count and sets grinv to null.

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

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

Increases the graph invariant change count but does not change grinv.

INCHI - Static variable in class chemaxon.formats.MFileFormat

IUPAC InChI files.

INCHIKEY - Static variable in class chemaxon.formats.MFileFormat

IUPAC InChIKey.

INCLUDE_ALL_ATOMS - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.

INCLUDE_ALL_BONDS - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Include all bonds: covalent and coordinate bonds in bond iteration.

INCLUDE_CHEMICAL_ATOMS_ONLY - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.

INCORRECT_AROMATIC_NITROGEN_REMARK - Static variable in class chemaxon.calculations.CalculatorPlugin

Incorrect aromatic nitrogen remark.

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

Represents that incorrect/impossible arrangement of wedge bonds around chiral centers have been found in the molecule

IncorrectTetrahedralStereoChecker - Class in chemaxon.checkers

Incorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.

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

Default constructor

incQProp(String) - Method in class chemaxon.struc.MolAtom

Increments the value of a query property.

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

Increments the value of the query aromaticity property.

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

Increments the value of the valence property.

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

Calculates the index of the bin specified by the arguments.

indexOf(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

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

Searches for an object in the document or in the chemical structure that belongs to the document.

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

Gets the index of the specified atom.

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

Gets the index of the specified node in the graph union.

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

Gets the index of the specified node in the graph union.

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

Gets the atom index in the S-group graph.

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

Returns the index of the specified bond in this atom.

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

Gets the index of the specified bond.

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

Gets the index of the specified edge in the graph union.

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

Gets the index of the specified edge in the graph union.

indexOf(MolBond) - Method in class chemaxon.struc.Sgroup

Gets the bond index in the S-group graph.

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

Returns the index of the specified bond in this atom.

indexOf(Sgroup) - Method in class chemaxon.struc.Molecule

Gets the array index of an S-group.

indexOfButtonB(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane

Gets the index of the button on the visible area of the viewer.

indexOfButtonC(AbstractButton) - Method in class chemaxon.marvin.beans.MViewPane

Gets the index of the checkbox in the visible area of the viewer.

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

Returns the index of the referenced bond in this atom.

INFO - Enum constant in enum class chemaxon.checkers.CheckerSeverity

This severity level should be used for StructureChecker implementations that search for standard information in a Molecule.

init() - Method in class chemaxon.descriptors.CDParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.CFParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.ECFPParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.RFParameters

This method is called by the constructors before processing the XML configuration.

init() - Method in class chemaxon.descriptors.SDParameters

This method is called by the constructors before processing the XML configuration.

init(int) - Method in interface chemaxon.core.util.ProgressMonitor

Initializes progress monitoring.

init(MolPanel) - Method in class chemaxon.marvin.beans.MarvinPane

Initializes the content pane.

init(MolPanel, boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Initializes the content pane.

init(String, int) - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

init(String, int) - Method in interface chemaxon.core.util.ProgressMonitor

Initializes progress monitoring.

initAccelerators(JComponent) - Method in class chemaxon.marvin.common.MAction

Initializes this action's accelerator keys for the specified component.

initAccelerators(KeyStroke[], JComponent) - Method in class chemaxon.marvin.common.MAction

initAction(Action, ResourceBundle, String, KeyStroke) - Static method in class chemaxon.marvin.util.SwingUtil

Initializes an action from information in a resource.

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

Initializes the list of brackets in this S-group.

initButton(AbstractButton, ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil

Utility method to initialize a button from information in a resource.

initButton(AbstractButton, ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil

Utility method to initialize a button from information in a resource.

initEmbeddedMD() - Method in class chemaxon.descriptors.ShapeParameters

This method is called by the constructors before processing the XML configuration.

initFields() - Method in class chemaxon.marvin.common.TableOptions

Initialize field information before update.

initGenerator() - Method in class chemaxon.descriptors.CDParameters

This method is void in this class as custom descriptors are opaque, their internal structure is not known.

initGenerator() - Method in class chemaxon.descriptors.CFParameters

Initializes the fingerprint generator.

initGenerator() - Method in class chemaxon.descriptors.ECFPParameters

Initializes the fingerprint generator.

initGenerator() - Method in class chemaxon.descriptors.RFParameters

Initializes the reaction fingerprint generator.

initGenerator() - Method in class chemaxon.descriptors.ShapeParameters

INITIAL_CAPACITY - Static variable in class chemaxon.struc.MoleculeGraph

Initial capacity of the atoms and bonds vectors.

initialize() - Method in class chemaxon.checkers.ComponentChecker

Empty default implementation

initialize() - Method in class chemaxon.reaction.ConcurrentReactorProcessor

For internal use only.

initializeReader(String) - Static method in class chemaxon.standardizer.StandardizerUtil

Initializes a configuration reader based on a configuration string

initMolImport(MolInputStream) - Method in class chemaxon.formats.MolImportModule

Initializes the import module.

initMolImport(MRecord, String) - Method in class chemaxon.formats.MolImportModule

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

Should not be public. Visibility will be restricted in RemovalDate.JUL_01_2027

initParameters() - Method in class chemaxon.descriptors.BCUTParameters

initParameters() - Method in class chemaxon.descriptors.CDParameters

Initializes data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.CFParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.ECFPParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

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

Initializes object after configuration parameters are loaded.

initParameters() - Method in class chemaxon.descriptors.PFParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.RFParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initParameters() - Method in class chemaxon.descriptors.scalars.HBParameters

initParameters() - Method in class chemaxon.descriptors.scalars.LDParameters

initParameters() - Method in class chemaxon.descriptors.SDParameters

Initializes those data members that depend on the XML configuration but are not directly taken from it.

initProgressMonitor(String, int, int) - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

Create a progress monitor.

initVariables(boolean) - Method in class chemaxon.alignment.AlignmentMolecule

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

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

Inserts a string.

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

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolAtom).

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

Inserts a bond at a specified index.

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

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by MoleculeGraph.add(MolBond).

insertBond(int, MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom

insertBondInOrder(MolBond, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Insert a bond in the order specified as the second argument.

insertDocument(MTextDocument) - Method in class chemaxon.struc.graphics.MReactionSign

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

Inserts document at the current cursor position.

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

Insert nulls into the atom array.

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

Insert nulls into the atom array.

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

Insert nulls into the bond array.

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

Insert nulls into the bond array.

insertTo(Container, int, int) - Method in class chemaxon.marvin.common.MAction

Insert menu item into the specified menu.

insideLabel(double, double) - Method in class chemaxon.struc.MolAtom

Tests whether the specified point is inside the atom label.

INSTABLE_TAUTOMERIC_FORM_REMARK - Static variable in class chemaxon.calculations.CalculatorPlugin

Instable tautomeric form remark.

INSTANCE - Static variable in class chemaxon.core.util.ValenceFilter

intDescr - Variable in class chemaxon.descriptors.CustomDescriptor

storage for the integer or binary descriptors

INTEGER_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters

internalSize - Variable in class chemaxon.descriptors.MDParameters

required memory size of one descriptor instance

intValue() - Method in class chemaxon.struc.prop.MIntegerProp

Gets the integer value.

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

Represents that the molecule is marked with invalid "absolute stereo" flag

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

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

StructureCheckerErrorType.INVALID_COORDINATION_SYSTEM is used instead

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

Represents that invalid coordination systems have been found in the molecule

INVALID_LINKNODE_MESSAGE - Static variable in class chemaxon.struc.MoleculeGraph

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

Represents that invalid reaction mapping has been found in the molecule

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

Represents that invalid R-groups have been found in the molecule

InvalidChecker - Class in chemaxon.checkers

An extremal checker implementation indicating error in the configuration imported from XML or action string

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

Initializes an invalid structure checker instance

InvalidStandardizerAction - Class in chemaxon.standardizer.actions

Implementation of StandardizerAction representing an invalid instance of a standardizer action.

InvalidStandardizerAction(String) - Constructor for class chemaxon.standardizer.actions.InvalidStandardizerAction

Initializes an invalid standardizer instance

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

Initializes an invalid standardizer instance

invert() - Method in class chemaxon.struc.Transform3D

Inverts the matrix.

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

invokeAndWait(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil

Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object, blocks until it is finished and returns the result (calling FutureTask.get()).

invokeLater(Callable<T>) - Static method in class chemaxon.marvin.util.SwingUtil

Calls SwingUtilities.invokeLater() for a Callable by wrapping it into a FutureTask object.

ionChargeOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the ion charge.

IonChargePlugin - Class in chemaxon.calculations

Plugin class for charge calculation on ionized microspecies.

IonChargePlugin() - Constructor for class chemaxon.calculations.IonChargePlugin

Constructor.

Ir - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Ir.

is3d() - Method in class chemaxon.struc.Transform3D

Tests whether the transformation is 3D.

isAbsoluteLabelsVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Is 'Absolute' label visible?.

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

Gets whether the placement of this attached data is absolute or relative to the objects it is attached.

isAbsStereo() - Method in class chemaxon.calculations.stereo.StereoAnalysis

Gets the absolute stereoconfiguration flag.

isAbsStereo() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Gets the absolute value of the action

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

Gets the absolute stereoconfiguration flag.

isAcceptableGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.MultipleSgroup

Decides whether the given molecule graph can be the graph of a multiple s-group.

isAcceptablePolymerGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Checks if the given molecular graph can be the graph of a polymer SRU

isAcceptableRSRUGraph(MoleculeGraph) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Checks if the given molecular graph can be the graph of an RSRU

isAcceptableSru(String) - Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

isAcceptedOptionName(String) - Static method in class chemaxon.search.hitdisplay.HitDisplayOptions

Checks if the given option name can be a hit coloring and alignment option.

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

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

isAcceptor(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isActinideMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is an actinide metal Actinium is included.

isActive() - Method in class chemaxon.standardizer.AbstractStandardizerAction

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

isActive() - Method in interface chemaxon.standardizer.StandardizerAction

Returns true if the action is active, and can be used

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

Gets wether the useres uses advanced save or not.

isAliphaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Returns true if aliphatic atom.

isAliphaticAtom(int) - Method in class chemaxon.core.calculations.Ring

Determines if an atom is not a member of an aromatic ring.

isAliphaticRC(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isAliphaticRingCenter(int) - Static method in class chemaxon.alignment.NodeColor

Determines if the given type is an aliphatic ring center.

isAlkaliMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is an alkali (group I.) metal.

isAlkalineEarthMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is an alkaline earth (group II.) metal.

isAllowTraditionalNitrogen() - Method in class chemaxon.checkers.ValenceErrorChecker

Gets whether the checker allows traditional N representation

isAllowValenceError() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Gets whether replace should be applied even in case of invalid valence in the result

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

Check if the atom has ambiguous stereo wedge configuration.

isAminoAcid() - Method in class chemaxon.standardizer.actions.GroupDefinition

Gets whether the group represents an amino-acid

isAminoAcidBondColoringEnabled() - Method in class chemaxon.marvin.beans.MolPrinter

Is peptide bridge coloring enabled?

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

Gets wether the user uses peptide bridge coloring or not.

isAnchor(int) - Method in class chemaxon.alignment.NodeColor

Determines if the given type is an anchor type based on the coloring scheme.

isAnchor(int) - Static method in class chemaxon.alignment.Pharmacophore3D

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

Selected cell is animated or not.

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

Gets the animation synchronization.

isAnnotationSupported() - Method in class chemaxon.naming.document.DocumentAnnotator

Checks whether annotation is supported for the current document type.

isApproximateCount() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Returns true if count is approximate due to multiple position bonds with multicenters of variable size, false otherwise.

isAromatic(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isAromaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Returns true if aromatic atom.

isAromaticAtom(int) - Method in class chemaxon.core.calculations.Ring

Determines if an atom is a member of an aromatic ring.

isAromaticBond(int) - Method in class chemaxon.core.calculations.Ring

Determines if a bond is a member of an aromatic ring.

isAromaticityChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects aromaticity atom query properties or not.

isAromaticRC(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isAromaticRingCenter(int) - Static method in class chemaxon.alignment.NodeColor

Determines if the given type is an aromatic ring center.

isAromaticSMILESSubset(int) - Static method in class chemaxon.struc.MolAtom

Is the atom can be aromatic according to the daylight specification: Only atoms on the following list can be considered aromatic: C, N, O, P, S, As, Se, and * (wildcard).

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

Checks if it is an arrow.

isAssociatedWith(Molecule) - Method in class chemaxon.struc.NoStructure

Verifies the reference equality of molecule and the component associated with this instance.

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

Returns whether current parametrized metric is asymmetric or not.

isAsymmetricAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Returns true if asymmetric atom.

isAtom(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets whether the arrow's terminus is at an atom.

isAtomicSymbol(String) - Static method in class chemaxon.struc.PeriodicTable

Returns whether the given string corresponds to an atomic number of an element in the periodic table specified by its symbol.

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

Checks whether the atom is in ring.

isAtomMapMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether atom map numbers are considered in search.

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

Determines the visibility of the atom mapping.

isAtomMappingVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Returns true if atom mapping is visible.

isAtomPropertiesVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Get the atom properties visibility

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

Tells wheter the atom properties are visible or not if exist.

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

Decides whether the atomset coloring mode is set.

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

Tests the visibility of the atom symbols in 3D.

isAtomSymbolsVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the atom symbol visibility of 3D mode.

isAtomTypeMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether atom types are considered in search.

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

Checks whether the given atom is an attachment atom or not.

isAutoAlign() - Method in class chemaxon.struc.graphics.MNameTextBox

Returns if the text-box is in automatic alignment mode.

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

Tells whether the automatic structure checking is enabled or not

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

Gets if it is autoHeight.

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

Gets the state of automatic fog calculation mode.

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

Gets the state of automatic reaction calculation mode.

isAutoResize() - Method in class chemaxon.struc.graphics.MNameTextBox

Returns if the text-box is in automatic resize mode.

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

isAvailable() - Method in class chemaxon.calculations.services.ServiceDescriptor

Returns true if service is available.

isAvailable() - Method in class chemaxon.checkers.AbstractStructureChecker

isAvailable() - Method in class chemaxon.checkers.InvalidChecker

isAvailable() - Method in interface chemaxon.checkers.StructureChecker

Returns true if the checker is available, and can be used

isAvailable() - Method in class chemaxon.checkers.SubstructureChecker

isAvailable() - Method in class chemaxon.standardizer.AbstractStandardizerAction

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

isAvailable() - Method in interface chemaxon.standardizer.StandardizerAction

Returns true if the action is available, and can be used

isBarredAtom(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Determines if an atom is is part of a certain functional group with high rotational barrier (amides, thioamides, sulphonamides).

isBold() - Method in class chemaxon.struc.graphics.MFont

Tests whether the font is bold.

isBold() - Method in class chemaxon.struc.MolBond

Decides whether this bond is bold or not.

isBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets whether the arrow's terminus is at a bond.

isBondDraggedAlong() - Method in class chemaxon.marvin.beans.MSketchPane

Is the currently used bond shown at the mouse cursor?

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

Is the currently used bond shown at the mouse cursor?

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

Gets the bond length display option.

isBondLengthVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Return whether the bond length is visible or not.

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

Checks if there is a bond parallel (having the same endpoints) with the given bond in this MoleculeGraph.

isBondTypeMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether bond types are considered in search.

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

Checks if this MolAtom is connected to another one or not.

isBracketCrossingBond(MolBond) - Method in class chemaxon.struc.Sgroup

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

Tests whether the bracket is visible.

isBracketVisible() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Tests whether the bracket is visible.

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

Tests whether the bracket is visible.

isBridgehead() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing bridgehead H

isBridgingRAllowed() - Method in class chemaxon.search.api.options.SearchOptions

Returns true if different undefined R-atoms can match the same group of atoms.

isCanceled() - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

Tests whether the user canceled the dialog.

isCanceled() - Method in interface chemaxon.core.util.ProgressMonitor

Tests whether the user canceled the progress.

isCancelled() - Method in class chemaxon.calculations.api.ProgressableCalculator

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

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

Gets boolean telling whether cell weights are to be generated for current parametrized metric.

isChainAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Returns true if chain atom.

isChainAtom(int) - Method in class chemaxon.core.calculations.Ring

Determines if an atom a ring bond or a chain bond.

isChainBond(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Determines if a bond is a ring bond or a chain bond.

isChainBond(int) - Method in class chemaxon.core.calculations.Ring

Determines if a bond is a ring bond or a chain bond.

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

Returns true if the charge angle is specified explicitly for the atom.

isChargeCalc() - Method in class chemaxon.calculations.IsoelectricPointPlugin

Returns true if pH-Charge calculation.

isCharged() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing charged H

isChargeMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether formal charges are considered in search.

isChargeWithCircle() - Method in class chemaxon.marvin.beans.MolPrinter

Get the visibility of Charge with Circle

isChecking() - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

isChecking() - Method in interface chemaxon.structurechecker.CheckerRunner

This function identifies the state of the checker thread

isChemicalFpType(String) - Static method in class chemaxon.descriptors.ChemicalFingerprint

Checks whether the given descriptor type name is considered as Chemical Fingerprint (e.g.

isChildOf(MObject) - Method in class chemaxon.struc.graphics.MMidPoint

Is this object a children of another one?

isChildOf(MObject) - Method in class chemaxon.struc.graphics.MRectanglePoint

Is this object a children of another one?

isChildOf(MObject) - Method in class chemaxon.struc.MObject

Is this object a children of another one?

isChildOf(MObject) - Method in class chemaxon.struc.MPoint

Is this object a children of another one?

isChiral() - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Determines if the molecule contains an atom with R or S stereo configuration.

isChiralCenter(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Determines if an atom can be a tetrahedral stereogenic center.

isChirality() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the chirality value of absolute stereo action

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

Tests whether cleaning is meaningful for the chosen output format.

isCleanable() - Method in class chemaxon.formats.MolExportModule

Tests whether 2D or 3D cleaning is meaningful for this output format.

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

Returns true if the H option for cleaning is enabled.

isCleanNeeded() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Returns true if clean is needed for GUI display.

isCloseEnabled() - Method in class chemaxon.marvin.beans.MSketchPane

Determines if the File->Close menu item is enabled or not.

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

Returns whether atom is collinear with the bond or not.

isCollinear(Point3D, Point3D, Point3D) - Static method in class chemaxon.struc.Point3D

Checks whether three 3D points can be connected with a line.

isColoringEnabled() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Specifies if substructure hit coloring should be used.

isCompatible(MTextAttributes, MTextAttributes, MFont) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether two attribute sets are compatible.

isConfirmExit() - Method in class chemaxon.marvin.beans.MSketchPane

Gets whether the confirmation dialog will be appear or not by exit.

isConjugated() - Method in class chemaxon.struc.MolBond

Gets the conjugation state of the bond set by the conjugation modul.

isConnected() - Method in class chemaxon.core.calculations.TopologyAnalyzer

Determines if the molecule is a connected graph or not.

isConnected(int, int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Returns true if two atoms are in the same connected component, false for atoms of disconnected structures.

isConnected(int, int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Determines if two atoms are members of a connected graph or not.

isConnectedGraph() - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Determines if the molecule is a connected graph or not.

isConnectedMode() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether the common substructures should be connected or they can consist of multiple fragments.

isConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects connection count atom query properties or not.

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

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

isContracted() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Is this S-group contracted?

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

Decides whether this S-group is contracted or not.

isCoordDependent() - Method in class chemaxon.struc.MProp

Tests whether the property depends on the molecular coordinates.

isCoordinate() - Method in class chemaxon.struc.MolBond

Tests whether the bond is coordinate.

isCopolymerMatching() - Method in class chemaxon.search.api.options.SearchOptions

Specifies whether matching mode is copolymer.

isCopyAsTransferable() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor

Determines whether the MTransferable is appearing as an option in the Copy As dialog.

isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionChecker

This method determines if a component of the reaction correct or not.

isCorrect(StructureCheckerResult) - Method in class chemaxon.checkers.ReactionMapErrorChecker

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

Tells whether the spectrum is coupled.

isCoupled() - Method in class chemaxon.calculations.nmr.NMRCalculator

Coupled/decoupled spectrum.

isCouplingNeeded() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns whether spin-spin couplings are taken into account.

isCreateRingCenters() - Method in class chemaxon.alignment.AlignmentMoleculeFactory

isCrossingBond(MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether the bond is a crossing bond in a ladder-type polymer bracket.

isCumulatedDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectCummulatedDoubleBonds

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

Gets whether the data should be displayed close to the objects or separately (detached).

isDataFlavorSupported(DataFlavor) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable

Checks whether the MarvinTransferable.flavor equals with the given parameter.

isDefault() - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether all attributes have default values.

isDefaultSelected() - Method in class chemaxon.formats.OptionDescriptor

Tests whether the option is selected by default.

isDefaultTransferable() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor

Determines whether the MTransferable instance should be used by the default copy operation.

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

Decides whether this is a descendant of another S-group.

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

Gets the detachable property.

isDetectCumulatedDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectCummulatedDoubleBonds

isDetectTransDoubleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTransDoubleBonds

isDetectTripleBonds() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTripleBonds

isDialogVisible() - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

Tests whether the dialog is visible.

isDirty() - Method in class chemaxon.search.api.options.SearchOptions

Returns the dirty flag.

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

isDisplayLabelsAndBoxes() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Gets whether bounding boxes and labels are to be displayed for the components of the search.

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

isDistancerangeSet() - Method in enum class chemaxon.alignment.AlignmentProperties

isDistinctFirstAtomMatching() - Method in class chemaxon.search.api.options.MolSearchOptions

Get option ensuring that upon the findNext() call the first atom must be stepped as well.

isDndTransferable() - Method in class chemaxon.marvin.datatransfer.TransferableDescriptor

isDocumentExport() - Method in class chemaxon.formats.MolExportModule

Tests if this export module is document export instead of a simple molecule export.

isDocumentImporter() - Method in class chemaxon.formats.MolImportModule

Tests whether this module is a document importer or not.

isDonor(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isDontRemoveLastComponent() - Method in class chemaxon.standardizer.actions.StripSaltsAction

isDoubleBond() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the double bond value of absolute stereo action

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

Determines whether mouse dragged evens are allowed or not.

isEcfpType(String) - Static method in class chemaxon.descriptors.ECFP

Checks whether the given descriptor type name is considered as ECFP Fingerprint (e.g.

isEditable() - Method in class chemaxon.standardizer.actions.TransformAction

Returns if this action is editable.

isEditable() - Method in class chemaxon.struc.graphics.MAnalysisBox

isEditable() - Method in class chemaxon.struc.graphics.MNameTextBox

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

Determines if this text box's content can be edited by the user.

isEmpty() - Method in class chemaxon.chemterms.ReactionContext

Returns true if the context is empty.

isEmpty() - Method in class chemaxon.search.mcs.McsSearchResult

Checks whether the common substructure contains any bonds or is empty.

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

Gets whether the configuration contains actions

isEmpty() - Method in class chemaxon.struc.graphics.MChemicalStruct

A chemical structure object is empty if the molecule graph is empty.

isEmpty() - Method in class chemaxon.struc.graphics.MMoleculeMovie

A chemical structure object is empty if the molecule graph is empty.

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

A polyline becomes empty if it has less than 2 points.

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

A text box is empty if the string contains only whitespace.

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

Tests whether the document is empty: the main molecule object in the document is empty no graphic object is included (neither simple nor extra)

isEmpty() - Method in class chemaxon.struc.MObject

An object may become empty if all the children are removed.

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

Tests whether the molecule is empty.

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

Tests whether the molecule graph is empty.

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

Ask if the molecule is empty or not.

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

Ask if the reaction is empty or not.

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

Is it an empty S-group?

isEnabled() - Method in class chemaxon.struc.PageSettings

isEnabledT(int, int) - Method in class chemaxon.marvin.common.MDocStorage

Tests whether a text field is enabled.

isEnableGenericTautomerInSSS() - Method in enum class chemaxon.search.api.options.TautomerSubstructureMode

isEnableTranslateAndRotate() - Method in class chemaxon.alignment.AlignmentMolecule

isEndgroupMatching() - Method in class chemaxon.search.api.options.SearchOptions

Get whether polymers end groups must match.

isEndReached() - Method in class chemaxon.calculations.CalculatorPluginMDocSource

Tests whether the end of input is already reached.

isEndReached() - Method in class chemaxon.formats.MDocSource

Tests whether the end of input is already reached.

isEndReached() - Method in class chemaxon.formats.MolImporter

Tests whether the end of input is already reached.

isEndReached() - Method in exception class chemaxon.marvin.common.MDocStorage.RecordUnavailableException

Tests whether the end of storage is reached.

isEnforceAbsStereo() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

isEnumerationNeeded() - Method in enum class chemaxon.search.api.options.TautomerTransformationMode

isExact() - Method in class chemaxon.standardizer.actions.TransformAction

Gets the exact value of the action

isExactBondMatching() - Method in class chemaxon.search.api.options.SearchOptions

Indicates whether bond types should match exactly - looking for query bonds target.

isExactBondMatchingAlwaysOn() - Method in enum class chemaxon.search.api.options.TautomerTransformationMode

isExactQueryAtomMatching() - Method in class chemaxon.search.api.options.SearchOptions

Returns whether exact matching of query atom information is set.

isExactQueryAtomMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether query atoms are matched only to query atoms of exactly the same type.

isExactQueryBondMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether query bonds are matched only to query bonds of exactly the same type.

isExcludedAtom(MolAtom) - Method in class chemaxon.struc.IteratorFactory

Deprecated.

By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more atoms, than it would normally.

isExcludedBond(MolBond) - Method in class chemaxon.struc.IteratorFactory

Deprecated.

By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to exclude more bonds, than it would normally.

isExclusionRegexp() - Method in class chemaxon.checkers.AttachedDataChecker

Tells how to interpret the exclusion list: a comma separated list or a regular expression.

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

Check whether exiting is allowed or not.

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

Tests if the molecule is expandable with the specified options.

isExpanded() - Method in interface chemaxon.struc.sgroup.Expandable

Is this S-group expanded?

isExpanded() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Is this S-group expanded?

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

Is this S-group expanded?

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

Tests whether experimental features are enabled.

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

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

Not supported anymore

isExplicitConnectionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects explicit connection count atom query properties or not.

isExplicitizedHydrogen() - Method in class chemaxon.reaction.AtomIdentifier

Gets whether the identifier represents an explicit H atom, that was implicit H atom in the input molecule, and was explicitized during the reaction, because it matched an explicit H atom in the reaction schema.

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

Decides whether a graphic object belongs to the main chemical structure of the document.

isEZLabelsVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the visibility state of absolute double bond stereo configuration labels.

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

Gets the E/Z display option.

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

Are E/Z labels visible?

isFallBackToBasic() - Method in class chemaxon.structurechecker.AdvancedCheckerRunner

Returns true if runner should fall back to basic runner when preferred fix failed.

isFiltered() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Return true if molecule filter is set.

isFixed(int) - Method in class chemaxon.marvin.common.MDocStorage

Tests whether a record is fixed.

isFlagSet(long) - Method in class chemaxon.formats.MFileFormat

Checks whether the format has a given (set of) flag(s) set.

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

Decides whether this S-group is flipped.

isFontDefault(MFont) - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether the default font is used.

isFontRegular() - Method in class chemaxon.struc.graphics.MTextAttributes

Tests whether the default font is used.

isFractionQuicklyAvailable(double) - Method in class chemaxon.marvin.common.MDocStorage

Tests whether the specified fraction of the total (estimated) number of records is quickly available.

isFree() - Method in class chemaxon.struc.sgroup.AttachmentPoint

Decides whether the attachment point is free or not.

isFree(int) - Method in class chemaxon.struc.graphics.MElectronContainer

True if MElectron referenced by the index is not occupied.

isFree(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

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

Checks whether the specified atom has free attachment point.

isFuzzyFingerprint() - Method in class chemaxon.descriptors.PFParameters

Gets whether the fuzzy fingerprints are used or not.

isGaussianSmoothing() - Method in class chemaxon.descriptors.PFParameters

Gets if fuzzy smmoothing is based on normal distribution.

isGenerateDistanceRanges() - Method in class chemaxon.alignment.AlignmentMoleculeFactory

isGenerateMinorProducts() - Method in class chemaxon.reaction.Reactor

Returns true if minor products are generated.

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

Tests whether the atom is a generic atom.

isGenNameShown() - Method in class chemaxon.marvin.common.TableOptions

Are IUPAC names shown in the table?

isGraphInvariantVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Return whether the graph invariant is visible or not.

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

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

Tests whether the graph invariant change count is valid.

isGrinvCCValid() - Method in class chemaxon.struc.SelectionMolecule

Tests whether the graph invariant change count is valid.

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

Gets the visibility of the graph invariants.

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

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

as of Marvin 6.2 replaced by Molecule.hasContractedSgroup()

isH(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isHalogen(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is a halogen (F, Cl, Br, I, At, Ts).

isHashed() - Method in class chemaxon.struc.MolBond

Decides whether this bond is hashed or not.

isHconnected() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing H connected H

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

Tests whether the property list contains subcollections like MListProp and MHashProp.

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

Is the specified object currently highlighted?

isHinderedBiarylBridgeBond(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Determines if a bond bridges two aryl systems having more than two ortho substituents.

isHomologyEnumerated() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Indicates if homology groups are enumerated or not.

isHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects hydrogen count atom query properties or not.

isHydrophobic(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isIdentity() - Method in class chemaxon.struc.Transform3D

isIgnoreAxialStereo() - Method in class chemaxon.search.api.options.SearchOptions

Retrieves if axial stereo is ignored during searching.

isIgnoreCumuleneOrRingCisTransStereo() - Method in class chemaxon.search.api.options.SearchOptions

Retrieves if cumulene cis-trans stereo is ignored during searching.

isIgnoreDoubleBondStereo() - Method in class chemaxon.search.api.options.SearchOptions

Retrieves if double bond stereo is ignored during searching.

isIgnoreSynAntiStereo() - Method in class chemaxon.search.api.options.SearchOptions

Retrieves if syn-anti stereo is ignored during searching.

isIgnoreTetrahedralStereo() - Method in class chemaxon.search.api.options.SearchOptions

Retrieves if tetrahedral stereo is ignored during searching.

isImplicitHcountImportant(MolAtom) - Static method in class chemaxon.formats.MolExportModule

Checks whether the number of implicit hydrogens is important information for an atom or not.

isImplicitHcountImportant(MoleculeGraph) - Method in class chemaxon.formats.MolExportModule

Checks whether the number of implicit hydrogens is important information for the atoms of mol or not.

isImplicitHydrogenCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects implicit hydrogen count atom query properties or not.

isImplicitHydrogenMode() - Method in class chemaxon.calculations.nmr.NMRSpectrum

Returns implicit hydrogen mode.

isImplicitizableH(int) - Method in class chemaxon.struc.MolAtom

Tests whether the hydrogen atom is implicitizable or not.

isIn3D() - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Returns true if structures are returned in 3D.

isIncipBond(Object) - Static method in class chemaxon.struc.graphics.MEFlow

Gets whether the arrow's sink is at an incipient bond.

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

Check whether the reaction is incomplete or not.

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

Check whether the reaction is incomplete or not.

isInputAvailable() - Method in class chemaxon.marvin.datatransfer.MarvinTransferable

Checks that the implementation supports input from clipboard.

isInputAvailable() - Method in interface chemaxon.marvin.datatransfer.MTransferable

Checks that the implementation supports input from clipboard.

isInputMoleculeAromatized() - Method in class chemaxon.calculations.CalculatorPlugin

Returns true if the input molecule has aromatic bond.

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

isInternalSelectable() - Method in class chemaxon.struc.MObject

Is it a selection only internal object?

isInternalSelectable() - Method in class chemaxon.struc.MPoint

Is it a selection only internal object?

isIsotopeMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether isotopes are considered in search.

isIsotopic() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing isotopic H

isItalic() - Method in class chemaxon.struc.graphics.MFont

Tests whether the font is italic.

isKeepMapping() - Method in class chemaxon.reaction.mapper.AutoMapper

Returns if the mapper will keep the initial mapping or not.

isKeepMapping() - Method in class chemaxon.reaction.mapper.AutoMapper.Options

isKeepMapping() - Method in class chemaxon.standardizer.actions.MapAction

Returns if underlying mapper keeps existing maps should be kept when mapping.

isKeepMapping() - Method in class chemaxon.standardizer.actions.MapReactionAction

Returns if underlying mapper keeps existing maps should be kept when mapping.

isKeepQueryOrder() - Method in class chemaxon.search.api.options.SearchOptions

Get options for rearranging query atoms for better search performance.

isLanthanideMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is a lanthanide metal Lanthanum is included.

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

Returns true if large molecule (number of atoms exceeds 1000).

isLastLine() - Method in class chemaxon.formats.Recognizer

Tests whether it is the last line of file.

isLicensed() - Method in class chemaxon.alignment.AlignmentBase

isLicensed() - Method in class chemaxon.alignment.AlignRigidEasy

isLicensed() - Method in class chemaxon.alignment.AtropIsomerDetector

isLicensed() - Method in class chemaxon.calculations.api.ProgressableCalculator

isLicensed() - Method in class chemaxon.calculations.CalculatorPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.calculations.ChargePlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.calculations.HBDAPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.calculations.HuckelAnalysisPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

isLicensed() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

isLicensed() - Method in class chemaxon.calculations.MSAPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.calculations.PolarizabilityPlugin

Returns true if the plugin is licensed.

isLicensed() - Method in class chemaxon.checkers.AbstractStructureChecker

isLicensed() - Method in class chemaxon.core.calculations.Ring

This method is for internal use only.

isLicensed() - Method in class chemaxon.core.calculations.TopologyAnalyzer

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

Returns information about the licensing of the product.

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

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.descriptors.ECFPGenerator

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.descriptors.pharmacophore.PMapper

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

Returns information about the licensing of the product.

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

isLicensed() - Method in interface chemaxon.license.api.Licensable

Checks if the required license is available for using this class or product.

isLicensed() - Method in class chemaxon.reaction.Reactor

isLicensed() - Method in class chemaxon.search.hitdisplay.HitDisplayTool

isLicensed() - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Returns information about the licensing of the product.

isLicensed() - Method in class chemaxon.search.MolSearch

isLicensed() - Method in class chemaxon.search.RgroupDecomposition

isLicensed() - Method in class chemaxon.standardizer.AbstractStandardizerAction

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

Gets whether the standardizer is licensed

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

Returns true if this action can be used in current license environment.

isLigandErrorVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Gets the bond's ligand error visibility

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

Tells wheter the bond's ligand error is visible or not.

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

The atom is a link node if the maximum number of repetitions is nonzero.

isLoadedMolModified() - Method in class chemaxon.marvin.beans.MSketchPane

Determines whether the original molecule that is loaded in is modified or not.

isLocalAromatic() - Method in class chemaxon.struc.ValenceCheckOptions

Do not calculate valence for ambiguous aromatic atoms behaving like aromatic Nitrogens (e.g.

isLonely() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing lonely H

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

isLonePairAsLine() - Method in class chemaxon.marvin.beans.MolPrinter

Get the visibility of Lone Pairs: dots/line

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

Returns the state of the automatic lone pair calculation.

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

isLonePairsAutoCalculated() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the state of the automatic calculation of lone pairs.

isLonePairsVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the visibility state of lone pairs.

isLP(int) - Static method in class chemaxon.alignment.Pharmacophore3D

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

Checks if this atom it a mappable.

isMapped() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing mapped H

isMarkBonds() - Method in class chemaxon.reaction.mapper.AutoMapper

Returns if the mapper marks the reaction center bonds or not.

isMarkBonds() - Method in class chemaxon.reaction.mapper.AutoMapper.Options

isMarkBonds() - Method in class chemaxon.standardizer.actions.MapAction

Returns if bonds are marked while mapping.

isMarkBonds() - Method in class chemaxon.standardizer.actions.MapReactionAction

Returns if bonds are marked while mapping.

isMarkush() - Method in enum class chemaxon.search.api.options.TautomerTransformationMode

isMarkushEnabled() - Method in class chemaxon.search.api.options.MolSearchOptions

Specifies whether a target containing Markush features should be treated as a Markush library.

isMarkushQuery() - Method in class chemaxon.search.RgroupDecomposition

Returns true if query contains Markush features which will be enumerated (all features except defined R-rgroups and homologies).

isMatchCountBetween(int, boolean, int, boolean) - Method in class chemaxon.search.AbstractSearch

Decides questions like "does the query match the target between 2 and 5 times (inclusively)" Makes this efficiently, which means it only searches for the number of hits necessary to decide the question.

isMatchCountInRelation(String, int) - Method in class chemaxon.search.AbstractSearch

Decides questions like "does the query match the target at least 3 times", "[] up to 5 times", "[] exactly once".

isMatching() - Method in class chemaxon.search.AbstractSearch

Checks if the query structure matches the target structure with respect to the search options.

isMatching() - Method in class chemaxon.search.FormulaSearch

Checks if the query formula matches the target formula according to the formula search type.

isMatching() - Method in class chemaxon.search.MolSearch

isMergedComponent(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Check whether given molecule is reaction component with a set of intentionally merged fragments or not.

isMetadataMol(Molecule) - Static method in class chemaxon.naming.document.DocumentToStructure

isMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Decides whether the element is a metal.

isMetalconnected() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing metal connected H

isMetalloid(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is a metalloid (B, Si, Ge, As, Sb, Te, Po).

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

Gets if it is minimumHeightSet.

isMixSgroupMatching() - Method in class chemaxon.search.api.options.SearchOptions

Get option whether search should consider consider COM, MIX and FOR sgroups during search.

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

Gets whether any modifications were applied on the molecule.

isModified() - Method in class chemaxon.struc.sgroup.AminoAcidSgroup

Checks whether the amino acid is modified or not.

isMolecular() - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Returns true if molecule output.

isMolMovie() - Method in class chemaxon.formats.MolImporter

Are the imported molecules merged into one multi-set molecule?

isMolNameShown() - Method in class chemaxon.marvin.common.TableOptions

Are molecule names shown in the table?

isMPLabelsVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the visibility state of M/P labels.

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

Gets the M/P display option.

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

isMsCalc() - Method in class chemaxon.calculations.CalculatorPlugin

Returns true if microspecies calculation.

isMsCalc() - Method in class chemaxon.calculations.HBDAPlugin

Returns true if microspecies calculation.

isMsCalc() - Method in class chemaxon.calculations.PkaPlugin

Returns true if microspecies calculation.

isMSpaceDisplayLabelOnlyOnHeavyAtoms() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Returns if mspace should display label only on heavy atoms.

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

Returns the multiple chirality flag.

isMultiPageEnabled() - Method in class chemaxon.struc.PageSettings

isMultipleDisplay() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Returns true if results for more molecules can be displayed in a single component, false if each molecule should be displayed in a separate component.

isMultiSet() - Method in class chemaxon.formats.MolImporter

Are the imported molecules merged into one multi-set molecule?

isMultiThreadedRunEnabled() - Method in class chemaxon.calculations.CalculatorPlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.calculations.GeometryPlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.calculations.MSAPlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.calculations.ResonancePlugin

For internal use only.

isMultiThreadedRunEnabled() - Method in class chemaxon.calculations.TautomerPlugin

For internal use only.

isNameShown() - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm

Returns whether the title of this term is shown in the analysis box.

isNegative(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isNegligible(double[]) - Method in class chemaxon.calculations.PkaPlugin

isNegligibleResult(Object, int, Object) - Method in class chemaxon.calculations.CalculatorPlugin

Returns whether the result can be ignored.

isNegligibleResult(Object, int, Object) - Method in class chemaxon.calculations.HBDAPlugin

Returns whether the result can be ignored.

isNegligibleResult(Object, int, Object) - Method in class chemaxon.calculations.PkaPlugin

Returns whether the result can be ignored.

isNobleGas(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is a noble gas.

isNonAromaticCovalentBond() - Method in enum class chemaxon.struc.BondType

Determines whether this bond is a non-aromatic covalent bond.

isNonAssociated() - Method in class chemaxon.struc.NoStructure

isNonPreferredStereoAtom(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Check if the atoms in the molecule is in SP2 hybridization state and has wedge whose getAtom1 is the specified atom, but wiggly bonds next to double bonds are allowed.

isNormal() - Method in enum class chemaxon.search.api.options.TautomerSubstructureMode

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

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

Returns whether current parametrized metric is normalized or not.

isOccupied(int) - Method in class chemaxon.struc.graphics.MElectronContainer

True if the MElectron referenced by the index is occupied.

isOccupied(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

ISOELECTRICPOINT - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

IsoelectricPointPlugin - Class in chemaxon.calculations

Plugin class for isoelectric point and pH - charge distribution calculation.

IsoelectricPointPlugin() - Constructor for class chemaxon.calculations.IsoelectricPointPlugin

Constructor.

isOK() - Method in class chemaxon.calculations.CalculatorPlugin

Returns true if no calculation error, false on error.

isOK() - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Returns true if the calculation has run without error.

isOK() - Method in interface chemaxon.calculations.output.CalculatorPluginOutputAccess

Returns true if the calculation has run without error.

isOkActionEnabled() - Method in interface chemaxon.calculations.gui.ParameterPanelHandler

Returns true if "OK" button is enabled.

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

Isolates atom: a more efficient way of removing an atom than MoleculeGraph.removeAtom(chemaxon.struc.MolAtom), especially for large molecule graphs.

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

Isolates bond: a more efficient way of removing a bond than MoleculeGraph.removeBond(chemaxon.struc.MolBond), especially for large molecule graphs.

isOneLetterPeptideDisplay() - Method in class chemaxon.marvin.beans.MolPrinter

Decides whether the Peptide display settings set to one letter.

isOnlyExpanded() - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

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

Get how the parity module interprets wedges.

isOptionsPaneLoaded(int) - Method in class chemaxon.calculations.gui.PluginFactory

Returns true is options pane is loaded for plugin, false otherwise.

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

Returns if the Sgroup is ordered component Sgroup.

isOrderSensitiveSearch() - Method in class chemaxon.search.api.options.SearchOptions

Indicates whether the search is order sensitive

isOrderSensitiveSearch() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether search is sensitive to the order of the matched atoms and bonds when searching for multiple hits.

isOrigTargetMayBeMarkush - Variable in class chemaxon.search.MolSearch

For internal use only.

isOrphanAtom() - Method in class chemaxon.reaction.AtomIdentifier

Gets whether the identifier represents an orphan atom.

isOtherMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is an "other metal", group IIIa-Va metal.

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

Represents that isotope atoms have been found in the molecule

ISOTOPE_2H3H - Enum constant in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

2H/3H isotope symbol

ISOTOPE_COMPOSITION - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType

Result type with the string id "isotopecomposition".

ISOTOPE_DT - Enum constant in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type

D/T isotope symbol

ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType

Result type with the string id "isotopeformalchargeformula".

ISOTOPE_FORMULA - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType

Result type with the string id "isotopeformula".

ISOTOPE_H - Static variable in class chemaxon.struc.MolAtom

Include Hydrogen isotope(s).

ISOTOPE_MATCHING_DEFAULT - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).

ISOTOPE_MATCHING_EXACT - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).

ISOTOPE_MATCHING_IGNORE - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for ignore isotope searching (isotope information is ignored during searching).

IsotopeChecker - Class in chemaxon.checkers

IsotopeChecker detects isotopes (non-elemental atoms).

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

Default constructor

isotopeComposition(int) - Method in class chemaxon.core.calculations.ElementalAnalyzer

Gets the molecular composition (w/w%).

isotopeComposition(int, boolean) - Method in class chemaxon.core.calculations.ElementalAnalyzer

Gets the molecular composition (w/w%).

isotopeDistribution() - Method in class chemaxon.calculations.elemental.ElementalAnalysis

Calculates the isotopic distributions for the molecule.

isotopeFormula() - Method in class chemaxon.core.calculations.ElementalAnalyzer

Calculates the molecular formula (isotopes are separated).

isotopeFormula(boolean) - Method in class chemaxon.core.calculations.ElementalAnalyzer

Calculates the molecular formula (isotopes are separated).

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

Sets whether isotopes of atoms should be considered in search.

isotopeType(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the type of an isotope.

isOuterAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether an atom is part of this repeating unit.

isOutputCleanable(String) - Static method in class chemaxon.formats.MFileFormatUtil

Tests whether the specified output format is cleanable.

isOverflowCalculation() - Method in class chemaxon.calculations.PkaPlugin

Returns true if overflow calculation: maximum number of ionizable atoms exceeded and protein ionization invoked.

isPartSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup

Decides if part of the S-group is selected or not.

isPassed() - Method in enum class chemaxon.common.annotations.RemovalDate

isPharmacophoreFpType(String) - Static method in class chemaxon.descriptors.PharmacophoreFingerprint

Checks whether the given descriptor type name is considered as Pharmacophore fingerprint (e.g.

isPhaseShiftedMatching() - Method in class chemaxon.search.api.options.SearchOptions

Get option whether phase shifted polymer matches on the original.

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

Returns true if the atom is plain Hydrogen (H or 1H).

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

isPolymerendgroup() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing polymer end group H

isPolymerMatching() - Method in class chemaxon.search.api.options.SearchOptions

Get option whether to search consider polymer sgroups during search.

isPositionVariation() - Method in class chemaxon.struc.MolBond

Decides whether this bond is a position variation bond.

isPositive(int) - Static method in class chemaxon.alignment.Pharmacophore3D

isPrefixModeSupported() - Method in interface chemaxon.naming.NameConverter

Returns true if prefix mode is supported.

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

Determines if the File->Print menu item is enabled or not.

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

Tests whether the atom is a pseudo atom.

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

For internal use only.

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

Tests whether it is a query atom.

isQuery() - Method in class chemaxon.struc.MolBond

Tests whether it is query bond or has query property: any single or double single or aromatic double or aromatic smarts bond ring or chain topology For more information on smarts bond and query bonds, see The JChem Query Guide

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

Indicates if the molecule has query features: query atoms or query bonds.

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

Indicates if the molecule has query features.

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

Indicates if the molecule has query features: query atoms or query bonds.

isQueryAbsoluteStereo() - Method in class chemaxon.search.api.options.MolSearchOptions

Returns whether the chiral flag is ignored or not for the query molecule.

isQueryBond() - Method in enum class chemaxon.struc.BondType

Determines whether this bond is a query bond.

isQueryDisplay() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Gets whether the query should be displayed in the upper left corner along with the hit.

isRadical() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing radical H

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

isRadicalMatching() - Method in class chemaxon.search.mcs.McsSearchOptions

Returns whether radicals are considered in search.

isRandomEnumeration() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Returns true if random enumeration is requested.

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

Checks if the structure represents a reaction or not.

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

Checks if the structure represents a reaction or not.

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

Checks if the structure represents a reaction or not.

isReactionArrow(MoleculeGraph) - Method in class chemaxon.struc.MObject

isReactionFpType(String) - Static method in class chemaxon.descriptors.ReactionFingerprint

Checks whether the given descriptor type name is considered as Reaction Fingerprint (e.g.

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

Returns true if reaction molecule was not mapped completely during reaction fingerprint generation.

isReactionUnpairedMapMatching() - Method in class chemaxon.search.api.options.SearchOptions

Get whether unpaired(orphan or widow) atom maps can match any atom.

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

Can it be a real atom parent?

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

R-group molecule objects cannot be real node parents.

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

Reaction molecules cannot be real node parents.

isRealAtomParent() - Method in class chemaxon.struc.SelectionMolecule

Selection molecules are not real atom parents.

isRegionalizedMatchingCompatible() - Method in enum class chemaxon.search.api.options.TautomerTransformationMode

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

Decides whether an S-group should be ungrouped if its structure changes.

isRemoveUnusedDefitions() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Gets whether unused definitions should be removed or not.

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

Checks if the specified atom object is in the paradigmatic repeating unit or not.

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

Informs whether the restH condition is set to the referenced R-group definition.

isReverse() - Method in class chemaxon.reaction.Reactor

Returns true if the reaction is to be processed in reversed direction.

isRewindable() - Method in class chemaxon.calculations.CalculatorPluginMDocSource

Tests whether rewinding (seeking backwards) is possible.

isRewindable() - Method in class chemaxon.formats.MDocSource

Tests whether rewinding (seeking backwards) is possible.

isRewindable() - Method in class chemaxon.formats.MolImporter

Tests whether rewinding (seeking backwards) is possible in the underlying input stream.

isRewindable() - Method in class chemaxon.marvin.common.MDocStorage

Tests whether the document storage is rewindable.

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

Tests whether the atom is an R-group atom.

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

Tests whether the atom is an R-group attachment point.

isRgrouped(Molecule) - Static method in class chemaxon.calculations.CalculatorPlugin

Returns true if molecule with R-groups.

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

Determines the visibility of R-group defintions.

isRgroupsVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Decides whether the R-group definitions are visible.

isRingAtom(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Returns true if ring atom.

isRingAtom(int) - Method in class chemaxon.core.calculations.Ring

Determines if an atom a ring bond or a chain bond.

isRingBond(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Determines if a bond is a ring bond or a chain bond.

isRingBond(int) - Method in class chemaxon.core.calculations.Ring

Determines if a bond is a ring bond or a chain bond.

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

Is this bond in a ring?

isRingBondCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects ring bond count atom query properties or not.

isRingCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects ring count atom query properties or not.

isRLogicVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Is R-logic visible?.

isRotatableBond(int) - Method in class chemaxon.alignment.RotatableBondDetector

Not flexible if:
double, aromatic, triple bond single bond neighboring a triple like at cyanide chain end bonds amide thioamide: -C(=S)-NR2 sulphonamide R-S(=O)2-NR2 aniline N : C(aromatic)-N(sp3) aromatic amidine : C(aromatic)-C(=NH)-NH2 aromatic nitroso : C(aromatic)-N=O aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable) C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature: Ring bonds may be rotatable also.

isRotatableBond(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Determines if a bond is a rotatable or not

isRotatableBond(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Determines if a bond is a rotatable or not

isRunning() - Method in class chemaxon.calculations.api.ProgressableCalculator

isSameParityClass(int, int, int, int, int, int, int, int) - Static method in class chemaxon.struc.MolAtom

Calculates if chirality centers in the structure and the query belong to the same parity class.

isSameType(int, int) - Method in class chemaxon.alignment.NodeColor.ExtendedAtomColoring

isSameType(int, int) - Method in class chemaxon.alignment.NodeColor

Determines if two types are considered the same based on the coloring scheme.

isSameTypeOrBothAnchor(int, int) - Method in class chemaxon.alignment.NodeColor

Determines if two types are considered the same or if both are anchor types based on the coloring scheme.

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

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

Automatically saves user settings to an initialization file.

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

Returns whether current parametrized metric is scaled or not.

isSearchAll() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects all R-atoms or not.

isSearchBridgehead() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for bridgehead explicit hydrogens

isSearchCharged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for charged explicit hydrogens

isSearchContracted() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Returns if the checker is searching for contracted SGroups or not

isSearchDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker

Returns if the checker detects valence properties with the default valence of the current atom type.

isSearchDisconnected() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms not connected to any other atoms or not.

isSearchExpanded() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Returns if the checker is searching for expanded SGroups or not

isSearchGeneric() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms without identifier numbers or not.

isSearchHConnected() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for H connected explicit hydrogens

isSearchIsotopic() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for isotopic explicit hydrogens

isSearchLinker() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms with more than one connection or not.

isSearchLonely() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for lonely explicit hydrogens

isSearchMapped() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for mapped explicit hydrogens

isSearchNested() - Method in class chemaxon.checkers.RatomChecker

Gets the option determining if the checker detects R-atoms within R-groups or not.

isSearchNonDefaultValence() - Method in class chemaxon.checkers.ValencePropertyChecker

Returns if the checker detects valence properties with a non-default valence of the current atom type.

isSearchPolymerEndGroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for polymer end group explicit hydrogens

isSearchRadical() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for radical explicit hydrogens

isSearchSgroup() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for S-group explicit hydrogens

isSearchSgroupEnd() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for S-group end explicit hydrogens

isSearchValenceError() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for valence errored explicit hydrogens

isSearchWedged() - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Returns if the checker search for wedged explicit hydrogens

isSeekable() - Method in class chemaxon.formats.PositionedInputStream

Tests whether the stream is seekable.

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

Are the cells selectable?

isSelectableNow() - Method in class chemaxon.struc.graphics.MMidPoint

isSelectableNow() - Method in class chemaxon.struc.graphics.MReactionSign

isSelectableNow() - Method in class chemaxon.struc.graphics.MRectanglePoint

isSelectableNow() - Method in class chemaxon.struc.MObject

Is the object selectable now?

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

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

isSelected() - Method in class chemaxon.struc.MObject

Is the object selected?

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

Tests whether this atom is selected.

isSelected() - Method in class chemaxon.struc.NoStructure

isSelected(int) - Method in class chemaxon.alignment.NodeColor.ExtendedAtomColoring

isSelected(int) - Method in class chemaxon.alignment.NodeColor

Determines if the given type is selected based on the coloring scheme.

isSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup

Is the S-group or part of the S-group selected?

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

Tests whether the specified property is a self-reference to the molecule.

isSelfReference(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether a property is a self reference to the containing molecule.

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

Tests whether the specified property is a self reference to the molecule.

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

Is the atom/bond set coloring enabled?

isSetColoringEnabled() - Method in class chemaxon.marvin.beans.MolPrinter

Returns true if atoms and bonds are colored according to the color of the pre-defined set they belong to.

isSgroup() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing s-group H

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

Returns whether the Sgroup data is formatted.

isSgroupDataFormatted() - Method in class chemaxon.marvin.beans.MolPrinter

Returns whether the Sgroup data is formatted.

isSgroupend() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing s-group end H

isShapeDescriptorType(String) - Static method in class chemaxon.descriptors.ShapeDescriptor

Checks whether the given descriptor type name is considered as Shape descriptor (e.g.

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

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

Tests if the molecule graph is similar to another graph.

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

Tests whether the document is equivalent to a simple molecule.

isSingle() - Method in class chemaxon.reaction.Reactor

Returns true if single mode is set.

isSingleCellLabelShown() - Method in class chemaxon.marvin.common.TableOptions

Tests whether label should be shown for a single cell.

isSingleUpOrDownBond() - Method in class chemaxon.standardizer.actions.ClearStereoAction

Gets the single wedge value of absolute stereo action

isSizeFinal() - Method in class chemaxon.marvin.common.MDocStorage

Tests whether the storage size is final.

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

Checks whether the molecule from the specified cell is opened in a sketcher window or not.

isSmallestRingSizeChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects smallest ring size atom query properties or not.

isSmartsQueryChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects SMARTS query properties or not.

isSMILESShown() - Method in class chemaxon.marvin.common.TableOptions

Are SMILES strings shown in the table?

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

Tests whether special symbol is used.

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

Tests whether special symbol is used.

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

Checks is Standardization of molecules is mandatory for the corresponding MolecularDescriptor before descriptor generation.

isStandardizerSpecified() - Method in class chemaxon.descriptors.pharmacophore.PMapper

Check if standardization is specified.

isStarAtom(MolAtom) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Decides whether an atom is a star atom in this S-group.

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

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

Gets whether last stereo fix should be applied

isStreamOutput() - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Returns true if stream output.

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

Tests whether a format is a sub-format of another format.

isSubsetChangable() - Method in class chemaxon.marvin.common.TableOptions

Returns whether startAt and maxSize can be changed.

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

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.

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

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.

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

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.

isSubstitutionCountChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects substitution count atom query properties or not.

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

Tests whether the molecule graph is symmetric.

isSymmetricalFuzzy() - Method in class chemaxon.descriptors.PFParameters

isTargetAbsoluteStereo() - Method in class chemaxon.search.api.options.MolSearchOptions

Returns whether the chiral flag is ignored or not for the target molecule.

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

Determines whether it is a terminal atom or not.

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

Checks if the line thickness is set.

isThreeLetterPeptideDisplay() - Method in class chemaxon.marvin.beans.MolPrinter

Decides whether the Peptide display settings set to three letter.

isThrowExceptionOnTimeout() - Method in class chemaxon.search.api.options.SearchOptions

Is search should throw exception upon timeout.

isTimeLoggingOn() - Method in class chemaxon.calculations.api.CalculatorLogger

isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.Sgroup

Decides if the whole S-group is selected or not.

isTotalSelected(MoleculeGraph) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Decides if the whole superatom sgroup is selected or not.

isTraditionalNitrogensAllowed() - Method in class chemaxon.struc.ValenceCheckOptions

Returns if the traditional way of the ylidene and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O, CN(=C)=O and c1ccccn1=O is accepted if false they are marked as valence error.

isTransDoubleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTransDoubleBonds

isTransformable() - Method in class chemaxon.struc.graphics.MAtomSetPoint

Is it a transformable object?

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

Is it a transformable object?

isTransformable() - Method in class chemaxon.struc.graphics.MRectanglePoint

isTransformable() - Method in class chemaxon.struc.MObject

Is it a transformable object?

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

Gets the transformation enabled/disabled.

isTransitionMetal(int) - Static method in class chemaxon.struc.PeriodicTable

Checks if the given atom is a transition metal, IB-VIIIB.

isTransparent() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the transparency state of the painting.

isTripleBond() - Method in class chemaxon.checkers.RingStrainErrorChecker

Returns the detectTripleBonds

isUndecided(Object) - Static method in class chemaxon.chemterms.ChemTermsExpression

Returns whether the result object is undecided.

isUndefinedRAtomMatchingGroup() - Method in class chemaxon.search.api.options.SearchOptions

Gets whether undefined R atom matches group of atoms.

isUndefinedRAtomUserDefined() - Method in class chemaxon.search.api.options.SearchOptions

Fot internal use only! Returns whether the undefined R-atom matching behavior was set externally (user-defined) or else internally as default for a specific query from

invalid reference

RgroupDecomposition#setQuery(chemaxon.struc.Molecule)

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

Gets whether the units string should be displayed.

isUnsaturationChecking() - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Gets the option determining if the checker detects unsaturation atom query properties or not.

isURLOrFileName(String) - Static method in class chemaxon.formats.MFileFormatUtil

Tests whether the specified string is an URL (absolute or relative) or file name.

isUseDefaultSalts() - Method in class chemaxon.standardizer.actions.StripSaltsAction

Gets whether default salt dictionary should be used

isUseDefaultSolvents() - Method in class chemaxon.standardizer.actions.RemoveSolventsAction

Gets whether default solvent dictionary should be used

isUsefulForQuery() - Method in class chemaxon.search.api.MolComparator

Decides based on the query and the search object if the comparator should be used or not.

isUsefulForTarget() - Method in class chemaxon.search.api.MolComparator

Decides based on the query, target and the search object if the comparator should be used or not.

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

Determines whether the valence check is enabled on this molecule graph.

isValenceerror() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing valence error H

isValenceErrorvisible() - Method in class chemaxon.marvin.beans.MolPrinter

Returns the visibility state of valence errors.

isValenceErrorVisible() - Method in class chemaxon.marvin.beans.MSketchPane

Are valence errors highlighted?

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

Are valence errors visible?

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

Are valence errors highlighted?

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

Are valence errors visible in MarvinView?

isValenceMatching() - Method in class chemaxon.search.api.options.SearchOptions

Get the valence matching option

isValencePropertyVisible() - Method in class chemaxon.marvin.beans.MolPrinter

Gets the atom valence property visibility

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

Tells wheter the atom valence property is visible or not.

isValid() - Method in class chemaxon.calculations.services.DynamicArgument

isValid() - Method in class chemaxon.calculations.services.ServiceArgument

Returns true if service argument is valid

isValid() - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Excluded object is initialized.

isValid() - Method in class chemaxon.checkers.AbstractStructureChecker

isValid() - Method in class chemaxon.checkers.AttachedDataChecker

isValid() - Method in class chemaxon.checkers.InvalidChecker

isValid() - Method in class chemaxon.checkers.PseudoAtomChecker

isValid() - Method in interface chemaxon.checkers.StructureChecker

Returns true if the checker's configuration is valid, false otherwise

isValid() - Method in class chemaxon.checkers.SubstructureChecker

isValid() - Method in class chemaxon.standardizer.AbstractStandardizerAction

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

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

Gets whether the configuration contains only valid elements

isValid() - Method in interface chemaxon.standardizer.StandardizerAction

Returns true if the action's parameters are valid, false otherwise

isValid(MProp) - Method in class chemaxon.struc.MPropertyContainer

Tests whether a coordinate dependent property is still valid.

isValid(InputStream) - Static method in class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlReader

Checks whether the contents of the provided input stream is a valid configuration XML

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

Is the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.

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

Checks whether the specified link atom is valid or not.

isValidList() - Method in class chemaxon.checkers.AttachedDataChecker.DataExclusionList

isValidQuery(String) - Static method in class chemaxon.search.FormulaSearch

Checks the given formula whether it is a valid query formula

isValidTarget(String) - Static method in class chemaxon.search.FormulaSearch

Checks the given formula whether it is a valid target formula

isValidXMLConfiguration(InputStream) - Static method in class chemaxon.standardizer.configuration.StandardizerConfigurationXmlReader

Checks whether the contents of the provided input stream is a valid configuration XML

isVerbose() - Method in class chemaxon.search.AbstractSearch

For debugging purposes only.

isVerbose() - Method in class chemaxon.search.api.options.SearchOptions

For debugging purposes only.

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

Returns true if atom mark and highlight is enabled in View.

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

Checks whether the view canvas of the specified cell is detached into a separate window or not.

isVirginAtom(Molecule[]) - Method in class chemaxon.reaction.AtomIdentifier

Gets whether the identifier represents a virgin atom.

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

Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.

isWedged() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Gets the value of property for removing wedged H

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

Returns whether current parametrized metric is weighted or not.

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

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

Italic font style.

iterator() - Method in class chemaxon.formats.MDocSource

Gets a molecule iterator for this document source.

iterator(Iterator<Molecule>) - Static method in class chemaxon.reaction.mapper.AutoMapper

Returns an auto-closeable result iterator that maps the reactions provided by the given input iterator.

iterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class chemaxon.reaction.mapper.AutoMapper

Returns an auto-closeable result iterator that maps the reactions provided by the given input iterator using the given options.

IteratorFactory - Class in chemaxon.struc

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

This class is deprecated and subject to removal in a future release. Please use the appropriate methods of MoleculeGraph and Molecule instead.

IteratorFactory(Molecule) - Constructor for class chemaxon.struc.IteratorFactory

Deprecated.

Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.

IteratorFactory(MoleculeGraph) - Constructor for class chemaxon.struc.IteratorFactory

Deprecated.

Constructs an iterator factory for the specified molecule with default atom and bond related behavior to include all atoms and bonds.

IteratorFactory(Molecule, int, int) - Constructor for class chemaxon.struc.IteratorFactory

Deprecated.

Constructs an iterator factory for the specified molecule with a specified atom and bond related behavior.

IteratorFactory.AtomIterator - Class in chemaxon.struc

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

IteratorFactory.AtomNeighbourIterator - Class in chemaxon.struc

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

IteratorFactory.BondIterator - Class in chemaxon.struc

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

IteratorFactory.BondNeighbourIterator - Class in chemaxon.struc

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

IteratorFactory.NeighbourIterator<E> - Class in chemaxon.struc

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

IteratorFactory.RgComponentIterator - Class in chemaxon.struc

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

IteratorFactory.RxnComponentIterator - Class in chemaxon.struc

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

IteratorFactory.SgroupIterator - Class in chemaxon.struc

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

J

JAN_01_2027 - Enum constant in enum class chemaxon.common.annotations.RemovalDate
jar - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
jar - Variable in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor
JPEG - Static variable in class chemaxon.formats.MFileFormat: JPEG format.
JsonServiceDescriptor - Class in chemaxon.calculations.services: Service descriptor of JSON type requests.
JsonServiceDescriptor() - Constructor for class chemaxon.calculations.services.JsonServiceDescriptor
JsonServiceDescriptor.Method - Enum Class in chemaxon.calculations.services: HTTP methods used for JSON RPC requests.
JsonServiceHandler - Class in chemaxon.calculations.services: Service handler for JSON type requests.
JsonServiceHandler() - Constructor for class chemaxon.calculations.services.JsonServiceHandler
JUL_01_2026 - Enum constant in enum class chemaxon.common.annotations.RemovalDate
JUL_01_2027 - Enum constant in enum class chemaxon.common.annotations.RemovalDate

K

K - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element K.
keep - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
KEEP_BOTH_FLEXIBLE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode: Keep both structures flexible during the alignment.
KEEP_BOTH_RIGID - Enum constant in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode: Keep both structures conformationally rigid during the alignment.
KEEP_FIRST_RIGID_SECOND_FLEXIBLE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode: Keep the first reference structure rigid, and the second as flexible during the alignment.
KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA - Enum constant in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode: As of AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).
KEEP_HYDROGENS - Static variable in class chemaxon.calculations.CalculatorPlugin
KEEP_MAPPING - Static variable in class chemaxon.standardizer.actions.MapAction: keep mapping property
KEEP_MAPPING - Static variable in class chemaxon.standardizer.actions.MapReactionAction: keep mapping property
KEEP_RINGS - Enum constant in enum class chemaxon.search.mcs.RingHandlingMode: This option specifies that rings should not be broken.
keepHydrogens - Variable in class chemaxon.calculations.CalculatorPlugin
KEEPLARGEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Keep largest fragment
keepLargestFragment(Molecule) - Static method in class chemaxon.alignment.MMPAlignment: Utility for preprocessing structure for alignment.
keeporiginalLineEnding - Variable in class chemaxon.formats.PositionedInputStream
KEEPSMALLEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Keep largest fragment
KEKULE_MATCH_AMBIG - Enum constant in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption: Ambiguous aromatic parts are not aromatized in the target Markush structures.
KEY_VALUE_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringReader: Parameter key and value separator token of the action string
KEY_VALUE_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: Parameter key and value separator token of the action string
KEY_VALUE_SEPARATOR - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: Parameter key and value separator token of the action string
KLOPMAN - Enum constant in enum class chemaxon.calculations.LogPMethod: Calculation method based on Klopman's model.
knownAtropStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the KNOWN atrop stereocenters.
knownAxialStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the KNOWN axial stereocenters.
knownResolvedStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the known, resolved tetrahedral stereogenic centers.
knownResolvedStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the known, resolved tetrahedral stereogenic centers (with attached data).
Kr - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Kr.

L

La - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element La.
LABEL - Static variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: Property display type: display in label.
LABEL - Static variable in class chemaxon.struc.NoStructure: Label for NoStructure.
LABEL_AUTO - Static variable in class chemaxon.struc.sgroup.SgroupAtom
LABEL_DEFAULT - Static variable in class chemaxon.struc.sgroup.SgroupAtom
labelAsAnchor(int) - Method in class chemaxon.alignment.NodeColor: Labels the given type as an anchor type.
labelAsAnchor(int) - Static method in class chemaxon.alignment.Pharmacophore3D
largestring - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
largestRing() - Method in class chemaxon.core.calculations.Ring: Identifies the atoms of the largest ring (number of atoms) in the molecule.
largestRingSize() - Method in class chemaxon.core.calculations.Ring: Calculates the size of the largest ring in the molecule (SSSR based).
largestRingSizeOfAtom(int) - Method in class chemaxon.core.calculations.Ring: Calculates the size of the largest ring an atom is a member of (SSSR based).
largestringsystem - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
largestRingSystem() - Method in class chemaxon.core.calculations.Ring: Identifies the atoms of the largest ring system (number of rings) in the molecule.
largestRingSystemSize() - Method in class chemaxon.core.calculations.Ring: Calculates the size of the largest ring system (number of rings) in the molecule.
lastPage - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions: The last page of the document that should be annotated.
lastPage(Integer) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
LAYOUT - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "layout".
LAYOUT_HEADER - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "layoutH".
LDIR_ABOVE - Static variable in class chemaxon.struc.MolAtom: Implicit Hydrogen(s) are above the element symbol.
LDIR_BELOW - Static variable in class chemaxon.struc.MolAtom: Implicit Hydrogen(s) are below the element symbol.
LDIR_LEFT - Static variable in class chemaxon.struc.MolAtom: Implicit Hydrogen(s) are left to element symbol.
LDIR_RIGHT - Static variable in class chemaxon.struc.MolAtom: Implicit Hydrogen(s) are right to element symbol.
LDParameters - Class in chemaxon.descriptors.scalars: Manages parameters for the LogD scalar descriptor class.
LDParameters() - Constructor for class chemaxon.descriptors.scalars.LDParameters: Creates an empty object.
LDParameters(File) - Constructor for class chemaxon.descriptors.scalars.LDParameters: Creates a new object based on a given configuration file.
LDParameters(String) - Constructor for class chemaxon.descriptors.scalars.LDParameters: Creates a new object based on a given configuration string.
LEAVE_COORDS_UNCHANGED - Static variable in interface chemaxon.struc.sgroup.Expandable: Coordinates are not calculated during expand or contract.
leftMul(Transform3D) - Method in class chemaxon.struc.Transform3D: Multiplies by another matrix from left.
length - Variable in class chemaxon.descriptors.MDParameters: the length of the descriptor: the number of cells
length() - Method in class chemaxon.formats.PositionedInputStream: Gets the file length.
length() - Method in class chemaxon.struc.graphics.MTextDocument: Gets the length of the document.
length() - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the number of characters.
length() - Method in class chemaxon.struc.graphics.MTextDocument.Section: Gets text length.
lengthSquare() - Method in class chemaxon.struc.Point3D: Calculates the square of the length of the vector defining the point.
lessOrEquals(RenderingStyle) - Method in enum class chemaxon.rendering.constants.RenderingStyle
Li - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Li.
Licensable - Interface in chemaxon.license.api: The common interface of license-protected classes of Chemaxon.
license() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the license required for this action.
LICENSE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "license".
LICENSE_FILE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "licenseFile".
licenseEnvironment - Variable in class chemaxon.calculations.api.ProgressableCalculator
licenseEnvironment - Variable in class chemaxon.calculations.CalculatorPlugin: Member storing license environment.
LicenseException - Exception Class in chemaxon.license.api: Thrown when the product is not properly licensed.
LicenseException(String) - Constructor for exception class chemaxon.license.api.LicenseException: Constructs an instance of LicenseException with the specified detail message.
LicenseException(String, String) - Constructor for exception class chemaxon.license.api.LicenseException
LIGAND_ERROR_VISIBILITY_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Flag for showing ligand error by coloring to red.
LIGAND_ERROR_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "ligandErrorVisible".
LIGAND_ORDER_MASK - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Ligand order visibility mask.
LIGAND_ORDER_OFF - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Ligand order visibility: Do not show ligand order.
LIGAND_ORDER_OFF_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: String constant for LIGAND_ORDER_OFF
LIGAND_ORDER_ON - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Ligand order visibility: Show ligand order on all R-groups.
LIGAND_ORDER_ON_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: String constant for LIGAND_ORDER_ON
LIGAND_ORDER_ONLY_WITH_DEFINITION - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Ligand order visibility: Show only on R-groups with definition.
LIGAND_ORDER_ONLY_WITH_DEFINITION_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: String constant for LIGAND_ORDER_ONLY_WITH_DEFINITION
LIGAND_ORDER_STYLES - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Array of ligand order visibility strings.
ligands() - Method in class chemaxon.struc.MolAtom: Provides an unmodifiable list view of the ligands of the atom.
Limitations: - Search tag in class chemaxon.alignment.AtropIsomerDetector: Section
limitRecordCount(int) - Method in class chemaxon.calculations.CalculatorPluginMDocSource: Limits the number of result docs.
limitsByTag() - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Returns the value of the limitsByTag record component.
lineByteBuffer - Variable in class chemaxon.formats.PositionedInputStream: Lines are read into this buffer.
lineCurrentColumn - Variable in class chemaxon.formats.PositionedInputStream: Column position of the next character to read.
LIST - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the inclusive atom list.
LISTEN_MOUSE_EVENT - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "listenmouseevent".
LISTEN_PROPERTY_CHANGE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "listenpropertychange".
listener - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions: A listener that will be notified of the progress of the annotation.
load() - Static method in class chemaxon.calculations.admet.HergActivityPredictor: Initializes the default hERG activity model.
load() - Static method in class chemaxon.calculations.admet.HergClassPredictor: Initializes the default hERG classification model.
load() - Method in class chemaxon.calculations.gui.PluginFactory: Loads default property file.
load(String, String) - Method in class chemaxon.calculations.gui.PluginFactory: Loads plugin data from property file.
load(Properties) - Method in class chemaxon.calculations.gui.PluginFactory: Loads plugin data from properties.
LOAD_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "loadMols".
loadPluginClass(String) - Static method in class chemaxon.calculations.CalculatorPlugin: Loads a plugin class from the classpath based on its fully qualified name.
LOCAL_MENU_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: local menu name property of checker
localMenuName() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the local menu name of the checker
LocalServiceDescriptor - Class in chemaxon.calculations.services: Service Descriptor for java based local services.
LocalServiceDescriptor() - Constructor for class chemaxon.calculations.services.LocalServiceDescriptor
LocalServiceHandler - Class in chemaxon.calculations.services: ServiceHandler implementation for LocalServiceDescriptor.
LocalServiceHandler() - Constructor for class chemaxon.calculations.services.LocalServiceHandler
log(Molecule, CalculatorLogger.Level, String, String...) - Method in class chemaxon.calculations.api.CalculatorLogger
log(Molecule, String, double) - Method in class chemaxon.calculations.api.CalculatorLogger
log(Molecule, String, String...) - Method in class chemaxon.calculations.api.CalculatorLogger
log(Molecule, String, Throwable) - Method in class chemaxon.calculations.api.CalculatorLogger
LogD - Class in chemaxon.descriptors.scalars: Implements logD value as a scalar descriptor.
LogD() - Constructor for class chemaxon.descriptors.scalars.LogD: Creates a new, empty logD descriptor.
LogD(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.LogD: Copy constructor.
LogD(LDParameters) - Constructor for class chemaxon.descriptors.scalars.LogD: Creates a new instance according to the parameters given.
LogD(String) - Constructor for class chemaxon.descriptors.scalars.LogD: Creates a new instance according to the parameters given.
LOGD - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Calculated distribution coefficient at pH 7.4.
LOGDCALCULATOR - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
LogDPlugin - Class in chemaxon.calculations: Plugin class for logD calculation.
LogDPlugin() - Constructor for class chemaxon.calculations.LogDPlugin: Constructor.
LogP - Class in chemaxon.descriptors.scalars: Implements LogP value as a scalar descriptor.
LogP() - Constructor for class chemaxon.descriptors.scalars.LogP: Creates a new, empty logP descriptor.
LogP(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.LogP: Copy constructor.
LogP(SDParameters) - Constructor for class chemaxon.descriptors.scalars.LogP: Creates a new instance according to the parameters given.
LogP(String) - Constructor for class chemaxon.descriptors.scalars.LogP: Creates a new instance according to the parameters given.
LOGP - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Lipophilicity, calculated partition coefficient.
LogPMethod - Enum Class in chemaxon.calculations: Enumeration of logP calculation methods.
LogPPlugin - Class in chemaxon.calculations: Plugin class for logP calculation.
LogPPlugin() - Constructor for class chemaxon.calculations.LogPPlugin: Constructor.
LOGS - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
LOGS - Enum constant in enum class chemaxon.calculations.solubility.SolubilityUnit: Solubility is expressed in base-10 logarithm unit.
logToDebug(System.Logger, System.Logger.Level, String, boolean) - Method in class chemaxon.alignment.DihedralScanResult: Append to log.
LONE_PAIRS_AS_LINE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "lonePairsAsLine".
LONE_PAIRS_AS_LINE_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts
LONE_PAIRS_AS_LINE_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts
LONE_PAIRS_AUTO_CALCULATION - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "lonePairsAutoCalc".
LONE_PAIRS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "lonePairsVisible".
LONELY_H - Static variable in class chemaxon.struc.MolAtom: Include lonely Hydrogen atom(s).
lonePairCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
lonePairRealCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
lonePairState - Static variable in class chemaxon.struc.graphics.MEFlow
LOOSE - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type: Loose aromatization
LOW - Enum constant in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory: Low solubility.
LOW_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor: low priority value
LOWEST_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor: the lowest priority value
lowestEigenvalues - Variable in class chemaxon.descriptors.BCUT
LP - Static variable in class chemaxon.alignment.Pharmacophore3D
LP - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the lone pair.
LP_AUTO_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Lone pair automatic calculation visible flag.
LP_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Lone pair visibility flag.
Lr - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Lr.
lt(RenderingStyle) - Method in enum class chemaxon.rendering.constants.RenderingStyle
Lu - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Lu.
Lv - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Lv.

M

m - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue
m - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue
M - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue
M - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue
M - Static variable in class chemaxon.chemterms.SearchContext
m00 - Variable in class chemaxon.struc.Transform3D: The m00 element of the matrix.
m01 - Variable in class chemaxon.struc.Transform3D: The m01 element of the matrix.
m02 - Variable in class chemaxon.struc.Transform3D: The m02 element of the matrix.
m03 - Variable in class chemaxon.struc.Transform3D: The m03 element of the matrix.
m10 - Variable in class chemaxon.struc.Transform3D: The m10 element of the matrix.
m11 - Variable in class chemaxon.struc.Transform3D: The m11 element of the matrix.
m12 - Variable in class chemaxon.struc.Transform3D: The m12 element of the matrix.
m13 - Variable in class chemaxon.struc.Transform3D: The m13 element of the matrix.
m20 - Variable in class chemaxon.struc.Transform3D: The m20 element of the matrix.
m21 - Variable in class chemaxon.struc.Transform3D: The m21 element of the matrix.
m22 - Variable in class chemaxon.struc.Transform3D: The m22 element of the matrix.
m23 - Variable in class chemaxon.struc.Transform3D: The m23 element of the matrix.
m30 - Variable in class chemaxon.struc.Transform3D: The m30 element of the matrix.
m31 - Variable in class chemaxon.struc.Transform3D: The m31 element of the matrix.
m32 - Variable in class chemaxon.struc.Transform3D: The m32 element of the matrix.
m33 - Variable in class chemaxon.struc.Transform3D: The m33 element of the matrix.
MAction - Class in chemaxon.marvin.common: Comman base class for Marvin actions.
MAction(String, String) - Constructor for class chemaxon.marvin.common.MAction: Creates an action.
MAction(String, String, KeyStroke) - Constructor for class chemaxon.marvin.common.MAction: Creates an action.
MAction(String, String, KeyStroke[]) - Constructor for class chemaxon.marvin.common.MAction: Creates an action.
main(String[]) - Static method in class chemaxon.common.version.VersionInfo: Main method that prints out the version information into the standard output.
main(String[]) - Static method in class chemaxon.formats.converter.MolConverter: Main method.
mainMChemicalStruct - Variable in class chemaxon.struc.MDocument
mainMMoleculeMovie - Variable in class chemaxon.struc.MDocument
mainWithoutExit(String[]) - Static method in class chemaxon.formats.converter.MolConverter: Same as main(), but never calls System.exit().
MajorMicrospeciesAccessorPlugin - Class in chemaxon.calculations: Common base class for all plugins with possible major microspecies input.
MajorMicrospeciesPlugin - Class in chemaxon.calculations: Plugin class that calculates the major microspecies on a given pH.
MajorMicrospeciesPlugin() - Constructor for class chemaxon.calculations.MajorMicrospeciesPlugin: Constructor.
makeColor(String) - Static method in class chemaxon.struc.MObject
makeEditMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane: Adds menu items to the specified Edit menu.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.Molecule: Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule: Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule: Copies some properties of this molecule to the other one specified as argument.
makeRecentFileListMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane: Read the recent file list from marvin.properties, and add it to the specified parent menu.
makeSaveAsMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane: Creates the "Save As" menu and adds it to the specified parent menu.
makeStructureMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane
makeTableMenu(Container) - Method in class chemaxon.marvin.common.TableSupport: Creates Table menu items.
makeViewMenu(Container) - Method in class chemaxon.marvin.beans.MViewPane: Adds menu items to the specified View menu.
MAnalysisBox - Class in chemaxon.struc.graphics: A special text box containing analysis results.
MAnalysisBox(Molecule, List<MAnalysisBoxTerm>) - Constructor for class chemaxon.struc.graphics.MAnalysisBox: Constructor.
MAnalysisBoxTerm - Class in chemaxon.struc.graphics: Represents a term in MAnalysisBox.
MAnalysisBoxTerm(String, String, MAnalysisBoxTerm.Formatter, boolean) - Constructor for class chemaxon.struc.graphics.MAnalysisBoxTerm: Constructor.
MAnalysisBoxTerm.Formatter - Interface in chemaxon.struc.graphics: Formatter interface for MAnalysisBoxTerm.
map(RxnMolecule) - Method in class chemaxon.reaction.mapper.AutoMapper: Maps the reaction.
map(RxnMolecule) - Method in interface chemaxon.reaction.mapper.ReactionMapper: Marks the matching parts of the given reaction with the same identifier (atom map number) in reactants and products.
MapAction - Class in chemaxon.standardizer.actions: Standardizer action that adds atom map numbers to the molecule.
MapAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MapAction: Initializes the action
MapMoleculeFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which maps the atoms of the molecule incrementally
MapMoleculeFixer() - Constructor for class chemaxon.fixers.MapMoleculeFixer
MAPPED_H - Static variable in class chemaxon.struc.MolAtom: Mapped Hydrogen atom(s).
MAPPING_STYLE - Static variable in class chemaxon.standardizer.actions.MapAction: mapping style property
MAPPING_STYLE - Static variable in class chemaxon.standardizer.actions.MapReactionAction: mapping style property
MAPPING_STYLE_CHANGING - Static variable in class chemaxon.reaction.Reactor: Output reaction mapping style: changing (Chemaxon).
MAPPING_STYLE_COMPLETE - Static variable in class chemaxon.reaction.Reactor: Output reaction mapping style: complete.
MAPPING_STYLE_MATCHING - Static variable in class chemaxon.reaction.Reactor: Output reaction mapping style: matching (Daylight).
MAPPING_STYLE_NONE - Static variable in class chemaxon.reaction.Reactor: Output reaction mapping style: none.
mapReaction(MolImporter, MolExporter) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
Use AutoMapper.mapReactions(MolImporter, MolExporter) instead. This method will be removed in a future release.
mapReaction(MolImporter, MolExporter, AutoMapper.Options) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
Use AutoMapper.mapReactions(MolImporter, MolExporter, Options) instead. This method will be removed in a future release.
mapReaction(MolImporter, MolExporter, ReactionMapper...) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
No replacement. This method will be removed in a future release.
mapReaction(AutoMapper.Options, Molecule...) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
Use AutoMapper.mapReactions(Collection, Options) instead. This method will be removed in a future release.
mapReaction(ReactionMapper[], Molecule...) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
No replacement. This method will be removed in a future release.
mapReaction(Molecule) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the given reaction.
mapReaction(Molecule...) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
Use AutoMapper.mapReactions(Molecule...) instead. This method will be removed in a future release.
mapReaction(Molecule, AutoMapper.Options) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the given reaction.
mapReaction(Collection<Molecule>) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
Use AutoMapper.mapReactions(Collection) instead. This method will be removed in a future release.
mapReaction(Collection<Molecule>, AutoMapper.Options) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
Use AutoMapper.mapReactions(Collection, Options) instead. This method will be removed in a future release.
mapReaction(Collection<Molecule>, ReactionMapper...) - Static method in class chemaxon.reaction.mapper.AutoMapper: Deprecated, for removal: This API element is subject to removal in a future version.
No replacement. This method will be removed in a future release.
MapReactionAction - Class in chemaxon.standardizer.actions: Standardizer action that adds atom-atom mapping to the reaction.
MapReactionAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MapReactionAction: Initializes the action
MapReactionFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which maps the reaction with AutoMapper.
MapReactionFixer() - Constructor for class chemaxon.fixers.MapReactionFixer: Default constructor
mapReactions(MolImporter, MolExporter) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the reactions read from the given importer and writes them to the given exporter.
mapReactions(MolImporter, MolExporter, AutoMapper.Options) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the reactions read from the given importer using the given options and writes them to the given exporter.
mapReactions(Molecule...) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the given reactions.
mapReactions(Collection<Molecule>) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the given reactions.
mapReactions(Collection<Molecule>, AutoMapper.Options) - Static method in class chemaxon.reaction.mapper.AutoMapper: Maps the given reactions using the given options.
MARGIN_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "marginSize".
MARK_BONDS - Static variable in class chemaxon.standardizer.actions.MapAction: mark bonds property
MARK_BONDS - Static variable in class chemaxon.standardizer.actions.MapReactionAction: mark bonds property
MarkAsMajorFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which adds an attached data to the bond: "STEREO = M"
MarkAsMajorFixer() - Constructor for class chemaxon.fixers.MarkAsMajorFixer: Initializes the fixer
MarkAsUnknownFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which adds an attached data to the bond: "STEREO = U"
MarkAsUnknownFixer() - Constructor for class chemaxon.fixers.MarkAsUnknownFixer: Initializes the fixer
markSingleTypes(BitSet, int) - Method in class chemaxon.alignment.NodeColor.ExtendedAtomColoring
markSingleTypes(BitSet, int) - Method in class chemaxon.alignment.NodeColor: Marks the given type in the provided BitSet according to the coloring scheme.
MARKUSH_HIT_INNER - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for returning hit indices of the inner, compiled representation of a Markush target.
MARKUSH_HIT_ORIGINAL - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for returning hit indices of the original Markush target.
MARKUSH_REDUCTION - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: Constant value specifying, that in case of markush searching the markush structure is expanded according to the query structure.
MARKUSH_REDUCTION_HGEXPANSION - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: Constant value specifying, that in case of markush searching the markush structure is expanded according to the query structure and homology groups are also replaced by the query structure matching on them.
MarkushAromaticityHandlingOption - Enum Class in chemaxon.search.api.options: Option type describing the way aromaticity is handled in Markush structures.
MarkushEnumerationPlugin - Class in chemaxon.calculations: Plugin class for enumerating Markush molecules.
MarkushEnumerationPlugin() - Constructor for class chemaxon.calculations.MarkushEnumerationPlugin: Constructor.
MarkushGenerator - Class in chemaxon.search: Generates RgMolecule output that covers the specified targets with the specified scaffold.
MarkushGenerator() - Constructor for class chemaxon.search.MarkushGenerator: Constructor.
MARVIN_CONFIG_DEFAULT_PATH - Static variable in class chemaxon.marvin.common.UserSettings: The default configuration file path inside the chemaxon settings directory in user home.
MarvinPane - Class in chemaxon.marvin.beans: Ancestor of the Marvin Beans.
MarvinPane() - Constructor for class chemaxon.marvin.beans.MarvinPane: Constructor.
MarvinPaneBeanInfo - Class in chemaxon.marvin.beans: Ancestor of Marvin's BeanInfo classes that are needed by GUI builders.
MarvinPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MarvinPaneBeanInfo
MarvinTransferable - Class in chemaxon.marvin.datatransfer: Abstract Adapter implementation of the MTransferable interface used by Marvin.
MarvinTransferable() - Constructor for class chemaxon.marvin.datatransfer.MarvinTransferable
mass() - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Calculates the molecular weight of the molecule.
mass() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the molecular weight of the molecule.
Mass - Class in chemaxon.descriptors.scalars: Implements Mass (total mass of molecule) value as a scalar descriptor.
Mass() - Constructor for class chemaxon.descriptors.scalars.Mass: Creates a new, empty logD descriptor.
Mass(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.Mass: Copy constructor.
Mass(SDParameters) - Constructor for class chemaxon.descriptors.scalars.Mass: Creates a new instance according to the parameters given.
Mass(String) - Constructor for class chemaxon.descriptors.scalars.Mass: Creates a new instance according to the parameters given.
MASS - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "mass".
MASS_SPECTRUM - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "massspectrum".
MAssigner - Class in chemaxon.struc.graphics: Atom assigner to connect two atoms.
MAssigner() - Constructor for class chemaxon.struc.graphics.MAssigner: Contructs an assigner.
MAssigner(MAssigner) - Constructor for class chemaxon.struc.graphics.MAssigner: Copy constructor.
MAssigner(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MAssigner: Contructs an assigner with the specified endpoints.
massNumber() - Method in record class chemaxon.calculations.elemental.FormulaAtom: Returns the value of the massNumber record component.
massPrecision() - Method in class chemaxon.core.calculations.ElementalAnalyzer: Calculates the precision of the molecular weight (number of decimal digits).
match(MolAtom, MolAtom) - Method in interface chemaxon.search.mcs.McsCustomMatcher: Returns true if the given atoms are matchable according to some custom matching criteria.
match(MolBond, MolBond) - Method in interface chemaxon.search.mcs.McsCustomMatcher: Returns true if the given bonds are matchable according to some custom matching criteria.
MATCH_AMBIG_IF_POSSIBLE - Enum constant in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption: Ambiguous aromatic parts can be matched by a query if it has the same aromaticity as the target Markush structure considering its reduction (enumeration) according to the hit candidate.
MATCH_COUNT_BETWEEN - Static variable in interface chemaxon.search.api.SearchConstants
MATCH_COUNT_RELATION - Static variable in interface chemaxon.search.api.SearchConstants
MATCH_RING_BONDS - Enum constant in enum class chemaxon.search.mcs.RingHandlingMode: This option allows the algorithm to match a query and a target bond only if both are in rings or both are in chains.
matches(MolAtom, MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction: Matches 2 atoms
matches(String, long, long) - Method in class chemaxon.formats.MFileFormat: Tests whether the format matches the specified pattern.
MATCHING - Enum constant in enum class chemaxon.reaction.mapper.ReactionMapper.MappingStyle: Map only the matching atoms.
MAtomSetPoint - Class in chemaxon.struc.graphics: Point fixed to the location of one or more atoms.
MAtomSetPoint() - Constructor for class chemaxon.struc.graphics.MAtomSetPoint: Contructs an empty point object.
MAtomSetPoint(MAtomSetPoint) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint: Copy constructor.
MAtomSetPoint(MolAtom[]) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint: Contructs a point object.
MAX_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings: The maximum size of sketchRecentFileList
MAX_SCALE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "maxscale".
maxAbsOxStateOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the oxidation state that has the maximum absolute value
MaxCliqueMcs - Class in chemaxon.search.mcs: Implements a heuristic MCS algorithm based on maximum clique detection.
MaxCliqueMcs(McsSearchOptions) - Constructor for class chemaxon.search.mcs.MaxCliqueMcs: Creates a MaxCliqueMcs object with the specified search options.
MaxCommonSubstructure - Class in chemaxon.search.mcs: Abstract base class of the algorithms for finding the maximum common substructure (MCS) of two molecules.
maxConsideredRingSize(int) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets the maximum size of rings considered for ring matching purposes.
MAXMAPS - Static variable in class chemaxon.chemterms.SearchContext: Maximal number of map values.
maxNonEmptyId - Variable in class chemaxon.descriptors.MDGenerator
maxNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator
maxParameterCount() - Element in annotation interface chemaxon.chemterms.ChemTermsContext.ProvidesFunction: The higher end of the allowed parameter count range (inclusive), or ChemTermsContext.VARARG to signal that there is no maximum.
maxParameterCount() - Method in interface chemaxon.chemterms.CustomFunction: Returns the maximum parameter count of this function (a non-negative integer), or CustomFunction.VARARG if there is no maximum.
maxScale(Dimension) - Method in class chemaxon.marvin.beans.MolPrinter: Calculates the maximum scaling factor for fitting the image in a rectangle of the specified size.
maxScale(Rectangle) - Method in class chemaxon.marvin.beans.MolPrinter: Calculates the maximum scaling factor for fitting the image in the specified rectangle.
maxStereoisomerCount() - Method in class chemaxon.calculations.stereo.StereoisomerSettings: Returns the adjusted maximum number of generated stereoisomers or Optional.empty().
MAYBE_USEFUL - Static variable in class chemaxon.search.api.MolComparator: Describes that the MolComparator may be needed with the current search object and the current query, depending on the target.
MBooleanProp - Class in chemaxon.struc.prop: String property.
MBooleanProp(boolean) - Constructor for class chemaxon.struc.prop.MBooleanProp: Constructs a property.
MBooleanProp(String) - Constructor for class chemaxon.struc.prop.MBooleanProp: Constructs a property.
MBracket - Class in chemaxon.struc.graphics: Bracket object.
MBracket() - Constructor for class chemaxon.struc.graphics.MBracket: Constructs a bracket.
MBracket(MBracket) - Constructor for class chemaxon.struc.graphics.MBracket: Copy constructor.
MBracket(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MBracket: Constructs a bracket with the specified corner points.
MBracket(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MBracket: Constructs a bracket with the specified corner points and color.
MByteArrayProp - Class in chemaxon.struc.prop: Byte array property.
MByteArrayProp(byte[]) - Constructor for class chemaxon.struc.prop.MByteArrayProp: Constructs a property object from an byte[] value.
MByteArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MByteArrayProp: Constructs a byte array property from a string value.
Mc - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Mc.
MChart - Class in chemaxon.calculations.gui: Wrapper for the EasyChart module.
MChart() - Constructor for class chemaxon.calculations.gui.MChart: Constructor.
MChemicalStruct - Class in chemaxon.struc.graphics: Molecule graph object.
MChemicalStruct(MChemicalStruct) - Constructor for class chemaxon.struc.graphics.MChemicalStruct: Copy constructor.
MChemicalStruct(MoleculeGraph) - Constructor for class chemaxon.struc.graphics.MChemicalStruct: Contructs a molecule graph object.
MCollectionProp - Class in chemaxon.struc.prop: Collection of properties.
MCollectionProp() - Constructor for class chemaxon.struc.prop.MCollectionProp
mcs - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes
MCS - Enum constant in enum class chemaxon.alignment.AlignmentProperties.OrientationType: Deprecated.
MCSAlignment - Interface in chemaxon.alignment: Align molecules using the maximum common substructure (MCS) of the given molecules.
MCSAlignment.Factory - Class in chemaxon.alignment: Factory class for ConformationAlignment.
MCSAlignmentResult - Interface in chemaxon.alignment: Result class for MCS alignment calculation.
McsCustomMatcher - Interface in chemaxon.search.mcs: Interface for custom matching of atoms and bonds for MaxCommonSubstructure search.
McsCustomMatcherFactory - Interface in chemaxon.search.mcs: Factory interface for creating McsCustomMatcher objects.
McsSearchMode - Enum Class in chemaxon.search.mcs: Enum type for search modes of MaxCommonSubstructure (MCS) algorithms.
McsSearchOptions - Class in chemaxon.search.mcs: Options class for MaxCommonSubstructure (MCS) search.
McsSearchOptions.Builder - Class in chemaxon.search.mcs: Builder class for creating immutable instances of the enclosing McsSearchOptions class.
McsSearchResult - Class in chemaxon.search.mcs: Class for representing the result of a MaxCommonSubstructure (MCS) search.
McsSearchResult(Molecule, int[], int[], int) - Constructor for class chemaxon.search.mcs.McsSearchResult: Creates a SearchResult object representing a common substructure of two molecules.
md - Variable in class chemaxon.descriptors.MDParameters: this object is needed to access default dissimilarity functions
Md - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Md.
MDGenerator - Class in chemaxon.descriptors: Base class for all kinds of MolecularDescriptor generators.
MDGenerator() - Constructor for class chemaxon.descriptors.MDGenerator: Created an object.
MDGeneratorException - Exception Class in chemaxon.descriptors: Exception definition for the MolecularDescriptor.generate() interface.
MDGeneratorException() - Constructor for exception class chemaxon.descriptors.MDGeneratorException: Creates new MDGeneratorException without detailed explanation.
MDGeneratorException(String) - Constructor for exception class chemaxon.descriptors.MDGeneratorException: Constructs a MDGeneratorException with the specified detailed message.
MDGeneratorException(String, Throwable) - Constructor for exception class chemaxon.descriptors.MDGeneratorException: Constructs a MDGeneratorException with the specified detail message and cause.
MDGeneratorException(Throwable) - Constructor for exception class chemaxon.descriptors.MDGeneratorException: Constructs a MDGeneratorException with the specified cause.
MDL_DOWNWEDGE_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: MDL style down wedge orientation.
MDL_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable: MDL like multiple group expansion flag.
MDocSource - Class in chemaxon.formats: Marvin document source.
MDocSource() - Constructor for class chemaxon.formats.MDocSource
MDocStorage - Class in chemaxon.marvin.common: Sparse dynamic document storage and reader.
MDocStorage() - Constructor for class chemaxon.marvin.common.MDocStorage: Constructs a document storage.
MDocStorage(int) - Constructor for class chemaxon.marvin.common.MDocStorage: Constructs a document storage.
MDocStorage.CancellationException - Exception Class in chemaxon.marvin.common: Exception indicating that records are not available because the user cancelled file reading.
MDocStorage.Listener - Interface in chemaxon.marvin.common: Document production listener.
MDocStorage.RecordUnavailableException - Exception Class in chemaxon.marvin.common: Requested record is not available in the source.
MDocument - Class in chemaxon.struc: Marvin document.
MDocument(MDocument) - Constructor for class chemaxon.struc.MDocument: Copy constructor.
MDocument(MDocument, boolean) - Constructor for class chemaxon.struc.MDocument: Copy constructor.
MDocument(Molecule[]) - Constructor for class chemaxon.struc.MDocument: Creates a document for the specified molecule animation.
MDocument(MoleculeGraph) - Constructor for class chemaxon.struc.MDocument: Creates a document for the specified molecule graph.
MDocument.CheckerMark - Class in chemaxon.struc: Provides information for Structure Checker highlight.
MDocument.Prop - Class in chemaxon.struc: Property that stores an MDocument.
MDoubleArrayProp - Class in chemaxon.struc.prop: Double array property.
MDoubleArrayProp(double[]) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp: Constructs a property object from a double array.
MDoubleArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MDoubleArrayProp: Constructs a double array property from a string value.
MDoubleProp - Class in chemaxon.struc.prop: Double floating point property.
MDoubleProp(double) - Constructor for class chemaxon.struc.prop.MDoubleProp: Constructs a property object from a double floating point value.
MDoubleProp(String) - Constructor for class chemaxon.struc.prop.MDoubleProp: Constructs a double floating point property from a string value.
MDParameters - Class in chemaxon.descriptors: MolecularDescriptor parameter settings.
MDParameters() - Constructor for class chemaxon.descriptors.MDParameters: Creates and initializes an empty object.
MDParametersException - Exception Class in chemaxon.descriptors: MDParametersException reports all kinds of parametrization related failures.
MDParametersException() - Constructor for exception class chemaxon.descriptors.MDParametersException: Creates an exception object with a default message.
MDParametersException(String) - Constructor for exception class chemaxon.descriptors.MDParametersException: Creates an exception object with a given message.
MDParametersException(String, Throwable) - Constructor for exception class chemaxon.descriptors.MDParametersException: Creates an exception object with a given message and cause.
MEASUREMENT_KEY - Static variable in class chemaxon.standardizer.actions.RemoveFragmentAction: Key of measurement for parsing and property change
MEDIUM - Enum constant in enum class chemaxon.calculations.nmr.NMRErrorClassification: Medium quality
MEFlow - Class in chemaxon.struc.graphics: Electron flow arrow.
MEFlow() - Constructor for class chemaxon.struc.graphics.MEFlow: Contructs an empty 2 electron flow arrow.
MEFlow(int) - Constructor for class chemaxon.struc.graphics.MEFlow: Contructs an empty electron flow arrow.
MEFlow(MEFlow) - Constructor for class chemaxon.struc.graphics.MEFlow: Copy constructor.
MEFlow(MPoint, MPoint, int) - Constructor for class chemaxon.struc.graphics.MEFlow: Contructs an electron flow arrow with the specified endpoints.
MEFlowBasePoint - Class in chemaxon.struc.graphics: Electron flow arrow base point.
MEFlowBasePoint() - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint: Contructs an empty point object.
MEFlowBasePoint(MEFlowBasePoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint: Copy constructor.
MEFlowBasePoint(MolAtom, MPoint) - Constructor for class chemaxon.struc.graphics.MEFlowBasePoint: Contructs a point object.
MElectron - Class in chemaxon.struc.graphics: Represents an electron associated with a molecular atom.
MElectron() - Constructor for class chemaxon.struc.graphics.MElectron
MElectron(Point3D, MolAtom) - Constructor for class chemaxon.struc.graphics.MElectron
MElectronContainer - Class in chemaxon.struc.graphics: Container for managing electrons and radicals in a molecular structure.
MElectronContainer() - Constructor for class chemaxon.struc.graphics.MElectronContainer: This constructor is only available for MRVImport
MElectronContainer(MElectron) - Constructor for class chemaxon.struc.graphics.MElectronContainer: Creates a Radical from one MElectron
MElectronContainer(MElectron, MElectron) - Constructor for class chemaxon.struc.graphics.MElectronContainer: Creates a LonePair by the clones of the MElectrons.
MElectronContainer(MElectron, MElectron, boolean) - Constructor for class chemaxon.struc.graphics.MElectronContainer: Creates a LonePair which can represent radicals or lonepairs by the clones of the MElectrons.
MEllipse - Class in chemaxon.struc.graphics: Ellipse object.
MEllipse() - Constructor for class chemaxon.struc.graphics.MEllipse: Constructs an ellipse.
MEllipse(MEllipse) - Constructor for class chemaxon.struc.graphics.MEllipse: Copy constructor.
MEllipse(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MEllipse: Constructs a ellipse with the specified corner points.
MEllipse(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MEllipse: Constructs a ellipse with the specified corner points and color.
MENU_CUSTOMIZATION_FILE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "menuconfig".
MENUBAR - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "menubar".
MER - Enum constant in enum class chemaxon.struc.SgroupType
merge(CheckerFixerFactory) - Method in class chemaxon.structurechecker.CheckerFixerFactory.Builder: Adds all checkers, fixers and properties registered in the given other factory instance.
MERGE_DISTANCE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "mergedst".
mergeBrackets(MolBond, MolBond) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Sets the crossing bonds of this S-group so that they will share a common bracket.
mergeComponentParts(MoleculeGraph, int, boolean) - Method in class chemaxon.struc.RxnMolecule: Finds those component parts that are contained in the molecule graph m and creates a new component containing all atoms of m, splitting them from the previous merges.
mergeFrags(int, int, int) - Method in class chemaxon.struc.MoleculeGraph: Merges two connected components of the given fragmentation type.
mergeProperties(UserSettings, MPropertyContainer, Rectangle) - Static method in class chemaxon.marvin.util.ImageExportUtil: Merge the properties of UserSettings with the GUI properties.
If both has a value for a given key, the value stored in GUI properties will be used.
MesomerizeAction - Class in chemaxon.standardizer.actions: Standardizer action that generates the canonical mesomeric form of the molecule.
MesomerizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.MesomerizeAction: Initializes the action
message - Variable in class chemaxon.naming.document.DocumentAnnotator.ProgressInfo: A message about the current state of the annotation.
METALCONNECTED_H - Static variable in class chemaxon.struc.MolAtom: Hydrogen atom(s) connected to metal.
METALLOCENE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that incorrectly drawn metallocenes have been found in the molecule
METALLOCENE_AMBIGUOUS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that incorrectly drawn metallocenes have been found in the molecule
MetalloceneCheckerResult - Class in chemaxon.checkers.result: Structure checker result for metallocene-related issues.
MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult: Deprecated.
use MetalloceneCheckerResult(StructureChecker, List, List, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List, List, int) instead
MetalloceneCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, List<List<MolAtom>>, List<MolAtom>, int) - Constructor for class chemaxon.checkers.result.MetalloceneCheckerResult: Constructor which initialize all the properties.
MetalloceneErrorChecker - Class in chemaxon.checkers: MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats, that are not coordinate multicenters.
MetalloceneErrorChecker() - Constructor for class chemaxon.checkers.MetalloceneErrorChecker: Default constructor
MetalloceneFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which converts a single incorrectly drawn metallocene into multicenter based coordinate bond representation.
MetalloceneFixer() - Constructor for class chemaxon.fixers.MetalloceneFixer
METHOD - Static variable in class chemaxon.calculations.services.ServiceDescriptor: Property key for Method name to call as String
METHOD_KEY - Static variable in class chemaxon.standardizer.actions.RemoveFragmentAction: Key of method for parsing and property change
metricIndexes - Variable in class chemaxon.descriptors.MDParameters: convert parameterized indexes to MolecularDescriptor metric indexes
Metrics - Class in chemaxon.descriptors: The Metrics class implements dissimilarity metrics for MolecularDescriptors.
Metrics() - Constructor for class chemaxon.descriptors.Metrics
MetricsType - Enum Class in chemaxon.descriptors: Enumeration of similarity metric types (Tanimoto, Tversky, Dice, Euclidean, etc.) used for molecular descriptor comparison.
MFileFormat - Class in chemaxon.formats: File format descriptor class.
MFileFormatUtil - Class in chemaxon.formats: File format related utility functions.
MFileFormatUtil() - Constructor for class chemaxon.formats.MFileFormatUtil
MFont - Class in chemaxon.struc.graphics: Font wrapper class that does not require an X server.
MFont(MFont) - Constructor for class chemaxon.struc.graphics.MFont: Copy constructor.
MFont(Font) - Constructor for class chemaxon.struc.graphics.MFont: Create a wrapper for the specified AWT font.
MFont(String) - Constructor for class chemaxon.struc.graphics.MFont: Parses a font from a string.
MFont(String, int, double) - Constructor for class chemaxon.struc.graphics.MFont: Contructs a font.
MFontProp - Class in chemaxon.struc.prop: Font property.
MFontProp(MFont) - Constructor for class chemaxon.struc.prop.MFontProp
MFontProp(Font) - Constructor for class chemaxon.struc.prop.MFontProp
MFontProp(String) - Constructor for class chemaxon.struc.prop.MFontProp
Mg - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Mg.
MGPERML - Enum constant in enum class chemaxon.calculations.solubility.SolubilityUnit: Solubility is expressed in mg/ml unit.
MHashProp - Class in chemaxon.struc.prop: Linked hash map of properties.
MHashProp() - Constructor for class chemaxon.struc.prop.MHashProp: Constructs a property object from an integer value.
MHashProp(MHashProp, Set) - Constructor for class chemaxon.struc.prop.MHashProp: Copy constructor.
MHCoords3DProp - Class in chemaxon.struc.prop: 3D coordinates array property.
MHCoords3DProp(String) - Constructor for class chemaxon.struc.prop.MHCoords3DProp: Constructs a point array property from a string value.
MHCoords3DProp(Map<MolAtom, Point3D[]>, MoleculeGraph) - Constructor for class chemaxon.struc.prop.MHCoords3DProp: Constructs a property object from a map.
MHCoords3DProp(Map<Integer, Point3D[]>, long) - Constructor for class chemaxon.struc.prop.MHCoords3DProp: Constructs a property object from a map.
MICROSPECIES_MAJORMS2 - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
MICROSPECIES_MSDISTR2 - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
MIN_RECENT_FILE_LIST_SIZE - Static variable in class chemaxon.marvin.common.UserSettings: The minimum size of sketchRecentFileList
MIN_RING_SIZE_FOR_TRANS_DB - Static variable in class chemaxon.struc.MoleculeGraph: The minimal size of the ring for the existence of TRANS double bond.
minFragmentSize(int) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets the minimum required size of the fragments of MCS.
MinMaxDistance - Class in chemaxon.alignment: Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.
MinMaxDistance() - Constructor for class chemaxon.alignment.MinMaxDistance
minNonEmptyId - Variable in class chemaxon.descriptors.MDGenerator
minNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator
MINOR_PRODUCT_TAG - Static variable in class chemaxon.reaction.Reactor
minParameterCount() - Element in annotation interface chemaxon.chemterms.ChemTermsContext.ProvidesFunction: The lower end of the allowed parameter count range (inclusive).
minParameterCount() - Method in interface chemaxon.chemterms.CustomFunction: Returns the minimum parameter count of this function (a non-negative integer).
MIntegerArrayProp - Class in chemaxon.struc.prop: Integer array property.
MIntegerArrayProp(int[]) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp: Constructs a property object from an integer value.
MIntegerArrayProp(String, int, int) - Constructor for class chemaxon.struc.prop.MIntegerArrayProp: Constructs an integer array property from a string value.
MIntegerProp - Class in chemaxon.struc.prop: Integer property.
MIntegerProp(int) - Constructor for class chemaxon.struc.prop.MIntegerProp: Constructs a property object from an integer value.
MIntegerProp(String) - Constructor for class chemaxon.struc.prop.MIntegerProp: Constructs an integer property from a string value.
MISSING_ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atoms without atom map numbers have been found in the molecule
MISSING_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that some R-group definitions are missing from the molecule
MissingAtomMapChecker - Class in chemaxon.checkers: MissingAtomMapChecker detects atoms without atom map numbers.
MissingAtomMapChecker() - Constructor for class chemaxon.checkers.MissingAtomMapChecker: Default constructor
MissingRGroupChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting missing R-group definition errors.
MissingRGroupChecker() - Constructor for class chemaxon.checkers.MissingRGroupChecker: Initializes the checker
MIXTURE - Enum constant in enum class chemaxon.struc.SgroupType
MListProp - Class in chemaxon.struc.prop: Property list property.
MListProp() - Constructor for class chemaxon.struc.prop.MListProp: Constructs a property object from a list.
MListProp(MListProp, Set) - Constructor for class chemaxon.struc.prop.MListProp: Copy constructor.
MM_MASK - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Mouse motion mask in display option flags.
MM_MODES - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Mouse motion modes.
MM_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Mouse motion mode offset in display option flags.
MM_ROT3D - Static variable in interface chemaxon.rendering.constants.DispOptConsts: 3D rotation motion mode.
MM_ROTZ - Static variable in interface chemaxon.rendering.constants.DispOptConsts: 2D rotation (about Z axis) motion mode.
MM_ZOOM - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Zoom mouse motion mode.
MM_ZOOMROT - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Zoom-rotate mouse motion mode.
MMF_FIELD - Static variable in class chemaxon.marvin.common.TableOptions: Main molecule is a field in at least one record.
MMF_NOT_FIELD - Static variable in class chemaxon.marvin.common.TableOptions: Main molecule is not a field in at least one record.
MMF_UNSET - Static variable in class chemaxon.marvin.common.TableOptions: Not yet decided whether the main molecule is a field or not.
MMidPoint - Class in chemaxon.struc.graphics: Middle point in a line.
MMidPoint(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint: Copy constructor.
MMidPoint(MPolyline, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MMidPoint: Contructs a middle point object.
MMidPoint.Sticky - Class in chemaxon.struc.graphics: Fixed middle point that can be a point of a polyline.
MMoleculeMovie - Class in chemaxon.struc.graphics: Molecule animation.
MMoleculeMovie(MMoleculeMovie) - Constructor for class chemaxon.struc.graphics.MMoleculeMovie: Copy constructor.
MMoleculeMovie(Molecule[]) - Constructor for class chemaxon.struc.graphics.MMoleculeMovie: Contructs a molecule animation.
MMoleculeProp - Class in chemaxon.struc.prop: Molecule property.
MMoleculeProp(Molecule) - Constructor for class chemaxon.struc.prop.MMoleculeProp: Constructs a property object from a molecule.
MMoleculeStringProp - Class in chemaxon.struc.prop: Molecule string property.
MMoleculeStringProp(String, String, String) - Constructor for class chemaxon.struc.prop.MMoleculeStringProp: Constructs a property.
MMPAlignment - Class in chemaxon.alignment: 3D Molecular alignment that uses the maximum common substructure to align a pair of structures.
MMPAlignment(Molecule, Molecule) - Constructor for class chemaxon.alignment.MMPAlignment: Constructs an MMPAlignment object for later alignment of two structures.
MMPAlignment(Molecule, Molecule, MMPAlignmentProperties) - Constructor for class chemaxon.alignment.MMPAlignment: Constructs an MMPAlignment object for later alignment of two structures.
MMPAlignmentProperties - Class in chemaxon.alignment: Input property settings for MMPAlignment.
MMPAlignmentProperties() - Constructor for class chemaxon.alignment.MMPAlignmentProperties: Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double) - Constructor for class chemaxon.alignment.MMPAlignmentProperties: Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean) - Constructor for class chemaxon.alignment.MMPAlignmentProperties: Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, boolean, int) - Constructor for class chemaxon.alignment.MMPAlignmentProperties: Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode, AlignmentAccuracyMode, double, int) - Constructor for class chemaxon.alignment.MMPAlignmentProperties: Constructs a MMPAlignmentProperties object.
MMPAlignmentResult - Class in chemaxon.alignment: Results of the MMPAlignment process.
Mn - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Mn.
MNameTextBox - Class in chemaxon.struc.graphics: Name Text box object to display IUPAC name.
MNameTextBox() - Constructor for class chemaxon.struc.graphics.MNameTextBox: Constructs an empty name text box.
MNameTextBox(MNameTextBox) - Constructor for class chemaxon.struc.graphics.MNameTextBox: Copy constructor.
Mo - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Mo.
MObject - Class in chemaxon.struc: Paintable object of a Marvin document.
MObject(MObject) - Constructor for class chemaxon.struc.MObject: Copy constructor.
MObject(Color, Color, Color) - Constructor for class chemaxon.struc.MObject: Contructs a paintable object with the specified color.
MObjectProp - Class in chemaxon.struc.prop: Property that stores any object.
MObjectProp(Object) - Constructor for class chemaxon.struc.prop.MObjectProp: Constructs a property object.
MObjectProp(String) - Constructor for class chemaxon.struc.prop.MObjectProp: Constructs a property from a string value.
MODE_COMBINATORIAL - Static variable in class chemaxon.reaction.ConcurrentReactorProcessor: Mode constant: combinatorial mode.
MODE_SEQUENTIAL - Static variable in class chemaxon.reaction.ConcurrentReactorProcessor: Mode constant: sequential mode.
MODEL_LARGE - Static variable in class chemaxon.calculations.PkaPlugin: Calculation model: large (always precise, can take more time).
MODEL_SMALL - Static variable in class chemaxon.calculations.PkaPlugin: Calculation model: small (precise up to the specified number of ionizable atoms).
MODERATE - Enum constant in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory: Moderate solubility.
MODIFICATION - Enum constant in enum class chemaxon.struc.SgroupType
modifyAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes: Adds atoms to the "modified atom" list.
modifyAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes: Adds atoms to the "modified atom" list.
modifyAtom(MolAtom) - Method in class chemaxon.standardizer.Changes: Adds an atom to the "modified atom" list.
modifyAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes: Adds an atom to the "modified atom" list.
MOL - Static variable in class chemaxon.chemterms.MolContext
MOL - Static variable in class chemaxon.formats.MFileFormat: MDL Molfiles and Rgfiles.
MOL_LOADER_FINISHED_EVENT - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "molLoaderFinishedEvent".
MOL_UID_PROPERTY - Static variable in class chemaxon.naming.document.DocumentAnnotator
MOL_V2_OUT - Static variable in class chemaxon.formats.MFileFormat
MOL_V3_OUT - Static variable in class chemaxon.formats.MFileFormat: MDL Extended Molfiles and Rgfiles.
MOL2 - Static variable in class chemaxon.formats.MFileFormat: Tripos Mol2 files.
MolAligner - Class in chemaxon.alignment: Tool for aligning a target molecule to a pattern molecule.
MolAligner() - Constructor for class chemaxon.alignment.MolAligner: Creates a new MolAligner object.
MolAligner(Molecule, Molecule) - Constructor for class chemaxon.alignment.MolAligner: Creates a new MolAligner object while setting the pattern and target molecules
MolAtom - Class in chemaxon.struc: Atom object in a molecule.
MolAtom(double, double) - Constructor for class chemaxon.struc.MolAtom: Construct a carbon atom at the specified location.
MolAtom(int) - Constructor for class chemaxon.struc.MolAtom: Construct an atom of the specified type at the origin.
MolAtom(int, double, double, double) - Constructor for class chemaxon.struc.MolAtom: Construct an atom.
MolBond - Class in chemaxon.struc: Bond object in a molecule.
MolBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.MolBond: Construct a single bond between two atoms.
MolBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.MolBond: Construct a bond between two atoms.
MolBond(MolAtom, MolAtom, BondType) - Constructor for class chemaxon.struc.MolBond: Construct a bond between two atoms.
MolBond(MolBond) - Constructor for class chemaxon.struc.MolBond: Copy constructor.
MolComparator - Class in chemaxon.search.api: Interface for comparing atoms, bonds, etc.
MolComparator() - Constructor for class chemaxon.search.api.MolComparator
MolContext - Class in chemaxon.chemterms: Expression evaluation context containing a single molecule.
MolContext() - Constructor for class chemaxon.chemterms.MolContext: Constructor.
MolContext(Molecule) - Constructor for class chemaxon.chemterms.MolContext: Creates a MolContext with the given input molecule.
MolConverter - Class in chemaxon.formats.converter: Converts between molecule file formats.
MolConverter(MolConverter.Builder) - Constructor for class chemaxon.formats.converter.MolConverter: Creates a MolConverter object.
MolConverter(InputStream, OutputStream, String, boolean) - Constructor for class chemaxon.formats.converter.MolConverter: Creates a MolConverter object.
MolConverter(InputStream, String, String, boolean) - Constructor for class chemaxon.formats.converter.MolConverter: Use this constructor if you do not need output buffering but want to determine output file positions.
MolConverter.Builder - Class in chemaxon.formats.converter: MolConverter builder.
molCount - Variable in class chemaxon.descriptors.MDGenerator: variables to collect statistical data in
MolecularDescriptor - Class in chemaxon.descriptors: Generic definition of molecular descriptors.
MolecularDescriptor() - Constructor for class chemaxon.descriptors.MolecularDescriptor: Default constructor, creates an empty object.
MolecularDescriptor(MDParameters) - Constructor for class chemaxon.descriptors.MolecularDescriptor: Creates a new MolecularDescriptor with the given parameters.
MolecularDescriptor(MolecularDescriptor) - Constructor for class chemaxon.descriptors.MolecularDescriptor: Copy constructor, creates am identical copy of the MolecularDescriptor passed as a parameter.
MolecularDynamicsPlugin - Class in chemaxon.calculations: Molecular Dynamics plugin.
MolecularDynamicsPlugin() - Constructor for class chemaxon.calculations.MolecularDynamicsPlugin: Creates a new instance of MolecularDynamicsPlugin
molecule - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable: The Molecule which will be transferred to the clipboard.
molecule - Variable in class chemaxon.structurechecker.BasicCheckerRunner: Deprecated.

The Molecule instance to check.
Molecule - Class in chemaxon.struc: Represents a molecule (a chemical structure).
Molecule() - Constructor for class chemaxon.struc.Molecule: Constructs an empty 2-dimensional molecule.
Molecule(Molecule, int, int) - Constructor for class chemaxon.struc.Molecule: Constructs a molecule or fragment with the specified capacity for storing atoms and bonds.
Molecule(Molecule, MolAtom) - Constructor for class chemaxon.struc.Molecule: Deprecated, for removal: This API element is subject to removal in a future version.
use Molecule() and MoleculeGraph.add(MolAtom)
Molecule(Molecule, MolBond) - Constructor for class chemaxon.struc.Molecule: Deprecated, for removal: This API element is subject to removal in a future version.
use Molecule() and Molecule.add(MolBond)
MOLECULE - Enum constant in enum class chemaxon.marvin.common.CellType
MOLECULE - Static variable in class chemaxon.calculations.CalculatorPlugin: Calculation domain type: calculation refers to the molecule.
MOLECULE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "mol".
MOLECULE_BACKGROUND - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "molbg".
MOLECULE_CHANGED - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "molChanged".
MOLECULE_CHARGE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the sum charge of the molecule is not zero
MOLECULE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "molFormat".
MoleculeChargeChecker - Class in chemaxon.checkers: MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.
MoleculeChargeChecker() - Constructor for class chemaxon.checkers.MoleculeChargeChecker: Default constructor
MoleculeGraph - Class in chemaxon.struc: A chemical graph consisting of MolAtom nodes and MolBond edges.
MoleculeGraph() - Constructor for class chemaxon.struc.MoleculeGraph: Construct a 2 dimensional molecule.
MoleculeImporter - Class in chemaxon.formats: Molecule importer.
MoleculeImporter(File) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the file.
MoleculeImporter(File, String) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the file.
MoleculeImporter(InputStream) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the input stream.
MoleculeImporter(InputStream, String) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the stream.
MoleculeImporter(InputStream, String, String) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the stream.
MoleculeImporter(String) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the file.
MoleculeImporter(String, String) - Constructor for class chemaxon.formats.MoleculeImporter: Constructs a new importer for the file.
MoleculeIterator - Interface in chemaxon.formats: Molecule iterator interface.
MoleculeIteratorFactory - Class in chemaxon.formats: Molecule iterator factory.
MoleculeIteratorFactory() - Constructor for class chemaxon.formats.MoleculeIteratorFactory
MOLECULES - Static variable in class chemaxon.calculations.CalculatorPlugin: Calculation domain type: calculation refers to multiple molecule output.
MolExporter - Class in chemaxon.formats: Molecule exporter class.
MolExporter(OutputStream, String) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExporter(OutputStream, String, boolean, String[]) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExporter(OutputStream, String, boolean, String[], String) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExporter(OutputStream, String, String) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExporter(Writer, String) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExporter(String, String) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExporter(String, String, int, String[], String) - Constructor for class chemaxon.formats.MolExporter: Creates a molecule exporter.
MolExportException - Exception Class in chemaxon.formats: Molecule export exception.
MolExportException(String) - Constructor for exception class chemaxon.formats.MolExportException: Creates a molecule export exception with the specified message.
MolExportException(String, Throwable) - Constructor for exception class chemaxon.formats.MolExportException: Creates a molecule export exception with the specified message and cause.
MolExportException(Throwable) - Constructor for exception class chemaxon.formats.MolExportException: Creates a molecule export exception with the specified cause.
MolExportModule - Class in chemaxon.formats: Abstract base class of molecule export modules.
MolExportModule() - Constructor for class chemaxon.formats.MolExportModule
MolFilter - Interface in chemaxon.core.util: Molecule filter interface.
MolFormatException - Exception Class in chemaxon.formats: Something's wrong with a molecule file format.
MolFormatException() - Constructor for exception class chemaxon.formats.MolFormatException: Creates a molecule format exception.
MolFormatException(String) - Constructor for exception class chemaxon.formats.MolFormatException: Creates a molecule format exception with the specified message.
MolFormatException(String, Throwable) - Constructor for exception class chemaxon.formats.MolFormatException: Creates a molecule format exception with the specified message and cause.
MolFormatException(Throwable) - Constructor for exception class chemaxon.formats.MolFormatException: Creates a molecule format exception with the specified cause.
MolImporter - Class in chemaxon.formats: Molecule file importer.
MolImporter(File) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for a file.
MolImporter(File, String) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for a file.
MolImporter(InputStream) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for an input stream.
MolImporter(InputStream, String) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for an input stream.
MolImporter(InputStream, String, String) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for an input stream.
MolImporter(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for an input stream.
MolImporter(String) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer for a file.
MolImporter(String, Component, String) - Constructor for class chemaxon.formats.MolImporter: Create a molecule importer with a progress monitor.
MolImporterInterface - Interface in chemaxon.formats: Interface for molecule importer classes.
MolImportModule - Class in chemaxon.formats: Base class of Molecule import modules.
MolImportModule() - Constructor for class chemaxon.formats.MolImportModule
MolInputStream - Class in chemaxon.formats: Molecule input stream that has the ability to determine the input file format.
MolInputStream(InputStream) - Constructor for class chemaxon.formats.MolInputStream: Create a molecule input stream from an ordinary one, and determine the format.
MolInputStream(InputStream, String) - Constructor for class chemaxon.formats.MolInputStream: Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(InputStream, String, String) - Constructor for class chemaxon.formats.MolInputStream: Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(InputStream, String, String, String) - Constructor for class chemaxon.formats.MolInputStream: Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MOLMASS - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement: Mass of the molecule
MOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil: Read multi-molecule files as movies.
molPanel - Variable in class chemaxon.marvin.beans.MarvinPane: Underlying panel.
MOLPERL - Enum constant in enum class chemaxon.calculations.solubility.SolubilityUnit: Solubility is expressed in mol/l unit.
MolPrinter - Class in chemaxon.marvin.beans: Molecule renderer that can draw a molecule to a graphics context using various display settings.
MolPrinter() - Constructor for class chemaxon.marvin.beans.MolPrinter: Constructs a molecule renderer for an empty molecule.
MolPrinter(MDocument) - Constructor for class chemaxon.marvin.beans.MolPrinter: Constructs a molecule renderer for the specified document.
MolPrinter(MoleculeGraph) - Constructor for class chemaxon.marvin.beans.MolPrinter: Constructs a molecule renderer for the specified molecule.
MolRenderer - Class in chemaxon.marvin.beans: MolRenderer is a simple TableCellRenderer component based on MolPrinter that can be used to render Molecule objects in JTables.
MolRenderer() - Constructor for class chemaxon.marvin.beans.MolRenderer
MolSearch - Class in chemaxon.search: Atom-by-atom structure search.
MolSearch() - Constructor for class chemaxon.search.MolSearch: Constructs a MolSearch object.
MolSearchOptions - Class in chemaxon.search.api.options: Class to encapsulate search options used by molecule search implementations.
MolSearchOptions(int) - Constructor for class chemaxon.search.api.options.MolSearchOptions: Creates a MolSearchOptions object while setting different search options according to a predefined search type.
molToScreenCoords(Point3D, Point2D) - Method in class chemaxon.marvin.beans.MolPrinter: Converts molecular coordinates to 2D screen coordinates.
monitor - Variable in class chemaxon.structurechecker.AdvancedCheckerRunner
MONO_SCHEME - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Monochrome color scheme in display option flags.
MONO_SCHEME_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Monochrome color scheme.
MONOMER - Enum constant in enum class chemaxon.struc.SgroupType
MONOVALENT - Enum constant in enum class chemaxon.struc.Radical: Monovalent radical center.
MORE_ENABLED - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "moreEnabled".
MORE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: multiple error message for checker
moreErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the more than one error message for the checker
moveCorners(double, double) - Method in class chemaxon.struc.MolAtom: Translates the coordinates of the atom label.
moveMainMoleculeGraphToFront() - Method in class chemaxon.struc.MDocument: Move the main molecule graph to the top of stack.
moveMoleculeMovieToFront() - Method in class chemaxon.struc.MDocument: Move the molecule movie (if exists) to the top of stack.
moveObject(MObject, int) - Method in class chemaxon.struc.MDocument: Move an object to another place in the stack.
moveTo(Point3D) - Method in class chemaxon.struc.MoleculeGraph: Move the molecule.
MP_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "mpVisible".
MP_VISIBLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "mpVisible" property.
MPoint - Class in chemaxon.struc: Point object in Marvin documents.
MPoint(double, double) - Constructor for class chemaxon.struc.MPoint: Contructs a point object.
MPoint(double, double, double) - Constructor for class chemaxon.struc.MPoint: Contructs a point object.
MPoint(MPoint) - Constructor for class chemaxon.struc.MPoint: Copy constructor.
MPoint(Point3D) - Constructor for class chemaxon.struc.MPoint: Constructs a point object.
MPolyline - Class in chemaxon.struc.graphics: Polyline object.
MPolyline() - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs an empty line.
MPolyline(boolean, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline: Creates a closed polyline.
MPolyline(MPolyline) - Constructor for class chemaxon.struc.graphics.MPolyline: Copy constructor.
MPolyline(MPolyline, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs a polyline from the specified starting polyline and endpoint.
MPolyline(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs a line with the specified endpoints.
MPolyline(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs a line with the specified endpoints.
MProgressMonitor - Interface in chemaxon.core.util: Deprecated, for removal: This API element is subject to removal in a future version.
Use ProgressMonitor instead.
MProp - Class in chemaxon.struc: Property base class.
MProp() - Constructor for class chemaxon.struc.MProp
MPropertyContainer - Class in chemaxon.struc: Property container.
MPropertyContainer() - Constructor for class chemaxon.struc.MPropertyContainer: Creates an empty property container.
MPropHandler - Class in chemaxon.formats: Property factory.
MPropHandler() - Constructor for class chemaxon.formats.MPropHandler
MRArrow - Class in chemaxon.struc.graphics: Reaction arrow object.
MRArrow() - Constructor for class chemaxon.struc.graphics.MRArrow: Constructs an empty reaction arrow where end points are not set.
MRArrow(MRArrow) - Constructor for class chemaxon.struc.graphics.MRArrow: Copy constructor.
MRArrow(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRArrow: Constructs a graphical reaction arrow between two points.
MReactionSign - Class in chemaxon.struc.graphics: Special MTextBox desdendant for displaying Reaction signs.
MReactionSign() - Constructor for class chemaxon.struc.graphics.MReactionSign
MReactionSign(Point3D) - Constructor for class chemaxon.struc.graphics.MReactionSign
MRectangle - Class in chemaxon.struc.graphics: Rectangle object.
MRectangle() - Constructor for class chemaxon.struc.graphics.MRectangle: Constructs a rectangle.
MRectangle(MRectangle) - Constructor for class chemaxon.struc.graphics.MRectangle: Copy constructor.
MRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRectangle: Constructs a rectangle with the specified corner points.
MRectangle(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MRectangle: Constructs a rectangle with the specified corner points.
MRectanglePoint - Class in chemaxon.struc.graphics: Rectangle point object.
MRectanglePoint(MRectangle, int, double, double, double) - Constructor for class chemaxon.struc.graphics.MRectanglePoint: Contructs a rectangle corner point object.
MRectanglePoint(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint: Copy constructor.
MRectanglePoint.Sticky - Class in chemaxon.struc.graphics: Fixed rectangle point that can be a point of a polyline.
MRoundedRectangle - Class in chemaxon.struc.graphics: Rounded rectangle object.
MRoundedRectangle() - Constructor for class chemaxon.struc.graphics.MRoundedRectangle: Constructs a rounded rectangle
MRoundedRectangle(MRoundedRectangle) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle: Copy constructor.
MRoundedRectangle(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle: Constructs a rounded rectangle with the specified corner points.
MRoundedRectangle(MPoint, MPoint, double, double) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle: Constructs a rounded rectangle with the specified corner points.
MRoundedRectangle(MPoint, MPoint, double, double, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle: Constructs a rounded rectangle with the specified corner points and color.
MRoundedRectangle(MPoint, MPoint, Color) - Constructor for class chemaxon.struc.graphics.MRoundedRectangle: Constructs a rounded rectangle with the specified corner points and color.
MRV - Static variable in class chemaxon.formats.MFileFormat: Chemaxon Marvin Document.
MRV_OUTPUT_LEVEL - Static variable in class chemaxon.search.AbstractSearch: MRV format of the query and target is logged at this level.
MSA - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
MSAPlugin - Class in chemaxon.calculations: Plugin class for molecular surface area calculation.
MSAPlugin() - Constructor for class chemaxon.calculations.MSAPlugin: Constructor.
MSBMP - Static variable in class chemaxon.formats.MFileFormat: Windows Bitmap format.
MSelectionDocument - Class in chemaxon.struc: Selection document.
MSelectionDocument(MSelectionDocument) - Constructor for class chemaxon.struc.MSelectionDocument: Copy constructor.
MSelectionDocument(SelectionMolecule) - Constructor for class chemaxon.struc.MSelectionDocument: Creates a document for the specified molecule graph.
MSketch - Class in chemaxon.marvin.beans: Java independent serialization of the sketcher bean.
MSketch() - Constructor for class chemaxon.marvin.beans.MSketch: Constructor used for deserialization.
MSketch(MSketchPane) - Constructor for class chemaxon.marvin.beans.MSketch: Constructor used for serialization.
MSketchPane - Class in chemaxon.marvin.beans: The MarvinSketch Bean.
MSketchPane() - Constructor for class chemaxon.marvin.beans.MSketchPane: Constructs the sketcher.
MSketchPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MSketchPane: Constructs the sketcher with the specified user settings object.
MSketchPane(UserSettings, boolean) - Constructor for class chemaxon.marvin.beans.MSketchPane: Constructs the sketcher with the specified user settings object.
MSketchPane(UserSettings, boolean, JComponent) - Constructor for class chemaxon.marvin.beans.MSketchPane: Constructs the sketcher with the specified user settings object.
MSketchPaneBeanInfo - Class in chemaxon.marvin.beans: MarvinSketch bean information.
MSketchPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MSketchPaneBeanInfo
MStringProp - Class in chemaxon.struc.prop: String property.
MStringProp(String) - Constructor for class chemaxon.struc.prop.MStringProp: Constructs a property.
Mt - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Mt.
MTextAttributes - Class in chemaxon.struc.graphics: Text attributes.
MTextAttributes() - Constructor for class chemaxon.struc.graphics.MTextAttributes: Constructs a default attributes object.
MTextAttributes(int, int, Color, MFont, double, double, double) - Constructor for class chemaxon.struc.graphics.MTextAttributes: Constructs an attributes object.
MTextBox - Class in chemaxon.struc.graphics: Text box object.
MTextBox() - Constructor for class chemaxon.struc.graphics.MTextBox: Contructs an empty text box.
MTextBox(MTextBox) - Constructor for class chemaxon.struc.graphics.MTextBox: Copy constructor.
MTextBoxTransformation - Class in chemaxon.struc.graphics: Handles affine transformation of text boxes in molecular graphics.
MTextBoxTransformation(MTextBox, Transform3D, double) - Constructor for class chemaxon.struc.graphics.MTextBoxTransformation
MTextDocument - Class in chemaxon.struc.graphics: Text document consisting of sections with different attributes.
MTextDocument() - Constructor for class chemaxon.struc.graphics.MTextDocument: Constructs an empty document.
MTextDocument(MTextDocument) - Constructor for class chemaxon.struc.graphics.MTextDocument: Copy constructor.
MTextDocument(String) - Constructor for class chemaxon.struc.graphics.MTextDocument: Constructs a document from the specified string.
MTextDocument.Portion - Class in chemaxon.struc.graphics: Selected text.
MTextDocument.Section - Class in chemaxon.struc.graphics: Plain text section with uniform attributes.
MTransferable - Interface in chemaxon.marvin.datatransfer: The interface of Marvin transferable implementations.
MTransformable - Interface in chemaxon.struc: Interface for classes that are transformable in 3D.
mul(Transform3D) - Method in class chemaxon.struc.Transform3D: Multiplies by another matrix from right.
MULTI_CENTER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that invalid R-group definitions have been found in the molecule
MULTI_COMPONENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Deprecated, for removal: This API element is subject to removal in a future version.
StructureCheckerErrorType.MULTIPLE_COMPONENT is used instead
MULTICENTER - Enum constant in enum class chemaxon.struc.SgroupType
MULTICENTER - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of a central atom of a MulticenterSgroup.
MultiCenterChecker - Class in chemaxon.checkers: MultiCenterChecker detects structures containing multicenter atoms.
MultiCenterChecker() - Constructor for class chemaxon.checkers.MultiCenterChecker
MulticenterSgroup - Class in chemaxon.struc.sgroup: Multicenter S-group to represent complexes like metallocenes and position variation in Markush structures.
MulticenterSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup: Constructs a Multicenter S-group.
MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup: Copy constructor.
MulticenterSgroup(MulticenterSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MulticenterSgroup: Copy constructor.
MultiComponentChecker - Class in chemaxon.checkers: MultiComponentChecker detects structures containing disconnected components/fragments.
MultiComponentChecker() - Constructor for class chemaxon.checkers.MultiComponentChecker: Default constructor
MULTIPLE - Enum constant in enum class chemaxon.struc.SgroupType
MULTIPLE - Static variable in class chemaxon.formats.MolExporter: Use this flag to produce multiple output files.
MULTIPLE_COMPONENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains multiple components
MULTIPLE_STEREO_CENTER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains multiple stereo centers
MultipleSgroup - Class in chemaxon.struc.sgroup: Multiple S-group.
MultipleSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup: Constructs a multiple S-group.
MultipleSgroup(MultipleSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup: Copy constructor.
MultipleStereocenterChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting molecules containing multiple stereocenters.
MultipleStereocenterChecker() - Constructor for class chemaxon.checkers.MultipleStereocenterChecker: Initializes a multiple stereo checker
multipliedScore() - Method in class chemaxon.calculations.bbb.BBB.Property
MULTISET - Static variable in class chemaxon.formats.MFileFormatUtil: The multi-molecule file really contains multiple atom sets of one molecule.
MView - Class in chemaxon.marvin.beans: Java independent serialization of the viewer bean.
MView() - Constructor for class chemaxon.marvin.beans.MView: Constructor used for deserialization.
MView(MViewPane) - Constructor for class chemaxon.marvin.beans.MView: Constructor used for serialization.
MViewCellEditor - Class in chemaxon.marvin.beans: Implementation of AbstractCellEditor and TableCellEditor that can be used to assign a cell editor to Molecule objects in JTables.
MViewCellEditor() - Constructor for class chemaxon.marvin.beans.MViewCellEditor: Creates the cell editor.
MViewCellRenderer - Class in chemaxon.marvin.beans: MViewCellRenderer is a TableCellRenderer component that can be used to render Molecule objects in JTables.
MViewCellRenderer() - Constructor for class chemaxon.marvin.beans.MViewCellRenderer: Creates the cell renderer.
MViewPane - Class in chemaxon.marvin.beans: The MarvinView Bean.
MViewPane() - Constructor for class chemaxon.marvin.beans.MViewPane: Constructs the viewer.
MViewPane(UserSettings) - Constructor for class chemaxon.marvin.beans.MViewPane: Constructs the viewer with the specified user settings.
MViewPaneBeanInfo - Class in chemaxon.marvin.beans: MarvinView bean information.
MViewPaneBeanInfo() - Constructor for class chemaxon.marvin.beans.MViewPaneBeanInfo
MViewParams - Class in chemaxon.marvin.beans: MViewParams is a helper tool to generate parameter string to MViewPane.
MViewParams() - Constructor for class chemaxon.marvin.beans.MViewParams: For each new parameter generation a new MViewParams instance is necessary to be created.
MW - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Molecular weight.
MWHBN - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction: MW^(-0.5) * (HBN), where HBN = HBA + HBD.

N

N - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element N.
Na - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Na.
name - Variable in class chemaxon.calculations.services.ServiceArgument: the name of the argument
name() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the name of the checker
name() - Element in annotation interface chemaxon.fixers.FixerInfo: Returns the name of the fixer.
name() - Method in class chemaxon.formats.Encoding: Gets the name of the encoding.
name() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the name of the action
NAME - Static variable in class chemaxon.calculations.services.ServiceDescriptor: Property key for Service name as String
NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: name property of checker
NAME - Static variable in class chemaxon.fixers.StructureFixerDescriptor: name property of fixer
NAME - Static variable in class chemaxon.formats.MFileFormat: IUPAC Name files.
NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: name property of action
NAME_IO_WEB_SERVICE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier for parameter: "namingWebServiceURL" See Parameters and Events documentation.
NameConverter - Interface in chemaxon.naming: The interface of a converter from names to structures.
NameConverters - Class in chemaxon.naming: Maintains the list of custom and built-in name-to-structures converters.
NameFormatException - Exception Class in chemaxon.naming: A failure to convert a name to a structure.
NameFormatException(String) - Constructor for exception class chemaxon.naming.NameFormatException
NameFormatException(String, String) - Constructor for exception class chemaxon.naming.NameFormatException
NameFormatException(String, Throwable) - Constructor for exception class chemaxon.naming.NameFormatException
NameFormatException(Throwable) - Constructor for exception class chemaxon.naming.NameFormatException
NameFormatException.FilteredCase - Exception Class in chemaxon.naming: Exception signaling that the given input name should not be converted.
nameOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the name of the specified element.
NamePrefixException - Exception Class in chemaxon.naming: This exception should be thrown by a NameConverter to indicate that even though a name cannot be converted to a structure, it is the prefix of a valid name.
NamePrefixException() - Constructor for exception class chemaxon.naming.NamePrefixException
NamePrefixException(String) - Constructor for exception class chemaxon.naming.NamePrefixException
NamePrefixException(String, String) - Constructor for exception class chemaxon.naming.NamePrefixException
names() - Element in annotation interface chemaxon.chemterms.ChemTermsContext.ProvidesFunction: The names of the functions which are registered by this annotation.
nameStructureFormat - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions: The structure format used to represent hits converted from names.
nameStructureFormat(String) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
NAN - Static variable in class chemaxon.calculations.CalculatorPlugin: Double constant for Double.NaN.
NAN - Static variable in interface chemaxon.chemterms.CustomFunction: Possible result with the value of Double.NaN.
naturalWeightOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the natural weight of the element.
NAVIGATION_MODE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "navmode".
Nb - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Nb.
NBasic - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType
Nd - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Nd.
Ne - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ne.
needError() - Method in class chemaxon.calculations.LogPPlugin
needsAnalysisBoxWarning() - Method in class chemaxon.marvin.common.UserSettings
needsConfig() - Method in class chemaxon.descriptors.MolecularDescriptor: Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.Heavy: Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.LogP: Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.Mass: Indicates if class takes parameters from configuration file.
needsConfig() - Method in class chemaxon.descriptors.scalars.TPSA: Indicates if class takes parameters from configuration file.
needsMore - Variable in class chemaxon.formats.Recognizer
needsMore() - Method in class chemaxon.formats.Recognizer: Should we read more lines?
NEG - Static variable in class chemaxon.alignment.Pharmacophore3D
negOxOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the negative oxidation number.
NeighbourIterator(MolAtom) - Constructor for class chemaxon.struc.IteratorFactory.NeighbourIterator: Deprecated.

Constructs an iterator to process the bonds connecting to the specified atom.
NeutralizeAction - Class in chemaxon.standardizer.actions: Standardizer action that neutralizes charged atoms in the molecule.
NeutralizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.NeutralizeAction: Initializes the action
NeutralizeChargeFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which neutralize the charge of the atoms of the molecule
NeutralizeChargeFixer() - Constructor for class chemaxon.fixers.NeutralizeChargeFixer
newInstance() - Method in interface chemaxon.core.util.MProgressMonitor: Deprecated.

Creates new monitor with same parent, message, levels.
newInstance() - Static method in class chemaxon.search.mcs.MaxCommonSubstructure: Creates a new instance of MCS search algorithm using the default search options.
newInstance() - Method in class chemaxon.struc.Molecule: Creates a new Molecule object.
newInstance() - Method in class chemaxon.struc.MoleculeGraph: Creates a new MoleculeGraph object.
newInstance() - Method in class chemaxon.struc.RgMolecule: Creates a new RgMolecule object.
newInstance() - Method in class chemaxon.struc.RxnMolecule: Creates a new RxnMolecule object.
newInstance() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets a new MultipleSgroup instance.
newInstance(McsSearchOptions) - Static method in class chemaxon.search.mcs.MaxCommonSubstructure: Creates a new instance of MCS search algorithm using the given search options.
newInstance(String) - Static method in class chemaxon.descriptors.MolecularDescriptor: Creates a MolecularDescriptor specified by its name.
newInstance(String, String) - Static method in class chemaxon.descriptors.MolecularDescriptor: Creates a MolecularDescriptor specified by its name and xml parameter.
newInstanceFromXML(String) - Static method in class chemaxon.descriptors.MolecularDescriptor: Creates a new MolecularDescriptor instance according to the given parameter string.
newSelectionMolecule() - Method in class chemaxon.struc.Molecule: Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
newSelectionMolecule() - Method in class chemaxon.struc.RgMolecule: Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
newToOld() - Method in class chemaxon.standardizer.Changes: Returns the new to old atom index mapping.
newToOld(List<Changes>, Molecule) - Static method in class chemaxon.standardizer.Changes: Calculates the new to old atom index mapping based on a list of changes.
next() - Method in class chemaxon.calculations.stereo.StereoisomerEnumeration
next() - Method in interface chemaxon.formats.MoleculeIterator: Gets the next molecule.
next() - Method in class chemaxon.struc.IteratorFactory.AtomIterator: Deprecated.

Returns the next atom in the iteration.
next() - Method in class chemaxon.struc.IteratorFactory.AtomNeighbourIterator: Deprecated.

Returns the next atom in the iteration.
next() - Method in class chemaxon.struc.IteratorFactory.BondIterator: Deprecated.

Returns the next bond in the iteration.
next() - Method in class chemaxon.struc.IteratorFactory.BondNeighbourIterator: Deprecated.

Returns the next bond in the iteration.
next() - Method in class chemaxon.struc.IteratorFactory.RgComponentIterator: Deprecated.

Returns the next component in the iteration.
next() - Method in class chemaxon.struc.IteratorFactory.RxnComponentIterator: Deprecated.

Returns the next component in the iterator.
next() - Method in class chemaxon.struc.IteratorFactory.SgroupIterator: Deprecated.

Returns the next s-group in the iteration.
nextBondIndex(int) - Method in class chemaxon.struc.IteratorFactory.NeighbourIterator: Deprecated.

Returns the next bond index in the iteration according to the atom and bond related behavior specified in the factory.
nextDoc() - Method in class chemaxon.calculations.CalculatorPluginMDocSource: Produces the next document.
nextDoc() - Method in class chemaxon.formats.MDocSource: Produces the next document.
nextDoc() - Method in class chemaxon.formats.MolImporter: Reads the next document.
nextOpt(String, int, String) - Static method in class chemaxon.formats.MolExportModule: Tests whether the option string contains the specified substring at the specified position.
nextResult() - Method in class chemaxon.search.mcs.MaxCommonSubstructure: Finds the next MCS search result according to the specified options.
Nh - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Nh.
NHAc - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType
Ni - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ni.
NMR_CNMR - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
NMR_HNMR - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
NMRCalculator - Class in chemaxon.calculations.nmr: Class for NMR spectrum calculation.
NMRCalculator.Builder - Class in chemaxon.calculations.nmr: Builder class for NMRCalculator.
NMRErrorClassification - Enum Class in chemaxon.calculations.nmr: Error classification categories for shifts.
NMRExporter - Class in chemaxon.calculations.nmr: Class for NMR spectrum export.
NMRExporter() - Constructor for class chemaxon.calculations.nmr.NMRExporter
NMRMultiplet - Class in chemaxon.calculations.nmr: Class for NMR multiplets.
NMRMultiplet(boolean) - Constructor for class chemaxon.calculations.nmr.NMRMultiplet: Constructor.
NMRShift - Class in chemaxon.calculations.nmr: NMR chemical shift class.
NMRShift(int, double) - Constructor for class chemaxon.calculations.nmr.NMRShift: Constructor.
NMRSpectrum - Class in chemaxon.calculations.nmr: Class for the representation of NMR spectra.
NMRSpectrum(Molecule) - Constructor for class chemaxon.calculations.nmr.NMRSpectrum: Constructor.
NMRSpectrum(Molecule, NMRSpectrum.Nucleus) - Constructor for class chemaxon.calculations.nmr.NMRSpectrum: Constructor.
NMRSpectrum.Nucleus - Enum Class in chemaxon.calculations.nmr: Nucleus enumeration type.
NMRSpectrum.Unit - Enum Class in chemaxon.calculations.nmr: Unit enumeration type.
No - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element No.
NO - Enum constant in enum class chemaxon.search.api.options.HaltOnErrorOption: Recover from record level errors if possible.
NO_ABAS - Static variable in interface chemaxon.search.api.SearchConstants: Substructure search that applies only screening.
NO_BOND - Enum constant in enum class chemaxon.struc.BondType: No bond type.
NO_DUPLICATE_FILTERING - Static variable in class chemaxon.reaction.Reactor: No duplicate product list filtering
NO_ERROR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Dummy error type representing no errors.
NO_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: no error message for checker
NO_LICENSE_REQUIRED - Static variable in annotation interface chemaxon.standardizer.StandardizerActionInfo: no license required
NO_MNEMONIC - Static variable in class chemaxon.marvin.common.MAction: Do not set the mnemonic.
NO_RADICAL - Enum constant in enum class chemaxon.struc.Radical: Not radical center.
NO_SCREEN - Static variable in interface chemaxon.search.api.SearchConstants: Substructure search that applies only atom-by-atom search.
NO_UNDEF_RGROUP - Static variable in class chemaxon.search.MarkushGenerator
NodeColor - Class in chemaxon.alignment: Defines the coloring of the nodes in the alignment graph.
NodeColor.ExtendedAtomColoring - Class in chemaxon.alignment
noErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the no error message for the checker
NoFreeAttachmentPointException - Exception Class in chemaxon.struc.sgroup: Exception thrown when a superatom method fails due to running out of free attachment points.
NoFreeAttachmentPointException() - Constructor for exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
NoFreeAttachmentPointException(SgroupAtom) - Constructor for exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
NoFreeAttachmentPointException(String) - Constructor for exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
NoFreeAttachmentPointException(String, SgroupAtom) - Constructor for exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
NoFreeAttachmentPointException(String, Throwable) - Constructor for exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
NoFreeAttachmentPointException(Throwable) - Constructor for exception class chemaxon.struc.sgroup.NoFreeAttachmentPointException
NOMINAL_MASS - Enum constant in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Result type with the string id "nominalmass".
nominalMass() - Method in class chemaxon.calculations.elemental.ElementalAnalysis: Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
NOMOLMOVIE - Static variable in class chemaxon.formats.MFileFormatUtil: Do not read multi-molecule XYZ files as movies.
NON_HIT_ATOM_SET - Static variable in class chemaxon.search.hitdisplay.HitDisplayTool: Set identifier for non-hit atoms
NON_HIT_BOND_SET - Static variable in class chemaxon.search.hitdisplay.HitDisplayTool: Set identifier for non hit bonds
NON_STANDARD_WEDGE_SCHEME - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that non-standard wedge configurations around chiral centers have been found in the molecule
NON_STEREO_WEDGE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that wedge bonds connected to non-stereo atoms have been found in the molecule
NONE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ProximityPotentialType
NONE - Enum constant in enum class chemaxon.search.api.options.HomologyTranslationOption: No atom can have translation.
NONE - Enum constant in enum class chemaxon.struc.EZConfiguration
NONE - Static variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: Property display type: no property display.
NONE - Static variable in class chemaxon.search.FormulaSearch: Constant value specifying the none search type.
NONNEGATIVE_REAL - Static variable in class chemaxon.formats.OptionDescriptor: Positive real number.
nonPositiveToInfinite(int) - Static method in class chemaxon.search.api.options.SearchOptions
NONRECURSIVE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable: Non recursive expansion of child groups.
NonStandardWedgeSchemeChecker - Class in chemaxon.checkers: Non-standard Wedge Scheme Checker detects wedge configurations not following the IUPAC recommendations.
NonStandardWedgeSchemeChecker() - Constructor for class chemaxon.checkers.NonStandardWedgeSchemeChecker: Default constructor
NonStereoWedgeBondChecker - Class in chemaxon.checkers: Non-stereo Wedge Bond Checker detects wedge bonds connected to non-stereo atoms.
NonStereoWedgeBondChecker() - Constructor for class chemaxon.checkers.NonStereoWedgeBondChecker: Default constructor
NOPARAMS - Static variable in class chemaxon.calculations.gui.PluginFactory: No parameter panel sign in property file: if present then no parameter panel belongs to the plugin.
NORMAL - Enum constant in enum class chemaxon.alignment.AlignmentAccuracyMode: Atomic contribution only, no correction terms.
NORMAL - Enum constant in enum class chemaxon.alignment.AtropIsomerDetector.Accuracy
NORMAL - Enum constant in enum class chemaxon.search.mcs.McsSearchMode: Normal search mode.
NORMAL_CANONICAL - Enum constant in enum class chemaxon.search.api.options.TautomerEqualityMode
NORMAL_CANONICAL - Enum constant in enum class chemaxon.search.api.options.TautomerTransformationMode
NORMAL_CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
NORMAL_GENERIC - Enum constant in enum class chemaxon.search.api.options.TautomerSubstructureMode
NORMAL_GENERIC - Enum constant in enum class chemaxon.search.api.options.TautomerTransformationMode
normalized - Variable in class chemaxon.descriptors.MDParameters: flags indicating if the metric is normalized or not
NORMALIZED_EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType
normalizedEuclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the normalized Euclidean distance.
normalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the normalized Euclidean distance.
NoStructure - Class in chemaxon.struc: This class represents NoStructure labels.
NoStructureFormat - Static variable in class chemaxon.naming.document.DocumentAnnotatorOptions: Use this format constant to avoid exporting any structural format in the HTML output.
NOT_USEFUL - Static variable in class chemaxon.search.api.MolComparator: Describes that the MolComparator is not needed with the current search object, the current query (and target).
NOTLIST - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the exclusive atom list.
Np - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Np.
numberOfAtoms() - Method in class chemaxon.struc.IteratorFactory: Deprecated.

Returns the number of atoms iterated by AtomIterator.
numberOfBonds() - Method in class chemaxon.struc.IteratorFactory: Deprecated.

Returns the number of bonds iterated by BondIterator.
numberOfNeighbours(MolAtom) - Method in class chemaxon.struc.IteratorFactory: Deprecated.

Returns the number of atoms/bonds iterated by (Atom/Bond)NeighbourIterator (the two values are the same).
numOf(String) - Static method in class chemaxon.struc.MolAtom: Deprecated.
As of Marvin 5.9, replaced by a similar method PeriodicTable.findAtomicNumber(String).
The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
numoxstatesOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the number of oxidation states for the specified element.

O

O - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element O.
OBasic - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType
objectContainingSelection - Variable in class chemaxon.struc.MDocument
objects - Variable in class chemaxon.struc.MDocument
OCRErrorChecker - Class in chemaxon.checkers: OCRErrorChecker detects structures which do not look like chemical structures.
OCRErrorChecker() - Constructor for class chemaxon.checkers.OCRErrorChecker: Default constructor
ODD - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoValue
ODD - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoValue
ODD - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoValue
ODD - Static variable in class chemaxon.core.calculations.stereo.Stereochemistry
of(CalculatorTag...) - Static method in interface chemaxon.calculations.api.TaggedCalculator: Creates a TaggedCalculator that always returns the given tags.
of(Object) - Static method in class chemaxon.struc.MProp: Factory method: creates an MProp object from the given object.
of(String, Predicate<Molecule>) - Static method in interface chemaxon.calculations.api.CalculatorInputChecker: Creates a new input checker that accepts those molecules which satisfy the given lambda.
of(Collection<CalculatorTag>) - Static method in interface chemaxon.calculations.api.TaggedCalculator: Creates a TaggedCalculator that always returns the given tags.
OFF - Enum constant in enum class chemaxon.calculations.api.CalculatorLogger.Level
OFFICE - Enum constant in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType
OFFSET - Static variable in class chemaxon.alignment.NodeColor.ExtendedAtomColoring
Og - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Og.
OHAc - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType
OLD_USER_DEFINED_CHECKERCONFIG_XML - Static variable in class chemaxon.structurechecker.CheckerFixerFactory: Old external checker configuration file name - backward compatibility
OLD_USER_DEFINED_FIXERCONFIG_XML - Static variable in class chemaxon.structurechecker.CheckerFixerFactory: Old external fixer configuration file name - backward compatibility
oldToNew() - Method in class chemaxon.standardizer.Changes: Returns the old to new atom index mapping.
oldToNew(List<Changes>, Molecule) - Static method in class chemaxon.standardizer.Changes: Calculates the old to new atom index mapping based on a list of changes.
OMIT_POSTCLEAN - Static variable in class chemaxon.struc.MolAtom: Omit arranging process after the hydrogen addition.
OMIT_POSTCLEAN - Static variable in class chemaxon.struc.MoleculeGraph: Omit the arranging process after the hydrogen addition.
ONE_ERROR_MESSAGE - Static variable in class chemaxon.checkers.StructureCheckerDescriptor: single error message for checker
ONE_LETTER_PEPTIDE_DISPLAY_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts
oneErrorMessage() - Element in annotation interface chemaxon.checkers.CheckerInfo: Returns the one error message for the checker
onFailure(ServiceException) - Method in interface chemaxon.calculations.services.AsyncCallback: Called when asynchronous call is failed
onFirstCheck(Molecule, List<StructureCheckerResult>) - Method in interface chemaxon.structurechecker.StructureCheckerMonitor: This method is called when the CheckerRunner checks a structure for the first time.
onFix(Molecule, Molecule, StructureCheckerResult, StructureFixer, boolean) - Method in interface chemaxon.structurechecker.StructureCheckerMonitor: This method is called then the CheckerRunner fixes a structure.
onLastCheck(Molecule, List<StructureCheckerResult>) - Method in interface chemaxon.structurechecker.StructureCheckerMonitor: This method is called then the CheckerRunner checks a structure for the last time.
onSuccess(T) - Method in interface chemaxon.calculations.services.AsyncCallback: Called when asynchronous call is completed successfully
open(String) - Method in class chemaxon.formats.MolExportModule: Opens the exporter stream.
open(String, MPropertyContainer) - Method in class chemaxon.formats.MolExportModule: Opens the exporter stream.
openSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane: Opens the sketcher window with the molecule from the specified cell if the viewer is editable.
openWindow(int) - Method in class chemaxon.marvin.beans.MViewPane: Detaches the view canvas of the specified cell into a separate window if the viewer is detachable.
Operations - Search tag in class chemaxon.descriptors.PharmacophoreFingerprint: Section
OPTIMIZATION_NORMAL - Static variable in class chemaxon.calculations.ConformerPlugin
OPTIMIZATION_STRICT - Static variable in class chemaxon.calculations.ConformerPlugin
OPTIMIZATION_VERY_LOOSE - Static variable in class chemaxon.calculations.ConformerPlugin
OPTIMIZATION_VERY_STRICT - Static variable in class chemaxon.calculations.ConformerPlugin
OPTION_NAME_STRING - Static variable in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption
OPTION_NAME_STRING - Static variable in enum class chemaxon.search.api.options.TargetHomologyMatchingMode
OptionDescriptor - Class in chemaxon.formats: General option descriptor class.
OptionDescriptor(String, String, int, String, String[], String[], String[]) - Constructor for class chemaxon.formats.OptionDescriptor: Creates an option.
Options() - Constructor for class chemaxon.reaction.mapper.AutoMapper.Options
OptionStringProvider - Interface in chemaxon.search.api.options: Interface for search option enum types that provide option strings.
OR - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.EnhancedStereoType: Stereogenic centers belonging to an ORn group (e.g.
OR - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
OrbitalElectronegativityPlugin - Class in chemaxon.calculations: Plugin class for orbital electronegativity calculation.
OrbitalElectronegativityPlugin() - Constructor for class chemaxon.calculations.OrbitalElectronegativityPlugin: Constructor.
order() - Method in class chemaxon.formats.Encoding: Gets the byte order ("endianness").
ORDER_INSENSITIVE_DUPLICATE_FILTERING - Static variable in class chemaxon.reaction.Reactor: Order insensitive duplicate product list filtering
ORDER_SENSITIVE_DUPLICATE_FILTERING - Static variable in class chemaxon.reaction.Reactor: Order sensitive duplicate product list filtering
orderSensitive(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.
ORIGINAL_MARKUSH - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: Constant value specifying, that in case of markush searching hit is displayed on the markush structure.
orix - Variable in class chemaxon.struc.MoleculeGraph: Origin x.
oriy - Variable in class chemaxon.struc.MoleculeGraph: Origin y.
oriz - Variable in class chemaxon.struc.MoleculeGraph: Origin z.
Os - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Os.
OSRA - Static variable in class chemaxon.formats.MFileFormat
otell() - Method in class chemaxon.formats.converter.MolConverter: Get the current file position.
outputIn3d() - Method in class chemaxon.calculations.stereo.StereoisomerSettings: Returns true if 3D structures will be generated.
outputPrecision - Variable in class chemaxon.descriptors.MDParameters: number of fraction digits in floating point output format
OVERLAPPING_ATOMS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that overlapping atoms have been found in the molecule
OVERLAPPING_BONDS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that overlapping bonds have been found in the molecule
OverlappingAtomsChecker - Class in chemaxon.checkers: OverlappingAtomsChecker detects atoms that are too close to each other.
OverlappingAtomsChecker() - Constructor for class chemaxon.checkers.OverlappingAtomsChecker
OverlappingBondsChecker - Class in chemaxon.checkers: OverlappingBondsChecker detects bonds that are too close to each other.
OverlappingBondsChecker() - Constructor for class chemaxon.checkers.OverlappingBondsChecker: Default constructor
ownOverlap(AlignmentAccuracyMode) - Method in class chemaxon.alignment.AlignmentMolecule
oxstateOf(int, int) - Static method in class chemaxon.struc.MolAtom: Gets the oxidation states.

P

p - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue
p - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue
P - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue
P - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue
P - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element P.
P_CENTER - Static variable in class chemaxon.struc.graphics.MRectangle: Central point ID.
P_E - Static variable in class chemaxon.struc.graphics.MRectangle: Middle point on right edge.
P_N - Static variable in class chemaxon.struc.graphics.MRectangle: Middle point on top edge.
P_NE - Static variable in class chemaxon.struc.graphics.MRectangle: Top-right corner index.
P_NW - Static variable in class chemaxon.struc.graphics.MRectangle: Top-left corner index.
P_S - Static variable in class chemaxon.struc.graphics.MRectangle: Middle point on bottom edge.
P_SE - Static variable in class chemaxon.struc.graphics.MRectangle: Botton-right corner index.
P_SW - Static variable in class chemaxon.struc.graphics.MRectangle: Bottom-left corner index.
P_W - Static variable in class chemaxon.struc.graphics.MRectangle: Middle point on left edge.
Pa - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pa.
pack() - Method in class chemaxon.struc.MolAtom: Reduce memory usage.
pack() - Method in class chemaxon.struc.MoleculeGraph: Reduce memory usage.
PAGE - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the page number, if applicable (e.g.
PageSettings - Class in chemaxon.struc: Page Settings of multipage molecular documents.
PageSettings() - Constructor for class chemaxon.struc.PageSettings: Constructor.
paint(Graphics2D, Dimension) - Method in class chemaxon.marvin.beans.MolPrinter: Paints the molecule on the specified graphics context in the given size.
paint(Graphics2D, Rectangle) - Method in class chemaxon.marvin.beans.MolPrinter: Paints the molecule into the center of the specified rectangle.
paint(Graphics, Rectangle) - Method in class chemaxon.marvin.beans.MolPrinter: Paints the molecule into the center of the specified rectangle.
paintComponent(Graphics) - Method in class chemaxon.marvin.beans.MolRenderer
PAIRED - Enum constant in enum class chemaxon.alignment.AlignmentProperties
PairwiseAlignment - Class in chemaxon.alignment: Align pairs of molecules (query and the target) using the shape Alignment
PairwiseAlignment() - Constructor for class chemaxon.alignment.PairwiseAlignment
PairwiseAlignment(AlignmentProperties) - Constructor for class chemaxon.alignment.PairwiseAlignment
PairwiseComparison - Interface in chemaxon.alignment: This interface designed for comparing two molecules in 3D by various overlay methodologies.
PairwiseSimilarity3D - Class in chemaxon.alignment: Align pairs of molecules (query and the target) using the atom/atom matcher Similarity3D
PairwiseSimilarity3D() - Constructor for class chemaxon.alignment.PairwiseSimilarity3D
PairwiseSimilarity3D(boolean) - Constructor for class chemaxon.alignment.PairwiseSimilarity3D
PARAM_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringReader: Parameter separator token of the action string
PARAM_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.StandardizerActionStringWriter: Parameter separator token of the action string
PARAM_SEPARATOR - Static variable in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter: Parameter separator token of the action string
ParameterConstants - Class in chemaxon.marvin.common: Parameters of Marvin components.
ParameterConstants() - Constructor for class chemaxon.marvin.common.ParameterConstants
ParameterPanelHandler - Interface in chemaxon.calculations.gui: Plugin parameter panel handler interface.
parameters - Variable in class chemaxon.descriptors.CDParameters: node in the DOM tree built from the XML configuration
PARAMETERS - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "param".
PARAMETERS_HEADER - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "paramH".
parametrizedMetricNodes - Variable in class chemaxon.descriptors.MDParameters
parametrizedMetrics - Variable in class chemaxon.descriptors.MDParameters: symbolic names (mnemonics) of parametrized metrics
parametrizedMetricsNode - Variable in class chemaxon.descriptors.MDParameters
params - Variable in class chemaxon.calculations.output.CalculatorPluginOutput: The plugin parameter table.
params - Variable in class chemaxon.descriptors.MolecularDescriptor: Parameter settings related to the descriptor.
params - Variable in class chemaxon.marvin.beans.MarvinPane: Parameter string.
parent - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: The parent component.
parentGraph - Variable in class chemaxon.struc.MoleculeGraph: The structure that contains this molecule graph as a substructure.
parentLine - Variable in class chemaxon.struc.graphics.MMidPoint
parentRect - Variable in class chemaxon.struc.graphics.MRectanglePoint
parentSgroup - Variable in class chemaxon.struc.Sgroup
PARITY_ALLENE - Static variable in interface chemaxon.struc.StereoConstants: Atom with allene like parity.
PARITY_EITHER - Static variable in interface chemaxon.struc.StereoConstants: Odd or even parity.
PARITY_EVEN - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of even parity (counterclockwise arrangement).
PARITY_MASK - Static variable in interface chemaxon.struc.StereoConstants: Parity mask in flags.
PARITY_NONE - Static variable in interface chemaxon.struc.StereoConstants: Atom with no parity.
PARITY_ODD - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of odd parity (clockwise arrangement).
PARITY_TETRAHEDRAL - Static variable in interface chemaxon.struc.StereoConstants: Atom with tetrahedral parity.
PARITY_UNSPEC - Static variable in interface chemaxon.struc.StereoConstants: Unspecified parity flag.
paritySign(int, int, int, int) - Static method in class chemaxon.struc.MolAtom: Calculates the sign of the parity for the specified indexes.
parse(String) - Static method in class chemaxon.checkers.AtomLabels: Parses the list of atom labels from a string.
parse(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
parse(String) - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type: Parses the type of the aromatize action
parse(String) - Static method in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Parses the type of the clean action
parse(String) - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type: Parses the type of the convert double bonds action
parse(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement: Parses the measurement of the remove fragment action
parse(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Parses the method of the remove fragment action
parse(String) - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type: Parses the hydrogen isotope representation type
parseCharIfOptionSign(String, int) - Method in class chemaxon.formats.MolExportModule: Parse the current character if it is an option sign.
ParseException - Exception Class in chemaxon.chemterms: This exception is thrown when parse errors are encountered.
ParseException() - Constructor for exception class chemaxon.chemterms.ParseException
ParseException(String) - Constructor for exception class chemaxon.chemterms.ParseException
ParseException(String, Throwable) - Constructor for exception class chemaxon.chemterms.ParseException
ParseException(Throwable) - Constructor for exception class chemaxon.chemterms.ParseException
parseGroupNames(String) - Method in class chemaxon.standardizer.AbstractSgroupAction
parseMolecule(String) - Static method in class chemaxon.formats.MPropHandler
parseOption(String, int) - Method in class chemaxon.formats.MolExportModule: Parses the following option in the option string.
parseType(String) - Static method in class chemaxon.formats.OptionDescriptor: Parses an option type from a string.
PARTIAL - Enum constant in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Partial clean
PARTIAL_CLEAN_KEY - Static variable in class chemaxon.standardizer.actions.Clean2DAction: Key for partial clean necessary property change
partialClean(MoleculeGraph, int, int[], String) - Static method in class chemaxon.core.calculations.clean.Cleaner: Calculates atom coordinates by using fixed atoms.
partialClean(MoleculeGraph, MoleculeGraph, int[], String) - Static method in class chemaxon.core.calculations.clean.Cleaner: Calculates atom coordinates by using the given template molecule.
partialClean(MoleculeGraph, MoleculeGraph, int[], String, Cleaner.AtomChangeEventListener) - Static method in class chemaxon.core.calculations.clean.Cleaner
partialClean(Molecule, Molecule[], String) - Static method in class chemaxon.core.calculations.clean.Cleaner: Calculates atom coordinates by using the given template molecule array.
partialClean(Molecule, Molecule[], String, Cleaner.AtomChangeEventListener) - Static method in class chemaxon.core.calculations.clean.Cleaner: A specific overloading for partial clean.
PartialCleanFixer - Class in chemaxon.fixers: Partial clean
PartialCleanFixer() - Constructor for class chemaxon.fixers.PartialCleanFixer
partialCleanWithStereo(MoleculeGraph, int, int[], String) - Static method in class chemaxon.core.calculations.clean.Cleaner: Calculates atom coordinates by using fixed atoms.
PATOM - Static variable in class chemaxon.chemterms.ReactionContext
Pb - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pb.
PBasic - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType
Pd - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pd.
PDB - Static variable in class chemaxon.formats.MFileFormat: Protein Data Bank format.
PDF - Enum constant in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType
PDF - Static variable in class chemaxon.formats.MFileFormat: Portable Document Format.
PEPTIDE_DISPLAY_SETTINGS_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts
PEPTIDE_DISPLAY_SETTINGS_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts
PEPTIDE_DISPLAY_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier for parameter: "peptideDisplayType" See Parameters and Events documentation.
PEPTIDE_IN - Static variable in class chemaxon.formats.MFileFormat: Peptide Sequence.
PEPTIDE1_OUT - Static variable in class chemaxon.formats.MFileFormat: Peptide Sequence (1-letter).
PEPTIDE3_OUT - Static variable in class chemaxon.formats.MFileFormat: Peptide Sequence (3-letter).
PeriodicTable - Class in chemaxon.struc: Periodic table of the elements.
PeriodicTable() - Constructor for class chemaxon.struc.PeriodicTable
PersistentProperty - Annotation Interface in chemaxon.checkers: This annotation signs if a property of a StructureChecker should be persisted.
PersistentProperty - Annotation Interface in chemaxon.standardizer: This annotation signs if a property of a StandardizerAction should be persisted.
PFGenerator - Class in chemaxon.descriptors: The PFGenerator class generates 2-dimensional pharmacophore fingerprints for molecular graphs.
PFGenerator(PMapper) - Constructor for class chemaxon.descriptors.PFGenerator: Creates a new instance of PFGenerator which can be used to generate fingerprints for an arbitrary number of molecules.
PFParameters - Class in chemaxon.descriptors: Manages 2D pharmacophore fingerprint parameters.
PFParameters() - Constructor for class chemaxon.descriptors.PFParameters: Creates an empty object.
PFParameters(File) - Constructor for class chemaxon.descriptors.PFParameters: Creates a new object based on a given configuration file.
PFParameters(String) - Constructor for class chemaxon.descriptors.PFParameters: Creates a new object based on a given configuration string.
PHARMACOPHORE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColoringScheme
Pharmacophore3D - Class in chemaxon.alignment: 3D Pharmacophore representation for 3D alignments.
Pharmacophore3D() - Constructor for class chemaxon.alignment.Pharmacophore3D
Pharmacophore3D(Molecule, int[]) - Constructor for class chemaxon.alignment.Pharmacophore3D
PharmacophoreFingerprint - Class in chemaxon.descriptors: The PharmacophoreFingerprint class implements 2D pharmacophoric fingerprints.
PharmacophoreFingerprint() - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint: Creates a new, empty instance of PharmacophoreFingerprint without allocating internal storage.
PharmacophoreFingerprint(PFParameters) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint: Creates a new instance of PharmacophoreFingerprint according to the parameters given.
PharmacophoreFingerprint(PharmacophoreFingerprint) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint: Copy constructor.
PharmacophoreFingerprint(String) - Constructor for class chemaxon.descriptors.PharmacophoreFingerprint: Creates a new instance of PharmacophoreFingerprint according to the parameters given.
PHYSPROP - Enum constant in enum class chemaxon.calculations.LogPMethod: Calculation method based on the PhysProp database.
PKA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction: PKa calculation for bbb score.
PKA - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Most basic center (pKa).
PKACALCULATOR - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
PkaPlugin - Class in chemaxon.calculations: Plugin class for macro/micro pKa calculation.
PkaPlugin() - Constructor for class chemaxon.calculations.PkaPlugin: Constructor.
PKAT - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
PkaTrainingResult - Class in chemaxon.calculations: Represents pKa training result.
PkaTrainingResult(String) - Constructor for class chemaxon.calculations.PkaTrainingResult: Generates an empty training result object
PkaTrainingResult.PkaType - Enum Class in chemaxon.calculations: Enumeration of pKa group types representing different acidic and basic functional groups in molecules.
PLAIN - Static variable in class chemaxon.struc.graphics.MFont: Plain font style.
plattIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
plugin - Variable in class chemaxon.calculations.output.CalculatorPluginOutput: The CalculatorPlugin object.
PLUGIN_CLASS_KEY - Static variable in class chemaxon.calculations.CalculatorPlugin: Plugin class key in manifest.
PLUGIN_DIR - Static variable in class chemaxon.calculations.CalculatorPlugin: Deprecated, for removal: This API element is subject to removal in a future version.
Not used anymore, no replacement.
PluginFactory - Class in chemaxon.calculations.gui: Plugin factory: responsible for plugin parameter panel and plugin creation and central management.
PluginFactory() - Constructor for class chemaxon.calculations.gui.PluginFactory: Constructor.
PluginFactory.PluginRecord - Class in chemaxon.calculations.gui: Stores plugin data.
Pm - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pm.
PMap - Class in chemaxon.descriptors.pharmacophore: Class representing the pharmacophore properties found for the atoms of a target molecule.
PMap(int, int) - Constructor for class chemaxon.descriptors.pharmacophore.PMap: Constructor.
PMap(int, BitSet[]) - Constructor for class chemaxon.descriptors.pharmacophore.PMap: Constructor.
PMapper - Class in chemaxon.descriptors.pharmacophore: Class for searching for pharmacophore properties in a molecule.
PMapper(File) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(File, Standardizer) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(String) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(String, Standardizer) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(Element) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(Element, Standardizer) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(Element, Standardizer, String) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(Element, String) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(Element, Element) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PMapper(Element, Element, String) - Constructor for class chemaxon.descriptors.pharmacophore.PMapper: Constructor.
PNG - Enum constant in enum class chemaxon.naming.document.DocumentAnnotatorOptions.ImageFormat
PNG - Static variable in class chemaxon.formats.MFileFormat: Portable Network Graphics.
Po - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Po.
Point3D - Class in chemaxon.struc: Point in three-dimensional space.
Point3D() - Constructor for class chemaxon.struc.Point3D: Construct a zero point.
Point3D(double, double, double) - Constructor for class chemaxon.struc.Point3D: Construct a point from the specified coordinates.
Point3D(Point3D) - Constructor for class chemaxon.struc.Point3D: Copy constructor.
points - Variable in class chemaxon.struc.graphics.MPolyline
POLARIZABILITY - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
POLARIZABILITY_GEOM3D - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
PolarizabilityPlugin - Class in chemaxon.calculations: Plugin class for atom polarizability calculation.
PolarizabilityPlugin() - Constructor for class chemaxon.calculations.PolarizabilityPlugin: Constructor.
polylinePointIndex - Variable in class chemaxon.struc.graphics.MMidPoint
POLYMERENDGROUP_H - Static variable in class chemaxon.struc.MolAtom: Hydrogen atom which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup) and the H is not in the same sgroup should be kept.
POOR - Enum constant in enum class chemaxon.calculations.nmr.NMRErrorClassification: Poor quality
pop() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay: Clears the last stored item from the display.
POPUP - Static variable in class chemaxon.marvin.common.MAction: Popup menu item, MAction.AUTORM, MAction.NO_MNEMONIC and MAction.IN_POPUP are set.
popupImageFormat - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions: The image format which should be used for popups in the annotated document.
popupImageFormat(DocumentAnnotatorOptions.ImageFormat) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
portionWidth(Graphics, MFont, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the width of this portion.
portionXAdvance(Graphics, MFont, FontMetrics) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the x coordinate change from the beginning to the end of this portion.
portionXAdvance(Graphics, MFont, FontMetrics, boolean) - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the width of this portion.
POS - Static variable in class chemaxon.alignment.Pharmacophore3D
POSITION_ON_0TH_HEAVY_ATOM - Static variable in interface chemaxon.search.api.SearchConstants: Hit constant denoting hit position of a non-heavy atom (e.g.
PositionedInputStream - Class in chemaxon.formats: Positioned input stream that has the ability to set / get the stream position as well as put back some parts already read.
PositionedInputStream(InputStream) - Constructor for class chemaxon.formats.PositionedInputStream: Constructor.
PositionedInputStream(InputStream, int) - Constructor for class chemaxon.formats.PositionedInputStream: Constructor.
PositionedInputStream(InputStream, int, String) - Constructor for class chemaxon.formats.PositionedInputStream: Constructor.
PositionedInputStream(InputStream, int, String, int) - Constructor for class chemaxon.formats.PositionedInputStream: Constructor.
PositionedInputStream(InputStream, String) - Constructor for class chemaxon.formats.PositionedInputStream: Constructor.
positionInRect - Variable in class chemaxon.struc.graphics.MRectanglePoint
posOxOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the smallest positive oxidation number.
POST - Enum constant in enum class chemaxon.calculations.services.JsonServiceDescriptor.Method: HTTP POST method
POVRAY - Static variable in class chemaxon.formats.MFileFormat: POVRay file.
ppm - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit: ppm unit
Pr - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pr.
PR_ATSYMS - Static variable in class chemaxon.struc.Sgroup: Print atom symbols.
PRE_CONFIGURED_TRANSFORMATIONS - Static variable in class chemaxon.standardizer.StandardizerActionFactory: Pre-configured transformation configuration path
preconvert(Molecule) - Method in class chemaxon.formats.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(Molecule, boolean) - Method in class chemaxon.formats.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(Molecule, boolean, int, boolean) - Method in class chemaxon.formats.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
predict(Molecule) - Method in class chemaxon.calculations.admet.HergActivityPredictor: Runs the prediction of the given molecule.
predict(Molecule) - Method in class chemaxon.calculations.admet.HergClassPredictor: Runs the prediction of the given molecule.
PRELOAD - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "preload".
preMatchMap - Variable in class chemaxon.search.AbstractSearch: Map for storing pre-match data.
preprocess(Molecule, boolean) - Static method in class chemaxon.alignment.MMPAlignment: Utility for preprocessing structure for alignment.
preprocessFormatAndOptions(String[]) - Static method in class chemaxon.formats.MFileFormatUtil: Parses options like "MULTISET", "MOLMOVIE" or "NOMOLMOVIE".
print() - Method in class chemaxon.marvin.beans.MViewPane: Prints the molecule table.
priority() - Element in annotation interface chemaxon.fixers.FixerInfo: Returns the priority of the fixer.
PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor: priority of fixer
probabilities() - Method in record class chemaxon.calculations.admet.HergClassPrediction: Returns the value of the probabilities record component.
process() - Method in class chemaxon.naming.document.DocumentAnnotator: Process the complete input at once, generating the annotated document.
process(String) - Static method in class chemaxon.naming.document.DocumentToStructure: Creates a MolImporter instance to import structures from a given text using the default format options.
process(String, String) - Static method in class chemaxon.naming.document.DocumentToStructure: Creates a MolImporter instance to import structures from a given text.
processDocument(boolean) - Method in class chemaxon.descriptors.CDParameters: Processes parts of the XML configuration that are specific to CustomDescriptor.
processDocument(boolean) - Method in class chemaxon.descriptors.CFParameters: Processes pars of the XML configuration specific to ChemicalFingerprint.
processDocument(boolean) - Method in class chemaxon.descriptors.ECFPParameters: Processes pars of the XML configuration specific to ECFP.
processDocument(boolean) - Method in class chemaxon.descriptors.MDParameters: Searches the DOM tree for relevant nodes and sets internal variables to some these nodes for the sake of easier information processing.
processDocument(boolean) - Method in class chemaxon.descriptors.PFParameters
processDocument(boolean) - Method in class chemaxon.descriptors.RFParameters: Processes pars of the XML configuration specific to ReactionFingerprint.
processDocument(boolean) - Method in class chemaxon.descriptors.SDParameters: Processes parts of the XML configuration specific to ScalarDescriptor.
processDocument(boolean) - Method in class chemaxon.descriptors.ShapeParameters: Processes pars of the XML configuration specific to Shape.
processError(Throwable) - Method in interface chemaxon.formats.ErrorProcessor: Error processing method.
processMolecule(Molecule) - Method in class chemaxon.descriptors.ECFPFeatureLookup: Performs the necessary preprocessing for the given molecule.
PRODUCT - Static variable in class chemaxon.chemterms.ReactionContext
PRODUCT_OUTPUT - Static variable in class chemaxon.reaction.Reactor: Output type: products.
PRODUCTS - Static variable in class chemaxon.struc.RxnMolecule: "Product" structure type.
progress - Variable in class chemaxon.naming.document.DocumentAnnotator.ProgressInfo: The estimated ratio of work that has already been done, between 0 and 1.
progress(DocumentAnnotator.ProgressInfo) - Method in interface chemaxon.naming.document.DocumentAnnotator.Listener
PROGRESS - Static variable in class chemaxon.calculations.api.ProgressableCalculator
ProgressableCalculator<T,R> - Class in chemaxon.calculations.api: An abstract calculator implementation which supports progress notification and cancellation.
ProgressableCalculator() - Constructor for class chemaxon.calculations.api.ProgressableCalculator
ProgressMonitor - Interface in chemaxon.core.util: Simple progress monitor interface.
Prop() - Constructor for class chemaxon.struc.MDocument.Prop
PROP_ALIGNHIT - Static variable in class chemaxon.search.hitdisplay.HitDisplayUtil: Atom property to store "align hit" option.
properties - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable: Display properties of the Molecule.
properties() - Method in class chemaxon.calculations.bbb.BBB: Returns the calculated phys-chem properties and scores.
properties() - Method in class chemaxon.calculations.cnsmpo.CnsMpo: Returns the calculated phys-chem properties and scores.
properties() - Method in class chemaxon.struc.MDocument: Gets the property container.
properties() - Method in class chemaxon.struc.MoleculeGraph: Gets the property container.
properties() - Method in class chemaxon.struc.RgMolecule: Gets the property container.
PROPERTY_KEY_ABSOLUTE - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction: Key of type for property change of mode
PROPERTY_KEY_ABSSTEREO - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction: Key of type for property change of mode
PROPERTY_KEY_ALLOW_VALENCE_ERROR - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction: Property key for serialization/deserialization an event changes for valence check (boolean value type)
PROPERTY_KEY_AROM_TYPE - Static variable in class chemaxon.checkers.AromaticityErrorChecker: This public constant String represents the name of the property which represents the arom type String property
PROPERTY_KEY_AROMATCITY - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Aromaticity atom query property.
PROPERTY_KEY_AROMATICITY_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Aromaticity checking property
PROPERTY_KEY_BRIDGEHEAD - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching Bridgehead property
PROPERTY_KEY_BRIDGEHEAD - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Bridgehead property
PROPERTY_KEY_CHARGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching charged explicit hydrogens in the molecule
PROPERTY_KEY_CHARGED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Charged property
PROPERTY_KEY_CHIRALITY - Static variable in class chemaxon.standardizer.actions.ClearStereoAction: Key of type for property change of mode
PROPERTY_KEY_CONNECTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Connection count atom query property.
PROPERTY_KEY_CONNECTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Connection count checking property
PROPERTY_KEY_CONTRACTED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker: This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups
PROPERTY_KEY_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker: Search for valence properties that are equal to the default valence.
PROPERTY_KEY_DETECT_CUMULATED_DOUBLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker: Property key detect cumulated double bonds
PROPERTY_KEY_DETECT_TRANS_DOUBLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker: Property key detect trans double bonds
PROPERTY_KEY_DETECT_TRIPLE_BONDS - Static variable in class chemaxon.checkers.RingStrainErrorChecker: Property key detect triple bonds
PROPERTY_KEY_DOUBLE_BOND - Static variable in class chemaxon.standardizer.actions.ClearStereoAction: Key of type for property change of mode
PROPERTY_KEY_ENFORCE_ABS - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction: Key of type for property change of mode
PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker: This public constant String represents the name of the property which is responsible for the list of excluded groups
PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.AttachedDataChecker: This public constant String represents the name of the property which is responsible for the list of excluded data.
PROPERTY_KEY_EXCLUDED - Static variable in class chemaxon.checkers.PseudoAtomChecker: This public constant String represents the name of the property which is responsible for the list of excluded pseudo atom labels
PROPERTY_KEY_EXPANDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker: This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups
PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Explicit connection count atom query property.
PROPERTY_KEY_EXPLICIT_CONNECTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Explicit connection count checking property
PROPERTY_KEY_H_CONNECTED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching H connected property
PROPERTY_KEY_H_CONNECTED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: H connected property
PROPERTY_KEY_HYDROGEN_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Hydrogen count atom query property.
PROPERTY_KEY_HYDROGEN_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Hydrogen count checking property
PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Implicit hydrogen count atom query property.
PROPERTY_KEY_IMPLICIT_HYDROGEN_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Implicit hydrogen count checking property
PROPERTY_KEY_IS_EXCLUSION_REGEXP - Static variable in class chemaxon.checkers.AttachedDataChecker: The name of the property, which is responsible for the decision if the excluded data should be treated as a regular expression instead of a (comma separated) list of strings.
PROPERTY_KEY_ISOTOPIC - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching isotopic explicit hydrogens in the molecule
PROPERTY_KEY_ISOTOPIC - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Isotopic property
PROPERTY_KEY_LONELY - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching lonely explicit hydrogens in the molecule
PROPERTY_KEY_LONELY - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Lonely property
PROPERTY_KEY_MAPPED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching mapped explicit hydrogens in the molecule
PROPERTY_KEY_MAPPED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Mapped property
PROPERTY_KEY_METAL_CONNECTED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Metal connected property
PROPERTY_KEY_NON_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker: Search for valence properties that are not equal to the default valence.
PROPERTY_KEY_POLYMER_END_GROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching Polymer end group property
PROPERTY_KEY_POLYMER_END_GROUP - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Polymer end group property
PROPERTY_KEY_QUERY_ATOM - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction: Property key for serialization/deserialization an event changes for query atom (MolAtom value type)
PROPERTY_KEY_RADICAL - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching radical explicit hydrogens in the molecule
PROPERTY_KEY_RADICAL - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Radical property
PROPERTY_KEY_REPLACE_ATOM - Static variable in class chemaxon.standardizer.actions.ReplaceAtomsAction: Property key for serialization/deserialization an event changes for replace atom (MolAtom value type)
PROPERTY_KEY_RING_BOND_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Ring bond count atom query property.
PROPERTY_KEY_RING_BOND_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Ring bond count checking property
PROPERTY_KEY_RING_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Ring count atom query property.
PROPERTY_KEY_RING_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Ring count checking property
PROPERTY_KEY_SEARCH_ALL - Static variable in class chemaxon.checkers.RatomChecker: This constant String represents the name of the property which is responsible for searching all ratoms in the molecule
PROPERTY_KEY_SEARCH_BRIDGEHEAD - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searchingBridgehead property
PROPERTY_KEY_SEARCH_CHARGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching charged explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_CONTRACTED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker: This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups
PROPERTY_KEY_SEARCH_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker: Search default valence property
PROPERTY_KEY_SEARCH_DISCONNECTED - Static variable in class chemaxon.checkers.RatomChecker: This constant String represents the name of the property which is responsible for searching disconnected ratoms in the molecule
PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker: This public constant String represents the name of the property which is responsible for the list of excluded groups
PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.AttachedDataChecker
PROPERTY_KEY_SEARCH_EXCLUDED - Static variable in class chemaxon.checkers.PseudoAtomChecker
PROPERTY_KEY_SEARCH_EXPANDED - Static variable in class chemaxon.checkers.AbbreviatedGroupChecker: This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups
PROPERTY_KEY_SEARCH_GENERIC - Static variable in class chemaxon.checkers.RatomChecker: This constant String represents the name of the property which is responsible for searching generic ratoms in the molecule
PROPERTY_KEY_SEARCH_H_CONNECTED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching H connected property
PROPERTY_KEY_SEARCH_ISOTOPIC - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching isotopic explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_LINKER - Static variable in class chemaxon.checkers.RatomChecker: This private constant String represents the name of the property which is responsible for searching linker ratoms in the molecule
PROPERTY_KEY_SEARCH_LONELY - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching lonely explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_MAPPED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching mapped explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_NESTED - Static variable in class chemaxon.checkers.RatomChecker: This private constant String represents the name of the property which is responsible for searching nested ratoms in the molecule
PROPERTY_KEY_SEARCH_NON_DEFAULT_VALENCE - Static variable in class chemaxon.checkers.ValencePropertyChecker: Search non default valence property
PROPERTY_KEY_SEARCH_POLYMER_END_GROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searchingPolymer end group property
PROPERTY_KEY_SEARCH_RADICAL - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching radical explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_SGROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searchingS-group property
PROPERTY_KEY_SEARCH_SGROUP_END - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searchingS-group end property
PROPERTY_KEY_SEARCH_VALENCE_ERROR - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searchingValence error property
PROPERTY_KEY_SEARCH_WEDGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the property which is responsible for searching wedged explicit hydrogens in the molecule
PROPERTY_KEY_SEARCH_WITH_REGEXP_EXCLUSION - Static variable in class chemaxon.checkers.AttachedDataChecker
PROPERTY_KEY_SGROUP - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching S-group property
PROPERTY_KEY_SGROUP - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: S-group property
PROPERTY_KEY_SGROUP_END - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching S-group end property
PROPERTY_KEY_SGROUP_END - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: S-group end property
PROPERTY_KEY_SINGLE_UP_OR_DOWN_BOND - Static variable in class chemaxon.standardizer.actions.ClearStereoAction: Key of type for property change of mode
PROPERTY_KEY_SMALLEST_RING_SIZE - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Smallest ring size atom query property.
PROPERTY_KEY_SMALLEST_RING_SIZE_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Smallest ring size checking property
PROPERTY_KEY_SMARTS_QUERY - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: SMARTS query property
PROPERTY_KEY_SMARTS_QUERY_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: SMARTS query checking property
PROPERTY_KEY_STEREO_GROUP - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction: Key of type for property change of mode
PROPERTY_KEY_SUBSTITUTION_COUNT - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Substitution count atom query property.
PROPERTY_KEY_SUBSTITUTION_COUNT_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Substitution count checking property
PROPERTY_KEY_TRADITIONAL_N_ALLOWED - Static variable in class chemaxon.checkers.ValenceErrorChecker: This public constant String represents the name of the configuration file property which is responsible for traditional N representation is allowed
PROPERTY_KEY_TYPE - Static variable in class chemaxon.checkers.AromaticityErrorChecker: This public constant String represents the name of the property which is responsible for using the given aromatization type during the check mechanism.
PROPERTY_KEY_TYPE - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction: Key of type for property change of mode
PROPERTY_KEY_TYPES - Static variable in class chemaxon.checkers.AtomTypeChecker: Types property
PROPERTY_KEY_UNSATURATION - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Unsaturation atom query property.
PROPERTY_KEY_UNSATURATION_CHECKING - Static variable in class chemaxon.checkers.AtomQueryPropertyChecker: Unsaturation checking property
PROPERTY_KEY_VALENCE_ERROR - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching Valence error property
PROPERTY_KEY_VALENCE_ERROR - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Valence error property
PROPERTY_KEY_VALID - Static variable in interface chemaxon.checkers.StructureChecker: This property key used to be the key of the property change event of valid property
PROPERTY_KEY_WEDGED - Static variable in class chemaxon.checkers.ExplicitHydrogenChecker: This public constant String represents the name of the configuration file property which is responsible for searching wedged explicit hydrogens in the molecule
PROPERTY_KEY_WEDGED - Static variable in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Wedged property
PROPERTY_TYPE_ALL - Static variable in class chemaxon.marvin.common.UserSettings: Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get all properties that are stored.
PROPERTY_TYPE_DEFAULT - Static variable in class chemaxon.marvin.common.UserSettings: Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the default properties.
PROPERTY_TYPE_PERSISTENT - Static variable in class chemaxon.marvin.common.UserSettings: Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the properties set by UserSettings.setProperty(String, String) method or by the setter methods.
PROPERTY_TYPE_TRANSIENT - Static variable in class chemaxon.marvin.common.UserSettings: Constant to use as the type parameter of UserSettings.getPropertyMap(String) method to get the properties that are being stored temporary, and will not be saved to the properties file.
propertyChange(PropertyChangeEvent) - Method in class chemaxon.checkers.AbstractStructureChecker
propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.beans.MarvinPane: Handles "ancestor" events or sets parameters if a bean property is changed.
propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.beans.MSketchPane: Handles property change events.
propertyChange(PropertyChangeEvent) - Method in class chemaxon.standardizer.AbstractStandardizerAction
propertyChangeSupport - Variable in class chemaxon.calculations.services.ServiceDescriptor: Property change support
propertyChangeSupport - Variable in class chemaxon.checkers.AbstractStructureChecker: property change support object bound to this
propertyContainer - Variable in class chemaxon.struc.MoleculeGraph
propertyCount() - Method in class chemaxon.struc.MObject: Returns the number of property (property key - property value) mappings of this MObject.
propertyCount() - Method in class chemaxon.struc.MolAtom: Returns the number of property (property key - property value) mappings of this atom.
propertyCount() - Method in class chemaxon.struc.MolBond: Returns the number of property (property key - property value) mappings of this bond.
propertyKeySet() - Method in class chemaxon.struc.MObject: Returns a set view of the property keys of this MObject.
propertyKeySet() - Method in class chemaxon.struc.MolAtom: Returns a set view of the property keys of this atom.
propertyKeySet() - Method in class chemaxon.struc.MolBond: Returns a set view of the property keys of this bond.
propertySet() - Method in class chemaxon.struc.MObject: Returns a collection view of the properties (property key - property value mappings) of this MObject.
propertySet() - Method in class chemaxon.struc.MolAtom: Returns a collection view of the properties (property key - property value mappings) of this atom.
propertySet() - Method in class chemaxon.struc.MolBond: Returns a set view of the properties (property key - property value mappings) of this bond.
protectDoubleBondStereo() - Method in class chemaxon.calculations.stereo.StereoisomerSettings: Returns the adjusted double bond stereo protection flag.
protectTetrahedralStereo() - Method in class chemaxon.calculations.stereo.StereoisomerSettings: Returns the adjusted tetrahedral stereo protection flag.
PROX_COMPLEX - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ProximityPotentialType
PROX_GAUSS - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ProximityPotentialType
PROX_SIMPLE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ProximityPotentialType
PSEUDO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that pseudo atoms have been found in the molecule
PSEUDO - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of a pseudoatom.
PSEUDO_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that pseudo atoms that could be converted to abbreviated groups have been found in the molecule
PSEUDO_NO_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Deprecated, for removal: This API element is subject to removal in a future version.
StructureCheckerErrorType.PSEUDO is used instead
PseudoAtomChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting pseudo atoms.
PseudoAtomChecker() - Constructor for class chemaxon.checkers.PseudoAtomChecker: Default constructor
PseudoAtomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.PseudoAtomChecker
PSymbols - Class in chemaxon.descriptors.pharmacophore: Class storing and sorting pharmacophore symbols.
PSymbols(String[]) - Constructor for class chemaxon.descriptors.pharmacophore.PSymbols: Constructor.
PSymbols(Collection<String>) - Constructor for class chemaxon.descriptors.pharmacophore.PSymbols: Constructor.
Pt - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pt.
Pu - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Pu.
PublicApi - Annotation Interface in chemaxon.common.annotations: Marks types that are part of the Chemaxon public API.
put(int, float) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Stores the given value in the specified hitogram bin.
put(int, int) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Stores the given value in the specified hitogram bin.
put(String, MProp) - Method in class chemaxon.struc.prop.MHashProp: Puts a value.
putBackLine() - Method in class chemaxon.formats.PositionedInputStream: Puts back the last line into the stream.
putBackLine(int) - Method in class chemaxon.formats.PositionedInputStream: Puts back the last line into the stream.
putProperty(String, Object) - Method in class chemaxon.struc.MObject: Associates the specified value with the specified key at this MObject.
putProperty(String, Object) - Method in class chemaxon.struc.MolAtom: Associates the specified value with the specified key at this atom.
putProperty(String, Object) - Method in class chemaxon.struc.MolBond: Associates the specified value with the specified key at this bond.

Q

QFINGERPRINT - Static variable in class chemaxon.chemterms.SearchContext
qpropCheck() - Method in class chemaxon.struc.MolAtom: Query property checking.
qpropCheck(List<MolAtom>) - Method in class chemaxon.struc.MoleculeGraph: Check for query property errors.
QUADRIVALENT - Enum constant in enum class chemaxon.struc.Radical: Quadrivalent radical center.
query - Variable in class chemaxon.search.api.MolComparator: The query molecule.
QUERY - Static variable in class chemaxon.chemterms.SearchContext
QUERY_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atoms with query properties have been found in the molecule
QUERY_ATOMS - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "queryAtoms".
QUERY_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that bonds with query properties have been found in the molecule
QUERY_LABEL - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: Label for the query part of a similarity hit.
QueryAtomChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting generic atoms or ones having query properties.
QueryAtomChecker() - Constructor for class chemaxon.checkers.QueryAtomChecker: Default constructor
QueryBond - Class in chemaxon.struc: Bond object with query features.
QueryBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.QueryBond: Construct an any bond between two atoms.
QueryBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.QueryBond: Construct an any bond between two atoms.
QueryBond(MolAtom, MolAtom, String) - Constructor for class chemaxon.struc.QueryBond: Construct a query bond between two atoms.
QueryBond(QueryBond) - Constructor for class chemaxon.struc.QueryBond: Copy constructor.
QueryBondChecker - Class in chemaxon.checkers: A descendant of BondChecker detecting query bonds.
QueryBondChecker() - Constructor for class chemaxon.checkers.QueryBondChecker: Default constructor

R

r - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue
R - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue
R_GROUPS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "rgroupsVisible".
Ra - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ra.
RA_IN_EXPAND - Static variable in class chemaxon.struc.Sgroup: Atom removal in expand.
RA_REMOVE_EXCEPT_RU - Static variable in class chemaxon.struc.Sgroup: Replace without duplicating.
RACEMATE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that asymmetric atoms without specific stereo configuration have been found in the molecule
RacemateChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting asymmetric tetrahedral atoms without specific stereochemistry.
RacemateChecker() - Constructor for class chemaxon.checkers.RacemateChecker: Creates a new RacemateChecker instance.
racemicStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the racemic tetrahedral stereogenic centers.
racemicStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the racemic tetrahedral stereogenic centers (with attached data).
RAD_COUNT_MASK - Static variable in class chemaxon.struc.MolAtom: Radical's free electron count bits in flags for valid radical values.
RAD_MASK - Static variable in class chemaxon.struc.MolAtom: Radical value bits in flags.
RAD_OFF - Static variable in class chemaxon.struc.MolAtom: Radical value offset in flags.
RAD1 - Static variable in class chemaxon.struc.MolAtom: Monovalent radical center.
RAD2 - Static variable in class chemaxon.struc.MolAtom: Divalent radical center.
RAD2_SINGLET - Static variable in class chemaxon.struc.MolAtom: Divalent radical center with singlet electronic configuration.
RAD2_TRIPLET - Static variable in class chemaxon.struc.MolAtom: Divalent radical center with triplet electronic configuration.
RAD3 - Static variable in class chemaxon.struc.MolAtom: Trivalent radical center.
RAD3_DOUBLET - Static variable in class chemaxon.struc.MolAtom: Trivalent radical center with doublet electronic configuration.
RAD3_QUARTET - Static variable in class chemaxon.struc.MolAtom: Trivalent radical center with quartet electronic configuration.
RAD4 - Static variable in class chemaxon.struc.MolAtom: Invalid value for radical center for students.
Radical - Enum Class in chemaxon.struc: Enumeration of the supported radicals.
RADICAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atoms with radicals have been found in the molecule
RADICAL_H - Static variable in class chemaxon.struc.MolAtom: Include radical Hydrogen atom(s).
RADICAL_MATCHING_DEFAULT - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).
RADICAL_MATCHING_EXACT - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).
RADICAL_MATCHING_IGNORE - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for ignore radical searching (radical information is ignored during searching).
RadicalChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting radical atoms.
RadicalChecker() - Constructor for class chemaxon.checkers.RadicalChecker: Default constructor
radicalCoordsLabel - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
radicalMatching(boolean) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets whether the radical information of atoms should be considered in search.
radicalState - Static variable in class chemaxon.struc.graphics.MEFlow
randicIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
randomizeRotatableDihedrals(Molecule, Random) - Static method in class chemaxon.alignment.Alignment: Rotates rotatable bonds by a random dihedral angle value.
RARE_ELEMENT - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that rare elements have been found in the molecule
RareElementChecker - Class in chemaxon.checkers: A descendant of AtomTypeChecker detecting structures containing elements which are usually rare in organic/drug molecules.
RareElementChecker() - Constructor for class chemaxon.checkers.RareElementChecker: Default constructor
RATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains R-atom
RATOM - Static variable in class chemaxon.chemterms.ReactionContext
RatomChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting R-atoms.
RatomChecker() - Constructor for class chemaxon.checkers.RatomChecker: Creates a new anyChecker instance detecting all R-atoms.
RatomChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RatomChecker: Creates a new anyChecker instance reading checking options from the params argument.
Rb - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Rb.
RC_CHANGE - Static variable in class chemaxon.struc.MolBond: The bond (order) has changed in the reaction.
RC_MAKE_AND_CHANGE - Static variable in class chemaxon.struc.MolBond: The bond is created and changed.
RC_MAKE_OR_BREAK - Static variable in class chemaxon.struc.MolBond: The bond is made or broken in the reaction.
RC_NOT_CENTER - Static variable in class chemaxon.struc.MolBond: The bond is not a reacting center.
RC_NOT_MODIFIED - Static variable in class chemaxon.struc.MolBond: The bond is not modified in the reaction.
RC_REACTING_CENTER - Static variable in class chemaxon.struc.MolBond: The bond is a reacting center.
RC_UNMAPPED - Static variable in class chemaxon.struc.MolBond: Unmapped bond in reacting center.
RDF - Static variable in class chemaxon.formats.MFileFormat: MDL RDfiles.
Re - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Re.
react() - Method in class chemaxon.reaction.ConcurrentReactorProcessor: Generates the product list(s) for all reactant sets.
react() - Method in class chemaxon.reaction.Reactor: Performs the reaction.
REACTANT - Static variable in class chemaxon.chemterms.ReactionContext
REACTANTS - Static variable in class chemaxon.struc.RxnMolecule: "Reactant" structure type.
REACTING_CENTER_BOND_MARK - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains reacting center bond marks
REACTING_CENTER_MASK - Static variable in class chemaxon.struc.MolBond: Mask for reacting center bits.
ReactingCenterBondMarkChecker - Class in chemaxon.checkers: Checker detects bonds with reacting center bond marks.
ReactingCenterBondMarkChecker() - Constructor for class chemaxon.checkers.ReactingCenterBondMarkChecker: Default constructor
REACTION_OUTPUT - Static variable in class chemaxon.reaction.Reactor: Output type: reaction.
REACTION_SUPPORT - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "reactionSupport".
reactionArrow - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: The reaction arrow endpoints, null if not a reaction.
ReactionChecker - Class in chemaxon.checkers: Descendants of ReactionChecker detect reaction scheme problems.
ReactionChecker(StructureCheckerErrorType, StructureChecker) - Constructor for class chemaxon.checkers.ReactionChecker: Default constructor.
ReactionContext - Class in chemaxon.chemterms: Expression evaluation context to evaluate reaction conditions.
ReactionContext() - Constructor for class chemaxon.chemterms.ReactionContext: Constructor.
ReactionContext(RxnMolecule) - Constructor for class chemaxon.chemterms.ReactionContext: Constructs a reaction context with specified reaction.
ReactionException - Exception Class in chemaxon.reaction: Reaction Exception class.
ReactionException() - Constructor for exception class chemaxon.reaction.ReactionException
ReactionException(String) - Constructor for exception class chemaxon.reaction.ReactionException
ReactionException(String, Throwable) - Constructor for exception class chemaxon.reaction.ReactionException
ReactionException(Throwable) - Constructor for exception class chemaxon.reaction.ReactionException
ReactionFingerprint - Class in chemaxon.descriptors: ReactionFingerprint class.
ReactionFingerprint() - Constructor for class chemaxon.descriptors.ReactionFingerprint: Creates a new, empty instance of ReactionFingerprint without allocating internal storage.
ReactionFingerprint(ReactionFingerprint) - Constructor for class chemaxon.descriptors.ReactionFingerprint: Copy constructor.
ReactionFingerprint(RFParameters) - Constructor for class chemaxon.descriptors.ReactionFingerprint: Creates a new instance of ReactionFingerprint according to the parameters given.
ReactionFingerprint(String) - Constructor for class chemaxon.descriptors.ReactionFingerprint: Creates a new instance of ReactionFingerprint according to the parameters given.
ReactionMapErrorChecker - Class in chemaxon.checkers: A descendant of ReactionChecker detecting reactions with invalid mapping.
ReactionMapErrorChecker() - Constructor for class chemaxon.checkers.ReactionMapErrorChecker: Default constructor
ReactionMapper - Interface in chemaxon.reaction.mapper: Interface of reaction mappers that identify the corresponding parts of reactants and products and mark them with the same identifier.
ReactionMapper.MappingStyle - Enum Class in chemaxon.reaction.mapper: Available mapping styles for ReactionMapper.
reactNext() - Method in class chemaxon.reaction.ConcurrentReactorProcessor: Reacts the next reactant set and returns all product sets in a list.
Reactor - Class in chemaxon.reaction: Executes a chemical reaction: creates products from reactants with reaction center data.
Reactor() - Constructor for class chemaxon.reaction.Reactor: Default constructor.
read() - Method in class chemaxon.formats.MoleculeImporter
read() - Method in class chemaxon.formats.MolImporter: Reads the next molecule from the stream/file.
read() - Method in interface chemaxon.formats.MolImporterInterface: Reads the next molecule from the stream/file.
read() - Method in class chemaxon.formats.PositionedInputStream: Reads a character.
read() - Method in class chemaxon.naming.document.DocumentAnnotator: Find the next structure in the source document and return it, or null when the end of the document has been reached.
read(byte[], int, int) - Method in class chemaxon.formats.PositionedInputStream: Reads a byte array.
read(ObjectInput) - Static method in class chemaxon.formats.Encoding: Reads an externalized encoding object.
read16doubles(ObjectInput) - Method in class chemaxon.struc.Transform3D: Reads the 4x4 matrix components as double precision floating point numbers.
read16floats(ObjectInput) - Method in class chemaxon.struc.Transform3D: Reads the 4x4 matrix components as single precision floating point numbers.
readDoc(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane
readDocument(MDocument) - Method in class chemaxon.formats.MolImportModule: Reads the next document.
readExternal(ObjectInput) - Method in class chemaxon.formats.Encoding: Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MarvinPane: Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketch: Restores the sketcher's state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MSketchPane: Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MView: Restores the viewer's state.
readExternal(ObjectInput) - Method in class chemaxon.marvin.beans.MViewPane: Restores object state.
readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextAttributes
readExternal(ObjectInput) - Method in class chemaxon.struc.graphics.MTextDocument: Restores the document.
readExternal(ObjectInput) - Method in class chemaxon.struc.MPropertyContainer: Restores the property container's state.
readExternal(ObjectInput) - Method in class chemaxon.struc.PageSettings
readExternal(ObjectInput) - Method in class chemaxon.struc.Point3D: Deserializes a 3D point.
readExternal(ObjectInput) - Method in class chemaxon.struc.Transform3D: Deserializes a transformation matrix.
readFromString(String) - Method in class chemaxon.struc.graphics.MTextDocument: Reads the document content from a string.
readFromXmlFile(File, boolean, boolean) - Method in class chemaxon.descriptors.MDParameters: Reads configuration from XML file.
readFromXmlString(String, boolean, boolean) - Method in class chemaxon.descriptors.MDParameters: Reads configuration from XML string.
readLine() - Method in class chemaxon.formats.PositionedInputStream: Reads a line.
readMetricParameters() - Method in class chemaxon.descriptors.MDParameters: Processes all ParametrizedMetric nodes in the DOM tree.
readMetricParameters() - Method in class chemaxon.descriptors.PFParameters
readMetricWeights(Element, int) - Method in class chemaxon.descriptors.MDParameters
readMetricWeights(Element, int) - Method in class chemaxon.descriptors.PFParameters
readMol(Molecule) - Method in class chemaxon.formats.MolImportModule: Reads the next molecule.
readMol(ObjectInput) - Static method in class chemaxon.marvin.beans.MarvinPane
readRecordAsText() - Method in class chemaxon.formats.MolImporter: Reads the next molecule in text format without creating a Molecule object.
readResources(Class<?>, String) - Static method in class chemaxon.marvin.beans.MarvinPane: Reads resources from the specified file.
readSaltDictionary() - Static method in class chemaxon.standardizer.actions.StripSaltsAction: Reads the default salt dictionary.
readServiceDescriptors(InputStream) - Method in interface chemaxon.calculations.services.ServiceDescriptorReader: Returns a list of configured ServiceDescriptor objects from specified InputStream
readSolventDictionary() - Static method in class chemaxon.standardizer.actions.RemoveSolventsAction: Reads the default solvent dictionary.
readValues(boolean) - Method in class chemaxon.descriptors.BCUTParameters: Retrieves relavant parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.CDParameters: Picks parameter values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.CFParameters: Picks parameter values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.ECFPParameters: Picks parameter values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.MDParameters: Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.
readValues(boolean) - Method in class chemaxon.descriptors.PFParameters
readValues(boolean) - Method in class chemaxon.descriptors.RFParameters: Picks parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.scalars.HBParameters: Picks relevant parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.scalars.LDParameters: Picks parameters values from the DOM tree.
readValues(boolean) - Method in class chemaxon.descriptors.SDParameters: Reads attribute values form the XML configuration.
readValues(boolean) - Method in class chemaxon.descriptors.ShapeParameters
RearomatizeFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which rearomatize the molecule
RearomatizeFixer() - Constructor for class chemaxon.fixers.RearomatizeFixer
RearrangeReactionAction - Class in chemaxon.standardizer.actions: Standardizer action that rearranges reaction components.
RearrangeReactionAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RearrangeReactionAction: Initializes the action
rearrangeSgroups(int[]) - Method in class chemaxon.struc.Molecule: For internal use only.
RearrangeWedgesFixer - Class in chemaxon.fixers: Rearranges stereo wedge bonds according to IUPAC recommendations.
RearrangeWedgesFixer() - Constructor for class chemaxon.fixers.RearrangeWedgesFixer
rebuildStructures() - Method in class chemaxon.struc.RxnMolecule: For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow.
rebuildStructures(Point3D[], int) - Method in class chemaxon.struc.RxnMolecule: Sets the reaction arrow.
recalcCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup: Recalculates and sets the coordinates of the central atom of this sgroup.
recalcReactionArrow() - Method in class chemaxon.struc.RxnMolecule: Recalculates the coordinates of the reaction arrow from the reactants and products, forced recalculation.
recognize(byte[], int, int) - Static method in class chemaxon.formats.Encoding: Tries to recognize the encoding of a byte array.
recognizeByBOM(byte[], int, int) - Static method in class chemaxon.formats.Encoding: Tries to recognize the encoding of a byte array by the byte order mark.
recognizeOneLineFormat(String) - Static method in class chemaxon.formats.MFileFormatUtil: Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
recognizeOneLineFormat(String, MFileFormat...) - Static method in class chemaxon.formats.MFileFormatUtil: Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
Recognizer - Class in chemaxon.formats: File format recognizer.
Recognizer() - Constructor for class chemaxon.formats.Recognizer
Recognizer.RecognizerResult - Record Class in chemaxon.formats: Represents the result of a format recognition attempt.
RecognizerResult(List<String>, List<String>) - Constructor for record class chemaxon.formats.Recognizer.RecognizerResult: Creates an instance of a RecognizerResult record class.
RECORD_NUMBER - Enum constant in enum class chemaxon.marvin.common.CellType
RECURSIVE_UNGROUP - Static variable in class chemaxon.struc.Molecule: Ungroup and expand (if possible) the child S-groups.
RED - Static variable in class chemaxon.calculations.CalculatorPlugin: Constant storing the red rgb value (the acidic pKa result color).
redo() - Method in class chemaxon.marvin.beans.MSketchPane: Invokes a redo command.
RefractivityPlugin - Class in chemaxon.calculations: Plugin class for refractivity calculation.
RefractivityPlugin() - Constructor for class chemaxon.calculations.RefractivityPlugin: Constructor.
regenBonds() - Method in class chemaxon.struc.MoleculeGraph: Regenerates the bond vector: remove its elements, then put the bond objects from the atoms into it.
regenBonds() - Method in class chemaxon.struc.RgMolecule: Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
regenBonds() - Method in class chemaxon.struc.RxnMolecule: Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
regenBtab() - Method in class chemaxon.struc.MoleculeGraph: Regenerates the bond table.
regenBtab() - Method in class chemaxon.struc.SelectionMolecule: Regenerates the bond table.
regenCtab() - Method in class chemaxon.struc.MoleculeGraph: Regenerates the connection table.
regenCtab() - Method in class chemaxon.struc.SelectionMolecule: Regenerates the connection table.
registerFormat(MFileFormat) - Static method in class chemaxon.formats.MFileFormatUtil: Registers a user defined file format.
registerNativeNames() - Method in class chemaxon.marvin.datatransfer.MarvinTransferable: Registers the Native names supported by the implementation.
registerNativeNames() - Method in interface chemaxon.marvin.datatransfer.MTransferable: Registers the Native names supported by the implementation.
REGULAR_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule: Regular double reaction arrow type.
REGULAR_SINGLE - Static variable in class chemaxon.struc.RxnMolecule: Regular single reaction arrow type.
reject(String...) - Static method in record class chemaxon.formats.Recognizer.RecognizerResult: Creates a Recognizer.RecognizerResult object rejecting the given formats.
reject(List<String>) - Static method in record class chemaxon.formats.Recognizer.RecognizerResult: Creates a Recognizer.RecognizerResult object rejecting the given formats.
rejectedFormats() - Method in record class chemaxon.formats.Recognizer.RecognizerResult: Returns the value of the rejectedFormats record component.
RELATIVE_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains multiple stereogenic center groups
RelativeStereoChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting molecules having multiple stereogenic center groups
RelativeStereoChecker() - Constructor for class chemaxon.checkers.RelativeStereoChecker: Initializes relative stereo checker
releaseBaseMElectrons() - Method in class chemaxon.struc.graphics.MEFlow
releaseNewEMFGenerator() - Static method in class chemaxon.marvin.util.ImageExportUtil: Releases and disposes native resources needed by the .NET based EMF generator.
reloadDefaultInstance() - Static method in class chemaxon.structurechecker.CheckerFixerFactory: Reloads the content of the default factory instance
reloadParameters() - Method in interface chemaxon.calculations.gui.ParameterPanelHandler: Reloads previously stored parameters to parameter panel.
RemovalDate - Enum Class in chemaxon.common.annotations: Date values accepted by the SubjectToRemoval annotation.
remove() - Method in class chemaxon.struc.IteratorFactory.AtomIterator: Deprecated.

Removes the next atom in the iteration.
remove() - Method in class chemaxon.struc.IteratorFactory.BondIterator: Deprecated.

Removes the next bond in the iteration.
remove() - Method in class chemaxon.struc.IteratorFactory.NeighbourIterator: Deprecated.

The remove operation is not supported by this Iterator implementation.
remove() - Method in class chemaxon.struc.IteratorFactory.RgComponentIterator: Deprecated.

The remove operation is not supported by this Iterator implementation.
remove() - Method in class chemaxon.struc.IteratorFactory.RxnComponentIterator: Deprecated.

The remove operation is not supported by this Iterator implementation.
remove() - Method in class chemaxon.struc.IteratorFactory.SgroupIterator: Deprecated.

Removes the next s-group in the iteration.
remove(int) - Method in class chemaxon.struc.prop.MListProp: Removes an element.
remove(int, int) - Method in class chemaxon.struc.graphics.MTextDocument: Deletes a substring in the document.
remove(NameConverter) - Static method in class chemaxon.naming.NameConverters: Remove the converter from the converter list.
remove(MProp) - Method in class chemaxon.struc.MPropertyContainer: Removes a property.
RemoveAbsoluteStereoAction - Class in chemaxon.standardizer.actions: Standardizer action that removes the absolute stereo flag from the molecule.
RemoveAbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAbsoluteStereoAction: Initializes a remove absolute stereo action
removeAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Removes an action of the configuration
removeActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane: Removes an action listener.
removeActionListener(ActionListener) - Method in class chemaxon.marvin.common.TableOptions: Removes an action listener.
removeActions(Collection<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration: Removes actions of the configuration
RemoveAliasFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the alias information from the atoms of the molecule
RemoveAliasFixer() - Constructor for class chemaxon.fixers.RemoveAliasFixer
removeAll() - Method in class chemaxon.struc.Molecule: Removes all the atoms and bonds.
removeAll() - Method in class chemaxon.struc.MoleculeGraph: Removes all the atoms and bonds.
removeAll() - Method in class chemaxon.struc.RgMolecule: Remove all the atoms and bonds from the root structure, and from all the R-groups.
removeAll() - Method in class chemaxon.struc.RxnMolecule: Remove all the atoms and bonds from the root structure, and from all the R-groups.
removeAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes: Adds atoms to the "removed atom" list
removeAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes: Adds atoms to the "removed atom" list
removeAllAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes all attachment points of the Superatom S-group.
removeAllBonds() - Method in class chemaxon.struc.MolAtom: Removes all bonds.
removeAllBonds() - Method in class chemaxon.struc.Molecule: Removes all bonds.
removeAllBonds() - Method in class chemaxon.struc.MoleculeGraph: Removes all bonds.
removeAllBonds() - Method in class chemaxon.struc.RgMolecule: Remove all bonds from the root structure, and from all the R-groups.
removeAllBonds() - Method in class chemaxon.struc.RxnMolecule: Removes all bonds from the reactants, products and agents.
removeAllBonds() - Method in class chemaxon.struc.sgroup.SgroupAtom: Remove all edges.
removeAllBonds(boolean) - Method in class chemaxon.struc.MolAtom: Removes all bonds.
removeAllBonds(boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom: Removes all edges.
removeAllConstraints() - Method in class chemaxon.alignment.Alignment
removeAllFromDocument(MDocument) - Static method in class chemaxon.struc.NoStructure: Removes all NoStructure labels from the target document.
removeAllGroups() - Method in class chemaxon.standardizer.actions.CreateGroupAction: Removes all group definitions from the group list of the action.
removeAllMolecules() - Method in class chemaxon.alignment.Alignment: before every new alignment the molecules have to be removed.
removeAllMolecules() - Method in class chemaxon.alignment.PairwiseAlignment
removeAllMolecules() - Method in interface chemaxon.alignment.PairwiseComparison
removeAllMolecules() - Method in class chemaxon.alignment.PairwiseSimilarity3D
removeAllPairs() - Method in class chemaxon.alignment.AlignOnPairedAtoms: Removes all user defined atom pairs.
removeAllProperty() - Method in class chemaxon.marvin.common.UserSettings: Removes all property that are stored in this UserSettings object.
removeAllSalts() - Method in class chemaxon.standardizer.actions.StripSaltsAction: Removes all salts from the salt list of the action.
removeAllSgroups() - Method in class chemaxon.struc.Molecule: Removes all S-groups.
removeAllSolvents() - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Removes all solvents from the solvents list of the action.
removeArgument(int) - Method in class chemaxon.calculations.services.ServiceDescriptor: Removes the specified argument from the argument list
removeAtom(int) - Method in class chemaxon.struc.MoleculeGraph: Removes an atom and its bonds by index.
removeAtom(int) - Method in class chemaxon.struc.SelectionMolecule: Removes an atom and its bonds from the graph.
removeAtom(int, int) - Method in class chemaxon.struc.Molecule: Removes an atom and its bonds by index.
removeAtom(int, int) - Method in class chemaxon.struc.MoleculeGraph: Removes an atom and its bonds with extra cleanup options.
removeAtom(int, int) - Method in class chemaxon.struc.RgMolecule: Removes an atom and its bonds from the root structure.
removeAtom(int, int) - Method in class chemaxon.struc.RxnMolecule: Removes an atom from the reactants, products or agents.
removeAtom(MolAtom) - Method in class chemaxon.standardizer.Changes: Adds an atom to the "removed atom" list.
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlow
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MElectron
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MElectronContainer
removeAtom(MolAtom) - Method in class chemaxon.struc.graphics.MMoleculeMovie
removeAtom(MolAtom) - Method in class chemaxon.struc.MDocument: Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
removeAtom(MolAtom) - Method in class chemaxon.struc.MObject: Removes the atom from the corresponding molecule object.
removeAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Removes an atom and its bonds by reference.
removeAtom(MolAtom) - Method in class chemaxon.struc.SelectionMolecule: Removes an atom and its bonds.
removeAtom(MolAtom) - Method in class chemaxon.struc.Sgroup: Removes an atom and its bonds from the S-group.
removeAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes: Adds an atom to the "removed atom" list.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.MDocument: Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.Molecule: Removes an atom and its bonds by reference.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.MoleculeGraph: Removes an atom and its bonds with extra cleanup options.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.RgMolecule: Removes an atom and its bonds from the root structure and from all the R-groups.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.RxnMolecule: Removes an atom from the reactants, products or agents.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Removes an atom from the S-group.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.Sgroup: Removes an atom and its bonds from the S-group.
removeAtom(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes an atom from the S-group.
removeAtom(Sgroup, MolAtom, int) - Static method in class chemaxon.struc.Sgroup: Wrapper method that calls Sgroup.removeAtom(MolAtom, int) of sg.
removeAtomAliases(Molecule) - Static method in class chemaxon.alignment.MMPAlignment: Utility for preprocessing structure for alignment.
RemoveAtomFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the atoms of the molecule signed in the result
RemoveAtomFixer() - Constructor for class chemaxon.fixers.RemoveAtomFixer
removeAtomFromChildren(Sgroup, MolAtom) - Method in class chemaxon.struc.Molecule: Removes the parameter atom from the parameter S-group and it's descendants.
removeAtomFromGraphs(MolAtom) - Method in class chemaxon.struc.MDocument: Removes the specified node from all molecule graphs.
RemoveAtomMapFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the atom maps from the molecule
RemoveAtomMapFixer() - Constructor for class chemaxon.fixers.RemoveAtomMapFixer
RemoveAtomQueryPropertyFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes query properties from the given atoms.
RemoveAtomQueryPropertyFixer() - Constructor for class chemaxon.fixers.RemoveAtomQueryPropertyFixer
RemoveAtomValueFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the atom value from the molecule
RemoveAtomValueFixer() - Constructor for class chemaxon.fixers.RemoveAtomValueFixer
RemoveAtomValuesAction - Class in chemaxon.standardizer.actions: Standardizer action that removes atom values from the molecule.
RemoveAtomValuesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAtomValuesAction: Initializes the action
RemoveAttachedDataAction - Class in chemaxon.standardizer.actions: Standardizer action that removes attached data from the molecule.
RemoveAttachedDataAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveAttachedDataAction: Initializes the action
RemoveAttachedDataFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the attached data from the molecule.
RemoveAttachedDataFixer() - Constructor for class chemaxon.fixers.RemoveAttachedDataFixer
removeAttachmentPoint(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes the attachment point with the given order.
removeAttachmentPoints(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes all attachment points of the given attachment atom.
removeBond(int) - Method in class chemaxon.struc.MolAtom: Removes a bond.
removeBond(int) - Method in class chemaxon.struc.MoleculeGraph: Removes a bond by index.
removeBond(int) - Method in class chemaxon.struc.SelectionMolecule: Removes a bond from the graph.
removeBond(int, boolean) - Method in class chemaxon.struc.MolAtom: Removes a bond.
removeBond(int, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom: Removes a bond.
removeBond(int, int) - Method in class chemaxon.struc.Molecule: Removes a bond by index.
removeBond(int, int) - Method in class chemaxon.struc.MoleculeGraph: Removes a bond by index.
removeBond(int, int) - Method in class chemaxon.struc.RgMolecule: Remove a bond from the root structure.
removeBond(int, int) - Method in class chemaxon.struc.RxnMolecule: Removes an edge from a reactant, agent or product.
removeBond(MolBond) - Method in class chemaxon.struc.MolAtom: Removes a bond by reference.
removeBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Removes a bond by reference.
removeBond(MolBond) - Method in class chemaxon.struc.SelectionMolecule: Removes a bond by reference.
removeBond(MolBond) - Method in class chemaxon.struc.Sgroup: Removes a bond from the S-group.
removeBond(MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes a the given bond from the S-group.
removeBond(MolBond, boolean) - Method in class chemaxon.struc.MolAtom: Removes a bond by reference.
removeBond(MolBond, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom: Removes a bond by reference.
removeBond(MolBond, int) - Method in class chemaxon.struc.Molecule: Removes a bond by reference.
removeBond(MolBond, int) - Method in class chemaxon.struc.MoleculeGraph: Removes a bond by reference.
removeBond(MolBond, int) - Method in class chemaxon.struc.RgMolecule: Remove a bond from the root structure, and from all the R-groups.
removeBond(MolBond, int) - Method in class chemaxon.struc.RxnMolecule: Removes a bond from the reactants, products or agents.
RemoveBondFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the bonds of the molecule signed by the result
RemoveBondFixer() - Constructor for class chemaxon.fixers.RemoveBondFixer
removeBonds() - Method in class chemaxon.struc.Sgroup: Removes the edge references.
RemoveBondTopologyFixer - Class in chemaxon.fixers: Fixer removes reactiong center bond marks from bonds.
RemoveBondTopologyFixer() - Constructor for class chemaxon.fixers.RemoveBondTopologyFixer
RemoveBracketsFixer - Class in chemaxon.fixers: Removes brackets from molecule by ungrouping S-groups surrounded by brackets.
RemoveBracketsFixer() - Constructor for class chemaxon.fixers.RemoveBracketsFixer
removeChild(MObject) - Method in class chemaxon.struc.graphics.MPolyline
removeChild(MObject) - Method in class chemaxon.struc.graphics.MRArrow
removeChild(MObject) - Method in class chemaxon.struc.graphics.MRectangle
removeChild(MObject) - Method in class chemaxon.struc.MObject: Removes a child object.
removeChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup: Removes an S-group from the children list.
RemoveChiralFlagFixer - Class in chemaxon.fixers: A StructureFixer implementation that removes the chiral flag ("absolute stereo" flag) from the molecule.
RemoveChiralFlagFixer() - Constructor for class chemaxon.fixers.RemoveChiralFlagFixer
removeColorsFromMolecules() - Method in class chemaxon.struc.MDocument: Removes coloring from all molecular objects in the document.
removeComparator(MolComparator) - Method in class chemaxon.search.MolSearch: Delete a comparator from the search object.
removeComponent(int, int) - Method in class chemaxon.struc.RxnMolecule: Removes a reactant, product or agent.
removeCTflagFromSmallRings(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Remove CIS|TRANS flag from bonds in rings smaller than size 8.
removeDependentRgroupDefinition(int) - Method in class chemaxon.struc.RgMolecule: Removes the dependent R-group definition of the referenced R-group definition.
removeElectronsOf(MolAtom) - Method in class chemaxon.struc.MDocument: Removes the Electron containers belongs to targetAtom,
removeElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct
removeEmptyComponents() - Method in class chemaxon.struc.RxnMolecule: Checks all the componentes and removes those that are empty (node count is zero).
RemoveExplicitHydrogenFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which implicitize the hydrogens in the molecule
RemoveExplicitHydrogenFixer() - Constructor for class chemaxon.fixers.RemoveExplicitHydrogenFixer
RemoveExplicitHydrogensAction - Class in chemaxon.standardizer.actions: Standardizer action that removes explicit hydrogens from the molecule.
RemoveExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction: Initializes the remove explicit H action
RemoveFragmentAction - Class in chemaxon.standardizer.actions: Standardizer action that removes fragments from the molecule.
RemoveFragmentAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveFragmentAction: Initializes the action with parameters
RemoveFragmentAction.Measurement - Enum Class in chemaxon.standardizer.actions: Type of measurement
RemoveFragmentAction.Method - Enum Class in chemaxon.standardizer.actions: Type of removal methods
removeFromDocument(NoStructure, MDocument) - Static method in class chemaxon.struc.NoStructure: Removes the given NoStructre from the target document.
removeGroup(GroupDefinition) - Method in class chemaxon.standardizer.actions.CreateGroupAction: Removes a group definition from the group list of the action
removeGroupedAtom(MoleculeGraph, MolAtom, MolBond[], int) - Static method in class chemaxon.struc.Sgroup: Removes an atom from the molecule and removes its specified bonds.
removeInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil: Removes the Standardizer tasks specified in the configuration parameter from the inactive tasks list.
removeIsolatedAtoms() - Method in class chemaxon.struc.MoleculeGraph: Removes the null atom entries in the atoms array and sets the index fields appropriately.
removeIsolatedBonds() - Method in class chemaxon.struc.MoleculeGraph: Removes the null bond entries in the bonds array and sets the index fields appropriately.
removeItemListener(ItemListener) - Method in class chemaxon.calculations.gui.MChart
REMOVELARGEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Remove largest fragment
removeListener(MDocStorage.Listener) - Method in class chemaxon.marvin.common.MDocStorage: Removes a listener.
removeLonePairs(Molecule) - Static method in class chemaxon.alignment.MMPAlignment: Utility for preprocessing structure for alignment.
removeMolecules() - Method in class chemaxon.alignment.AlignOnPairedAtoms
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MEFlow
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MElectronContainer
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint: Point removed from a document.
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MPolyline
removeNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint: Point removed from a document.
removeNotify(MDocument) - Method in class chemaxon.struc.MObject: Called when the object is removed from a document.
removeObject(int) - Method in class chemaxon.struc.MDocument: Removes an object from the document.
removeObject(int) - Method in class chemaxon.struc.MSelectionDocument: Removes an object from the document.
removeObject(MObject) - Method in class chemaxon.struc.MDocument: Removes an object from the document or from the chemical structure of the document.
removeObject(MObject) - Method in class chemaxon.struc.Molecule: Removes the given MObject that belongs to this molecule.
removeObject(MObject) - Method in class chemaxon.struc.MSelectionDocument: Removes an object from the document.
removeObject(MObject) - Method in class chemaxon.struc.RgMolecule
removeObject(MObject) - Method in class chemaxon.struc.RxnMolecule: Removes a graphical object from this.
removeObject(MObject) - Method in class chemaxon.struc.Sgroup: Removes the specified MObject from this Sgroup.
removeOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings: Removes an owner.
removeProperty(String) - Method in class chemaxon.struc.MObject: Removes the mapping for this property key from this MObject if present.
removeProperty(String) - Method in class chemaxon.struc.MolAtom: Removes the mapping for this property key from this atom if present.
removeProperty(String) - Method in class chemaxon.struc.MolBond: Removes the mapping for this property key from this bond if present.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.calculations.api.ProgressableCalculator: Removes a listener previously added with ProgressableCalculator.addPropertyChangeListener(PropertyChangeListener), so the listener will not receive property changes of this calculation
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker: Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor: Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor: Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings: Remove a property change listener
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
removePropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction: Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Remove a PropertyChangeListener from the listener list.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.calculations.api.ProgressableCalculator: Removes a listener previously added with ProgressableCalculator.addPropertyChangeListener(String, PropertyChangeListener), so the listener will not receive changes of specified property
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker: Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor: Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor: Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
removePropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction: Remove a PropertyChangeListener for a specific property.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor: Remove a PropertyChangeListener for a specific property.
RemoveRadicalFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes the radicals from the atoms of the molecule
RemoveRadicalFixer() - Constructor for class chemaxon.fixers.RemoveRadicalFixer
RemoveReactingCenterBondMarkFixer - Class in chemaxon.fixers: Fixer removes reactiong center bond marks from bonds.
RemoveReactingCenterBondMarkFixer() - Constructor for class chemaxon.fixers.RemoveReactingCenterBondMarkFixer
removeReactionArrow() - Method in class chemaxon.struc.RxnMolecule: Removes the reaction arrow of this reacion.
removeRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Removes an atom from the list of paradigmatic repeating unit atoms.
removeRestH(int) - Method in class chemaxon.struc.RgMolecule: Removes the restH condition from an R-group definition.
removeRgroup(int) - Method in class chemaxon.struc.RgMolecule: Removes an R-group.
removeRgroupBridge(RgroupBridgeId) - Method in class chemaxon.struc.RgMolecule: Removes an R-group bridge.
removeRgroupBridgeMember(RgroupBridgeId, int) - Method in class chemaxon.struc.RgMolecule: Removes a definition member of an R-group bridge.
RemoveRGroupDefinitionsAction - Class in chemaxon.standardizer.actions: Standardizer action that removes R-group definitions from the molecule.
RemoveRGroupDefinitionsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveRGroupDefinitionsAction: Initializes the action
removeRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule: Removes an R-group definition member.
removeRgroupMembers(int, int[]) - Method in class chemaxon.struc.RgMolecule: Removes R-group members.
removeSalt(int) - Method in class chemaxon.standardizer.actions.StripSaltsAction: Removes a salt from the salt list of the action
removeSalts(int...) - Method in class chemaxon.standardizer.actions.StripSaltsAction: Removes a salt from the salt list of the action
removeSelectedFrom(MDocument) - Static method in class chemaxon.struc.NoStructure: Removes the selected NoStructres from the document.
removeSgroupFromList(Sgroup) - Method in class chemaxon.struc.Molecule: Removes an S-group from the sgroupVector.
removeSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule: Removes S-groups that are contained in a given molecule but not contained in another molecule.
removeSgroupsOf(Molecule, int) - Method in class chemaxon.struc.Molecule: Removes S-groups that are contained in a given molecule but not contained in another molecule.
removeSketchRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings: Remove a file from marvinsketch's recent file list
REMOVESMALLEST - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Remove smallest fragment
removeSolvent(int) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Removes a solvent from the solvent list of the action
removeSolvents(int...) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction: Removes a solvent from the solvent list of the action
RemoveSolventsAction - Class in chemaxon.standardizer.actions: Standardizer action that removes common solvents from the molecule.
RemoveSolventsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveSolventsAction: Initializes remove solvents action
removeStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup: Changes terminal star atoms (*) to carbon atoms (C).
RemoveStereoCareBoxAction - Class in chemaxon.standardizer.actions: Standardizer action that removes the stereo care boxes from the bonds in the molecule.
RemoveStereoCareBoxAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.RemoveStereoCareBoxAction: Initializes the action
RemoveStereoCareBoxFixer - Class in chemaxon.fixers: Fixer for molecules containing Stereo-Care Boxes.
RemoveStereoCareBoxFixer() - Constructor for class chemaxon.fixers.RemoveStereoCareBoxFixer
RemoveStereoInversionRetentionMarkFixer - Class in chemaxon.fixers: Removes stereo inversion retention marks from atoms.
RemoveStereoInversionRetentionMarkFixer() - Constructor for class chemaxon.fixers.RemoveStereoInversionRetentionMarkFixer
RemoveUnreferencedRgroupDefinitionsFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer that removes unused R-group definitions.
RemoveUnreferencedRgroupDefinitionsFixer() - Constructor for class chemaxon.fixers.RemoveUnreferencedRgroupDefinitionsFixer
removeUnSelectedFrom(MDocument) - Static method in class chemaxon.struc.NoStructure: Removes the non-selected NoStructures from the document.
RemoveValencePropertyFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which removes valence properties from the given atoms.
RemoveValencePropertyFixer() - Constructor for class chemaxon.fixers.RemoveValencePropertyFixer
removeViewRecentFile(File) - Method in class chemaxon.marvin.common.UserSettings: Remove a file from marvinview's recent file list
removeWhitespace(String) - Static method in class chemaxon.calculations.CalculatorPlugin: Removes whitespace characters from the given string.
REMOVEZCOORDINATE - Enum constant in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Convert 3D to 2D
RemoveZCoordinateFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which sets the z-coordinates of atoms to zero.
RemoveZCoordinateFixer() - Constructor for class chemaxon.fixers.RemoveZCoordinateFixer
RENDERING - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "rendering".
RenderingStyle - Enum Class in chemaxon.rendering.constants: Enum representing the available molecular rendering styles.
reparentSgroups(Molecule) - Method in class chemaxon.struc.Molecule: Change parents of all S-groups in this molecule.
RepeatingUnitSgroup - Class in chemaxon.struc.sgroup: Source-based and structure-based representation of repeating unit groups (polymers and repeating units with repetition ranges).
RepeatingUnitSgroup(Molecule, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup: Constructs an SRU S-group.
RepeatingUnitSgroup(Molecule, String, int) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup: Constructs an SRU S-group with connectivity.
RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup: Copy constructor.
RepeatingUnitSgroup(RepeatingUnitSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.RepeatingUnitSgroup: Copy constructor.
replace(int, int, String) - Method in class chemaxon.struc.graphics.MTextDocument: Replaces a substring in the document.
replace(MolAtom, MolAtom, Molecule) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction: Replaces an atom to the replace atom in the target molecule
replace(MProp, MProp) - Method in class chemaxon.struc.MPropertyContainer: Replaces or removes a property.
replace(MProp, MProp) - Method in class chemaxon.struc.prop.MCollectionProp: Replaces or removes a property.
replace(MProp, MProp) - Method in class chemaxon.struc.prop.MHashProp: Replaces or removes a property.
replace(MProp, MProp) - Method in class chemaxon.struc.prop.MListProp: Replaces or removes a property.
REPLACE_COORDINATE_BONDS - Static variable in class chemaxon.struc.IteratorFactory: Deprecated.

Replace coordinate bonds to multicenter atoms with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).
replaceAtom(int, MolAtom) - Method in class chemaxon.struc.Molecule: Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.
replaceAtom(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MElectronContainer
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MPolyline: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.MObject: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.Sgroup: Replace an existing atom by a new one in this S-group and its parent(recursively).
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Replace an existing atom by a new one.
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.Sgroup: Replace an existing atom by a new one in this S-group and its parent (recursively).
replaceAtom(MolAtom, MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Replace an existing atom by a new one.
ReplaceAtomsAction - Class in chemaxon.standardizer.actions: Standardizer action that replaces specified atoms in the molecule.
ReplaceAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ReplaceAtomsAction: Initializes a replace atom standardizer action
replaceAtomsWithNewRgroup(SelectionMolecule, int) - Method in class chemaxon.struc.RgMolecule: Replaces selected atoms with a new R-group.
replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.MoleculeGraph: Deprecated.
as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.
replaceBond(MolBond, MolBond) - Method in class chemaxon.struc.RgMolecule: Deprecated.
as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.
replaceSgroup(Sgroup, Sgroup) - Method in class chemaxon.struc.Molecule: For internal use only.
requireBinaryVector() - Method in class chemaxon.descriptors.ECFP: Checks the binary vector storage and generates it from the identifier list if necessary.
reset() - Method in class chemaxon.formats.PositionedInputStream: Repositions this stream to the position at the time the mark method was last called on this input stream.
reset() - Method in class chemaxon.struc.PageSettings: Resets the settings of multipage molecular documents.
resetBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow
resetCtab() - Method in class chemaxon.struc.MoleculeGraph: An operation performed that changed the connection table and the graph invariants.
resetFilePointer() - Method in class chemaxon.formats.PositionedInputStream: Resets file pointer to zero.
resetGrinvInParents() - Method in class chemaxon.struc.MoleculeGraph: Graph invariants must be recalculated for this graph and all parent graphs.
resetMap() - Method in class chemaxon.alignment.MinMaxDistance
residueSymbolOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the name of a residue.
residueSymbolOf(int) - Static method in class chemaxon.struc.Molecule: Gets the name of a residue.
residueTypeOf(String) - Static method in class chemaxon.struc.MolAtom: Gets the residue identifier for a residue name.
residueTypeOf(String) - Static method in class chemaxon.struc.Molecule: Gets the residue identifier for a residue name.
RESONANCE - Static variable in class chemaxon.struc.RxnMolecule: Resonance arrow, the same as the two-headed single reaction arrow.
RESONANCE_ALL - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
RESONANCE_CANONICAL - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
RESONANCE_MAJORCONTRIBUTORS - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
ResonancePlugin - Class in chemaxon.calculations: Plugin class for finding resonant structures.
ResonancePlugin() - Constructor for class chemaxon.calculations.ResonancePlugin: Constructor.
RESSEQ_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum residue sequence number is currently 8191.
restart() - Method in class chemaxon.reaction.Reactor: Restarts the reactor: the following call to Reactor.react() will return the first product set.
restoreCache(int) - Method in class chemaxon.struc.MoleculeGraph: Restores caches like connection table, bond table, etc.
restoreCoords(MoleculeGraph, double[]) - Static method in class chemaxon.core.calculations.clean.CleanUtil: Restores atomic coordinates.
restoreDefaultParameters() - Method in interface chemaxon.calculations.gui.ParameterPanelHandler: Restores default parameters to parameter panel.
restoreExplicitHydrogens(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin: When the input molecule is set, the explicit H-s may be stored CalculatorPlugin.setMolecule(Molecule, boolean, boolean, boolean) The parameter should be topologically equal to the input molecule for a successfull restore.
RESTYPE_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum residue type is currently 63.
resultMolList - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: The result molecules to be displayed.
resultValues - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: The result values to be displayed in MarvinSpace.
RETROSYNTHETIC - Static variable in class chemaxon.struc.RxnMolecule: Retrosynthetic arrow, the same as the regular double reaction arrow.
returnOptionString(boolean) - Method in class chemaxon.search.api.options.SearchOptions
reuseAtom(int, int) - Method in class chemaxon.struc.Molecule: Reuse an atom or create a new one.
reuseAtom(int, int) - Method in class chemaxon.struc.RgMolecule: Reuse an atom or create a new one.
reuseFont(String, int, double) - Method in class chemaxon.struc.graphics.MTextDocument
revalidateCoordDependentProps() - Method in class chemaxon.struc.MoleculeGraph: Revalidate coordinate-dependent properties.
revalidateCoordDependentProps() - Method in class chemaxon.struc.RgMolecule: Revalidate coordinate dependent properties.
revalidateCoordDependentProps() - Method in class chemaxon.struc.RxnMolecule: Revalidate coordinate dependent properties.
reverse() - Method in class chemaxon.struc.graphics.MPolyline: Reverses the order of points.
Rf - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Rf.
RFGenerator - Class in chemaxon.descriptors: Generator class for the ReactionFingerprint descriptor.
RFGenerator() - Constructor for class chemaxon.descriptors.RFGenerator
RFParameters - Class in chemaxon.descriptors: Manages reaction fingerprint parameters.
RFParameters() - Constructor for class chemaxon.descriptors.RFParameters: Creates an empty object.
RFParameters(File) - Constructor for class chemaxon.descriptors.RFParameters: Creates a new object based on a given configuration file.
RFParameters(String) - Constructor for class chemaxon.descriptors.RFParameters: Creates a new object based on a given configuration string.
Rg - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Rg.
RG_ID_MASK - Static variable in class chemaxon.struc.RgMolecule: R-group id mask in R-logic.
RG_ID2_FLAG - Static variable in class chemaxon.struc.RgMolecule: Other R-group ID's presence flag in R-logic.
RG_ID2_MASK - Static variable in class chemaxon.struc.RgMolecule: Mask of the other R-group's id in R-logic.
RG_ID2_OFF - Static variable in class chemaxon.struc.RgMolecule: Offset of the other R-group's id in R-logic.
RG_RESTH - Static variable in class chemaxon.struc.RgMolecule: The RestH flag in R-logic.
RgComponentIterator() - Constructor for class chemaxon.struc.IteratorFactory.RgComponentIterator: Deprecated.

Constructs an iterator to process the rgroup definition components, if the specified molecule in the factory is an RgMolecule, the iterator is empty otherwise.
RgMolecule - Class in chemaxon.struc: A molecule or reaction containing R-groups.
RgMolecule() - Constructor for class chemaxon.struc.RgMolecule: Creates a 2 dimensional RgMolecule.
RgMolecule(Molecule) - Constructor for class chemaxon.struc.RgMolecule: Creates an RgMolecule with the given root structure.
RgMoleculeGraph - Interface in chemaxon.struc: R-group container interface.
RGROUP - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the R-group query "atom".
RGROUP_ATTACHMENT - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of an ordered R-group attachment point.
RGROUP_ATTACHMENT_ERROR - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that invalid attachments in R-group definitions have been found in the molecule
RGROUP_BRIDGE_RATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that invalid R-atoms corresponding to R-group bridge definitions have been found in the molecule
RGROUP_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum R-group number (32767).
RgroupAttachmentErrorChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting invalid attachments in R-group definitions.
RgroupAttachmentErrorChecker() - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker: Creates a new RgroupAttachmentErrorChecker instance.
RgroupAttachmentErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RgroupAttachmentErrorChecker: Parameterized constructor.
RgroupAttachmentFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer that can fix attachment errors in R-group definition members.
RgroupAttachmentFixer() - Constructor for class chemaxon.fixers.RgroupAttachmentFixer
RgroupBridgeId - Class in chemaxon.struc: Identifies an R-group bridge position by storing a pair of R-group IDs.
RgroupBridgeId(int, int) - Constructor for class chemaxon.struc.RgroupBridgeId: Constructor.
RgroupBridgeRatomChecker - Class in chemaxon.checkers: Checker for R-atoms that form R-group bridges.
RgroupBridgeRatomChecker() - Constructor for class chemaxon.checkers.RgroupBridgeRatomChecker
RgroupCheckerResult - Class in chemaxon.checkers.result: A descendant of DefaultStructureCheckerResult providing information of R-group issues.
RgroupCheckerResult(StructureChecker, StructureCheckerErrorType, List<MolAtom>, List<MolBond>, List<Integer>, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.RgroupCheckerResult: Constructor which initialize all the properties.
RgroupDecomposition - Class in chemaxon.search: R-group decomposition.
RgroupDecomposition() - Constructor for class chemaxon.search.RgroupDecomposition: Constructor.
RgroupDecompositionResults - Class in chemaxon.search: Convenience class for generating, storing and returning results of a search in different forms: as r-group decomposition or Markush molecule.
RgroupDecompositionResults(Molecule, int, Molecule[][], RgMolecule, int[]) - Constructor for class chemaxon.search.RgroupDecompositionResults: This constructor is used only for storing results.
RgroupDecompositionResults(Molecule, int, Molecule[][], RgMolecule, int[], int[]) - Constructor for class chemaxon.search.RgroupDecompositionResults: This constructor is used only for storing results.
RgroupDecompositionResults(Molecule, Molecule[], SearchOptions, int) - Constructor for class chemaxon.search.RgroupDecompositionResults: Constructor used for generating results.
RgroupDecompositionResults(Molecule, Molecule[], SearchOptions, int, int[]) - Constructor for class chemaxon.search.RgroupDecompositionResults: Constructor used for generating results.
RGROUPED - Static variable in class chemaxon.struc.RxnMolecule: Add R-groups to component structure.
rgroupIdOf(MolAtom) - Method in class chemaxon.struc.RgMolecule: Finds the ID of the R-group (the number in R#) that contains the specified atom.
rgroupIdOf(MolAtom) - Method in interface chemaxon.struc.RgMoleculeGraph: Finds the ID of the R-group (the number in R#) that contains the specified atom.
rgroupIndexOf(MolAtom) - Method in class chemaxon.struc.RgMolecule: Finds the index of the R-group (the number in R#) that contains the specified atom.
rgroupIndexOf(MolAtom) - Method in interface chemaxon.struc.RgMoleculeGraph: Finds the index of the R-group (the number in R#) that contains the specified atom.
RGROUPS_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R-group definitions visible flag.
Rh - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Rh.
RICH_GENERIC - Enum constant in enum class chemaxon.search.api.options.TautomerSubstructureMode
Ring - Class in chemaxon.core.calculations: The ring class provides information of the ring types in a molecule.
Ring() - Constructor for class chemaxon.core.calculations.Ring
ringAtomCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of ring atoms in the molecule.
ringBondCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of ring bonds in the molecule.
ringCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of rings (SSSR smallest set of smallest rings) in the molecule.
ringCount(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
ringCountOfAtom(int) - Method in class chemaxon.core.calculations.Ring: Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
ringHandlingMode(RingHandlingMode) - Method in class chemaxon.search.mcs.McsSearchOptions.Builder: Sets how rings should be handled during the search.
RingHandlingMode - Enum Class in chemaxon.search.mcs: Enum type for the ring handling modes of MaxCommonSubstructure (MCS) algorithms.
rings() - Method in class chemaxon.core.calculations.Ring: Identifies the rings in the molecule.
rings(int) - Method in class chemaxon.core.calculations.Ring: Identifies rings in the molecule having a given size.
RingStrainErrorChecker - Class in chemaxon.checkers: RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.
RingStrainErrorChecker() - Constructor for class chemaxon.checkers.RingStrainErrorChecker: Default constructor
RingStrainErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.RingStrainErrorChecker: Parameterized constructor.
If params contains "transDoubleBond"/"cumulatedDoubleBond"/"tripelBond" key with value "true" then trans double bonds/cummulated double bonds/triple bonds will be checked.
ringSystemCount() - Method in class chemaxon.core.calculations.Ring: Calculates the number of ring systems.
ringSystemCount(int) - Method in class chemaxon.core.calculations.Ring: Identifies ring systems having a given size (number of rings) in the molecule.
ringSystems() - Method in class chemaxon.core.calculations.Ring: Identifies the ring systems in the molecule.
ringSystems(int) - Method in class chemaxon.core.calculations.Ring: Indentifies the ring systems in the molecule having a given size (number of rings).
RLOGIC_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R-Logic visibility flag.
RLOGIC_VISIBLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "RLogicVisible" or "RLogic".
RMCLEANUP_ALL - Static variable in class chemaxon.struc.MoleculeGraph: Perform all cleanup methods when removing an atom or a bond.
RMCLEANUP_EDGES - Static variable in class chemaxon.struc.MoleculeGraph: When removing an atom or a bond, also remove the bond(s) from the atom object(s).
RMCLEANUP_FIXCOMPONENT - Static variable in class chemaxon.struc.MoleculeGraph: Remove called from RxnMolecule.fixComponent.
RMCLEANUP_FROMSGROUPS - Static variable in class chemaxon.struc.Molecule: Remove atoms from S-groups.
RMCLEANUP_MOBJECT - Static variable in class chemaxon.struc.MoleculeGraph: Remove graphics objects containing the removed atom.
RMCLEANUP_NONE - Static variable in class chemaxon.struc.MoleculeGraph: Do not perform any cleanup methods when removing an atom or a bond.
RMCLEANUP_PARENTDOC - Static variable in class chemaxon.struc.MoleculeGraph: Remove atom from parent document.
RMCLEANUP_SGROUPATOMS - Static variable in class chemaxon.struc.Molecule: Remove S-groups of removed superatoms.
RMCLEANUP_STEREO - Static variable in class chemaxon.struc.MoleculeGraph: When removing an H atom, keep stereo information unchanged.
rmsd() - Method in class chemaxon.alignment.AlignRigidEasy: calculates the rmsd value
rmsd() - Method in interface chemaxon.alignment.MCSAlignmentResult: Root mean square deviation from the reference molecule.
RMSG_DEFAULT - Static variable in class chemaxon.struc.Molecule: Remove S-group's children and remove S-group from its parent.
RMSG_KEEP_ALL - Static variable in class chemaxon.struc.Molecule: Do not remove S-group parent, children and central atom (in the case of multicenter S-groups).
RMSG_KEEP_CHILDREN - Static variable in class chemaxon.struc.Molecule: Do not remove S-group's children.
RMSG_KEEP_MULTICENTER - Static variable in class chemaxon.struc.Molecule: Do not remove central atom of multicenter S-groups.
RMSG_KEEP_PARENT - Static variable in class chemaxon.struc.Molecule: Do not remove S-group from its parent.
Rn - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Rn.
RNA - Static variable in class chemaxon.formats.MFileFormat: RNA sequence.
rotatableBondCount() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the number of rotatable bonds in the molecule.
RotatableBondDetector - Class in chemaxon.alignment: Detects rotatable bonds in a molecule, used for conformer generation and flexible alignment.
RotatableBondDetector(Molecule, boolean) - Constructor for class chemaxon.alignment.RotatableBondDetector
rotateBy(double, int, int, int, int) - Method in class chemaxon.alignment.DihedralRotator: Rotates the selected dihedral by the defined angle
rotatedAndReferenceFused() - Method in interface chemaxon.alignment.MCSAlignmentResult: Fuse the rotated and the reference molecule.
rotatedMolecule() - Method in interface chemaxon.alignment.MCSAlignmentResult: The rotated molecule.
rotateTo(double, int, int, int, int) - Method in class chemaxon.alignment.DihedralRotator: Sets the dihedral defined by the atoms a1-a4 to the angle
roundTo(int) - Method in class chemaxon.struc.Point3D: Rounds the represented value to the given decimal precision.
ROWS - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "rows".
RS_ALL - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R/S shown always.
RS_ALL_POSSIBLE - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R/S shown always.
RS_ALL_POSSIBLE_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R/S shown always and highlight possible stereocenters as wee.
RS_ALL_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R/S shown always.
RS_MASK - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Chirality support mask in display option flags.
RS_OFF - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R/S not shown.
RS_OFF_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: R/S not shown.
RS_OFFSET - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Chirality support offset in display option flags.
RS_OPTIONS - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Array of chirality support levels.
RS_SELECTED - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported, use DispOptConsts.RS_ALL option instead.
RS_SELECTED_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Deprecated, for removal: This API element is subject to removal in a future version.
No longer supported, use DispOptConsts.RS_ALL_S option instead.
Ru - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ru.
run() - Method in class chemaxon.calculations.AlignmentPlugin
run() - Method in class chemaxon.calculations.CalculatorPlugin: Runs the tool.
run() - Method in class chemaxon.calculations.ChargePlugin: Runs the charge calculation.
run() - Method in class chemaxon.calculations.ChemicalNamePlugin
run() - Method in class chemaxon.calculations.ConformerPlugin: Runs the conformer calculation.
run() - Method in class chemaxon.calculations.ElementalAnalysisPlugin: Runs the tool.
run() - Method in class chemaxon.calculations.GeometryPlugin: Runs the tool.
run() - Method in class chemaxon.calculations.HBDAPlugin: Runs the charge calculation.
run() - Method in class chemaxon.calculations.HLBPlugin
run() - Method in class chemaxon.calculations.HuckelAnalysisPlugin: Runs the Huckel analysis calculation.
run() - Method in class chemaxon.calculations.IonChargePlugin: Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH.
run() - Method in class chemaxon.calculations.IsoelectricPointPlugin: Runs the isoelectric point and charge distribution calculations.
run() - Method in class chemaxon.calculations.LogDPlugin: Runs the logD calculation.
run() - Method in class chemaxon.calculations.LogPPlugin: Runs the logP calculation.
run() - Method in class chemaxon.calculations.MajorMicrospeciesPlugin: Stores the input molecule with ungrouped sgroups.
run() - Method in class chemaxon.calculations.MarkushEnumerationPlugin: Creates enumerated structures.
run() - Method in class chemaxon.calculations.MolecularDynamicsPlugin: Runs the tool.
run() - Method in class chemaxon.calculations.MSAPlugin: Runs the surface area calculation.
run() - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin: Runs the orbital electornegativity calculation.
run() - Method in class chemaxon.calculations.PkaPlugin: Runs the macro pKa calculation.
run() - Method in class chemaxon.calculations.PolarizabilityPlugin: Runs the charge calculation.
run() - Method in class chemaxon.calculations.RefractivityPlugin: Runs the refractivity calculation.
run() - Method in class chemaxon.calculations.ResonancePlugin: Calculates the resonant structures.
run() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.

Runs the plugin.
run() - Method in class chemaxon.calculations.StructuralFrameworksPlugin: Run calculation
run() - Method in class chemaxon.calculations.TautomerPlugin: Calculates the tautomers.
run() - Method in class chemaxon.calculations.TopologyAnalysisPlugin: Runs the tool.
run() - Method in class chemaxon.calculations.TPSAPlugin: Runs the surface area calculation.
run() - Method in class chemaxon.search.RgroupDecompositionResults: Generates the results if no valid results are available (see RgroupDecompositionResults.hasResults())
running - Variable in class chemaxon.calculations.api.ProgressableCalculator
RUNNING - Static variable in class chemaxon.calculations.api.ProgressableCalculator
runScript(String) - Method in class chemaxon.chemterms.ChemTermsEvaluator: Runs a script, variables will be added to the base variable table and can be referenced by chemical expressions.
RXN - Static variable in class chemaxon.formats.MFileFormat: MDL Rxnfiles.
RXN_V3_OUT - Static variable in class chemaxon.formats.MFileFormat: MDL Extended Rxnfiles.
RxnComponentIterator() - Constructor for class chemaxon.struc.IteratorFactory.RxnComponentIterator: Deprecated.

Constructs an iterator to process the components (reactant, product and agent components), if the specified molecule in the factory is an RxnMolecule, the iterator is empty otherwise.
RxnMolecule - Class in chemaxon.struc: Chemical reaction structure.
RxnMolecule() - Constructor for class chemaxon.struc.RxnMolecule: Create a reaction.
RXNSTEREO_INVERSION - Static variable in class chemaxon.struc.MolAtom: The stereo configuration of the atom is inverted during the reaction.
RXNSTEREO_NONE - Static variable in class chemaxon.struc.MolAtom: The stereo configuration of the atom is not considered during the reaction.
RXNSTEREO_RETENTION - Static variable in class chemaxon.struc.MolAtom: The stereo configuration of the atom is retained during the reaction.

S

s - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue

S - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue

S - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element S.

SAFE - Enum constant in enum class chemaxon.calculations.admet.HergClass

SALT_ID_PROPERTY - Static variable in class chemaxon.standardizer.actions.StripSaltsAction

Property key for salt ID

SALT_LIST_KEY - Static variable in class chemaxon.standardizer.actions.StripSaltsAction

Property key for salt list modification

SAME - Enum constant in enum class chemaxon.alignment.AlignmentProperties.ColoringScheme

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

Save the persistent properties to the config file set by the constructor.

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

Save the persistent properties to the file given as the first parameter.

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

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

Saves caches like connection table, bond table, etc.

saveCoords(MoleculeGraph, double[]) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Saves atomic coordinates.

saveParameters() - Method in interface chemaxon.calculations.gui.ParameterPanelHandler

Saves parameters from parameter panel.

saveParameterSettings() - Method in class chemaxon.calculations.gui.PluginFactory.PluginRecord

saveParameterSettings() - Method in class chemaxon.calculations.gui.PluginFactory

Saves plugin parameter settings to file $HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or $HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).

Sb - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Sb.

SBasic - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType

Sc - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Sc.

scalar(Point3D, Point3D) - Static method in class chemaxon.struc.Point3D

Calculates the scalar product of the two vectors

ScalarDescriptor - Class in chemaxon.descriptors

Base class for all scalar descriptors.

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

Creates a new, empty instance of ScalarDescriptor.

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

Copy constructor.

ScalarDescriptor(SDParameters) - Constructor for class chemaxon.descriptors.ScalarDescriptor

Creates a new instance of ScalarDescriptor according to the parameters given.

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

Creates a new instance of ScalarDescriptor according to the parameters given.

scale(double) - Method in class chemaxon.struc.Point3D

Scales the vector with the given factor.

SCALE - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "scale".

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

Calculates the scaled asymmetric Tanimoto dissimilarity for floating point values.

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

Calculates the scaled asymmetric Tanimoto dissimilarity for floating point values.

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

Calculates the scaled Tanimoto dissimilarity for floating point values.

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

Calculates the scaled Tanimoto dissimilarity for floating point values.

scaleFactors - Variable in class chemaxon.descriptors.MDParameters

scale factor of scalable parametrized metrics

scaleShift(double) - Method in class chemaxon.calculations.nmr.NMRShift

Scales the stored chemical shift and shift standard deviation values.

ScanStep(double, double) - Constructor for class chemaxon.alignment.DihedralScanResult.ScanStep

Construct.

scheduler - Variable in class chemaxon.marvin.common.TableSupport

Record access task scheduler.

SCN_EITHER_UNKNOWN - Static variable in class chemaxon.struc.Sgroup

Either unknown S-group connectivity.

SCN_HEAD_TO_HEAD - Static variable in class chemaxon.struc.Sgroup

Head-to-head S-group connectivity.

SCN_HEAD_TO_TAIL - Static variable in class chemaxon.struc.Sgroup

Head-to-tail S-group connectivity.

score() - Method in class chemaxon.calculations.bbb.BBB.Property

score() - Method in class chemaxon.calculations.bbb.BBB

Calculates the BBB score from properties.

score() - Method in class chemaxon.calculations.cnsmpo.CnsMpo.Property

score() - Method in class chemaxon.calculations.cnsmpo.CnsMpo

Calculates the CNS MPO score from properties.

screeningConfigurationNode - Variable in class chemaxon.descriptors.MDParameters

SCRIPT - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "script".

SDF - Static variable in class chemaxon.formats.MFileFormat

MDL SDfiles.

SDParameters - Class in chemaxon.descriptors

Manages ScalarDescriptor parameters.

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

Creates an empty object.

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

Creates a new object from the given configuration file.

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

Creates a new object from the given configuration string.

Se - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Se.

SEARCH_OPTIONS_KEY - Static variable in class chemaxon.standardizer.actions.TransformAction

Key of search options for parsing and property change

SEARCH_TYPE_NAMES - Static variable in interface chemaxon.search.api.SearchConstants

The names of the search types.

SearchConstants - Interface in chemaxon.search.api

Constants for structure searching

SearchContext - Class in chemaxon.chemterms

Expression evaluation context containing search hit data: the target, the query and the hit.

SearchContext() - Constructor for class chemaxon.chemterms.SearchContext

Constructor.

SearchException - Exception Class in chemaxon.search.api

Exception denoting errors during the search process.

SearchException() - Constructor for exception class chemaxon.search.api.SearchException

Constructs a new exception with null as its detail message.

SearchException(String) - Constructor for exception class chemaxon.search.api.SearchException

Constructs a new exception with the specified detail message.

SearchException(String, Throwable) - Constructor for exception class chemaxon.search.api.SearchException

Constructs a new exception with the specified detail message and cause.

SearchException(Throwable) - Constructor for exception class chemaxon.search.api.SearchException

Constructs a new exception with the specified cause and a detail message of (cause==null ? null : cause.toString()) (which typically contains the class and detail message of cause).

SearchHit - Class in chemaxon.search.api

Search hit object.

SearchHit(int[]) - Constructor for class chemaxon.search.api.SearchHit

Constructor: creates a hit object from a single (1 dimensional) hit mapping array.

SearchHit(int[][]) - Constructor for class chemaxon.search.api.SearchHit

Constructor: creates a hit object from a group (2 dimensional) hit mapping array.

searchOptions - Variable in class chemaxon.search.AbstractSearch

Object to store all search parameters.

searchOptions - Variable in class chemaxon.search.api.MolComparator

The search options.

SearchOptions - Class in chemaxon.search.api.options

Class to encapsulate common search options.

SearchOptions(int) - Constructor for class chemaxon.search.api.options.SearchOptions

Creates a SearchOptions object while setting different search options according to a predefined search type.

SearchTimeoutException - Exception Class in chemaxon.search.api

Exceptions indicating timeout during the search process.

SearchTimeoutException() - Constructor for exception class chemaxon.search.api.SearchTimeoutException

Constructs a new exception with null as its detail message.

SearchTimeoutException(String) - Constructor for exception class chemaxon.search.api.SearchTimeoutException

Constructs a new exception with the specified detail message.

secondaryBonds - Variable in class chemaxon.struc.IteratorFactory.BondIterator

Deprecated.

Secondary bonds that replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).

secondaryBonds - Variable in class chemaxon.struc.IteratorFactory.NeighbourIterator

Deprecated.

Secondary bonds that replace a coordinate bond to the multicenter with coordinate bonds from the metal to the represented atoms (in the MulticenterSgroup of the multicenter).

Section(int, String) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section

Constructs a text section.

Section(int, String, MTextAttributes) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section

Constructs a text section.

Section(MTextDocument.Section) - Constructor for class chemaxon.struc.graphics.MTextDocument.Section

Copy constructor.

SECTION - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the section of the document where the structure was found.

seek(long, int) - Method in class chemaxon.formats.PositionedInputStream

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

seekForward(int, ProgressMonitor, int, Runnable) - Method in class chemaxon.formats.MDocSource

Seeks in forward direction.

seekRecord(int, ProgressMonitor) - Method in class chemaxon.calculations.CalculatorPluginMDocSource

seekRecord(int, ProgressMonitor) - Method in class chemaxon.formats.MDocSource

Seeks the specified record.

seekRecord(int, ProgressMonitor) - Method in class chemaxon.formats.MolImporter

Seek the specified record.

seekRecordAtFraction(double, int, int, int, ProgressMonitor) - Method in class chemaxon.formats.MDocSource

Seeks an approximate file position.

seekVisitedRecord(int) - Method in class chemaxon.calculations.CalculatorPluginMDocSource

seekVisitedRecord(int) - Method in class chemaxon.formats.MDocSource

Seeks an already visited position in case of rewindable input.

seekVisitedRecord(int) - Method in class chemaxon.formats.MolImporter

Seeks an already visited position in case of rewindable input.

SELECTABLE - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "selectable".

selectAllConnectedObjects(boolean) - Method in class chemaxon.struc.MDocument

Selects or unselects all objects in this document and objects that belong to the chemical structure of this document.

selectAllObjects(boolean) - Method in class chemaxon.struc.MDocument

Selects or unselects all objects.

selectAllObjects(boolean) - Method in class chemaxon.struc.Molecule

Selects or deselects all MObjects that belong to this molecule.

selectAllObjects(boolean) - Method in class chemaxon.struc.RgMolecule

selectAllObjects(boolean) - Method in class chemaxon.struc.RxnMolecule

selectAllObjects(boolean) - Method in class chemaxon.struc.Sgroup

Sets the selection state of the MObject-s that belong to this Sgroup.

SELECTED - Static variable in class chemaxon.struc.MolAtom

The atom is selected if this flag is set.

SELECTED_INDEX - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "selectedIndex".

SELECTION - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "selection".

SelectionMolecule - Class in chemaxon.struc

A selection object which can contain atoms and bonds without real parent relationship (the real parent of atoms and bonds is another MoleculeGraph ancestor).

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

sendProgress(float) - Method in class chemaxon.calculations.api.ProgressableCalculator

separator - Variable in class chemaxon.calculations.output.CalculatorPluginOutput

The separator string separating the results for different result types.

SEPARATOR - Static variable in class chemaxon.calculations.gui.PluginFactory

Menuitem separator in Tools menu: if present then separator will be added to the Tools menu after the plugin menuitem.

SEPARATOR - Static variable in enum class chemaxon.descriptors.MetricsType

SEPARATOR - Static variable in class chemaxon.descriptors.SimilarityCalculatorFactory

This character is used to separate fields of the parameter string.

SEPARATOR - Static variable in class chemaxon.search.RgroupDecomposition

Separator in atom color code property string representation.

seqCis - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue

seqTrans - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue

SERVICE_CONFIGURATION_PATH_PROPERTY_KEY - Static variable in class chemaxon.calculations.services.ServiceDescriptorTools

Java System Property key to globally override default configuration path.

ServiceArgument<T> - Class in chemaxon.calculations.services

Describes an argument passed to services

ServiceArgument(Class<T>, T) - Constructor for class chemaxon.calculations.services.ServiceArgument

Constructs a service argument with specified type and value

ServiceArgument(Class<T>, T, boolean) - Constructor for class chemaxon.calculations.services.ServiceArgument

Constructs a service argument with specified type and value

ServiceDescriptor - Class in chemaxon.calculations.services

Descriptor class for marvin services

ServiceDescriptor() - Constructor for class chemaxon.calculations.services.ServiceDescriptor

Subclasses must have public argless constructor.

ServiceDescriptorReader - Interface in chemaxon.calculations.services

Reader for ServiceDescriptors

ServiceDescriptorTools - Class in chemaxon.calculations.services

Helper class for accessing ServiceDescriptorReader and ServiceDescriptorWriter implementations and various configuration data for services.

ServiceDescriptorTools() - Constructor for class chemaxon.calculations.services.ServiceDescriptorTools

ServiceDescriptorWriter - Interface in chemaxon.calculations.services

Writer for ServiceDescriptors

ServiceException - Exception Class in chemaxon.calculations.services

Exception thrown when a service invocation fails.

ServiceException(String) - Constructor for exception class chemaxon.calculations.services.ServiceException

Creates a ServiceException with specified message

ServiceException(String, Throwable) - Constructor for exception class chemaxon.calculations.services.ServiceException

Creates a ServiceException with specified message and cause

ServiceException(Throwable) - Constructor for exception class chemaxon.calculations.services.ServiceException

Creates a ServiceException with specified cause

serviceHandler - Variable in class chemaxon.calculations.services.ServiceDescriptor

ServiceHandler<DT> - Class in chemaxon.calculations.services

Manages service calls.

ServiceHandler() - Constructor for class chemaxon.calculations.services.ServiceHandler

SERVICES_CONFIG_URL_PROPERTY_KEY - Static variable in class chemaxon.marvin.common.UserSettings

set(float) - Method in class chemaxon.descriptors.ScalarDescriptor

Set the value of the descriptor.

set(int) - Method in enum class chemaxon.rendering.constants.AnyBondStyle

set(int) - Method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle

set(int) - Method in enum class chemaxon.rendering.constants.CoordinateBondStyle

set(int) - Method in enum class chemaxon.rendering.constants.RenderingStyle

set(int, float) - Method in class chemaxon.descriptors.CustomDescriptor

Sets the value of one cell of the descriptor.

set(int, float[]) - Method in class chemaxon.descriptors.CustomDescriptor

Sets values of the descriptor.

set(int, int) - Method in class chemaxon.descriptors.CustomDescriptor

Sets the value of one cell of the descriptor.

set(int, int[]) - Method in class chemaxon.descriptors.CustomDescriptor

Sets values of the descriptor.

set(int, GroupDefinition) - Method in class chemaxon.standardizer.actions.CreateGroupAction

Sets the group definition at specified index, and returns the previous value.

set(int, MProp) - Method in class chemaxon.struc.prop.MListProp

Sets an element.

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

Set all atom properties except the coordinates.

set(MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom

Set properties of this S-group superatom.

set(Point3D) - Method in class chemaxon.struc.Point3D

Set coordinates.

set(Transform3D) - Method in class chemaxon.struc.Transform3D

Copy.

set(String, MProp) - Method in class chemaxon.struc.MPropertyContainer

Sets a property object.

set(String, MProp, int) - Method in class chemaxon.struc.MPropertyContainer

Sets a property object.

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

Identifier of parameter: "setColoringEnabled".

SET_SCHEME_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Set coloring flag in display options.

setAbbreviation(int, String) - Method in class chemaxon.standardizer.actions.CreateGroupAction

Sets the abbreviation of the group at the provided index

setAbbreviation(String) - Method in class chemaxon.standardizer.actions.GroupDefinition

Sets the abbreviation of the group.

setAbsoluteLabelsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Set 'Absolute' label visibility.

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

Show or hide Abolute labels

setAbsolutePlacement(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets whether the placement of this attached data is absolute or relative to the objects it is attached.

SetAbsoluteStereoAction - Class in chemaxon.standardizer.actions

Standardizer action that sets the absolute stereo flag on the molecule.

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

Initializes a set absolute stereo action

setAbsoluteXY(double, double) - Method in class chemaxon.struc.sgroup.DataSgroup

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

setAbsoluteXY(Point3D) - Method in class chemaxon.struc.sgroup.DataSgroup

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

setAbsStereo(boolean) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Sets the absoluteLegacy value of the action

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

Sets the absolute stereoconfiguration flag.

setAbsStereo(boolean) - Method in class chemaxon.struc.RgMolecule

Sets the absolute stereoconfiguration flag for the root structure and the R-groups.

setAbsStereo(boolean) - Method in class chemaxon.struc.RxnMolecule

Sets the absolute stereoconfiguration flag for all the structures.

setAccuracyMode(AlignmentAccuracyMode) - Method in class chemaxon.calculations.AlignmentPlugin

setAcidicpKaUpperLimit(double) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setAcidicPkaUpperLimit(double) instead. This method will be removed in a future version.

setAcidicPkaUpperLimit(double) - Method in class chemaxon.calculations.PkaPlugin

Sets the maximum acidic pKa (default: 20).

setAction(StandardizerAction) - Method in class chemaxon.standardizer.Changes

Sets the base StandardizerAction of the changes

setActionB(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets the action string (URL or JavaScript expression) of a button in a GridBagView table.

setActionC(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets one of the two action strings (JavaScript expressions) of a checkbox in a GridBagView table.

setActionCommand(String) - Method in class chemaxon.marvin.common.MAction

Sets the action command string.

setActionState(ActionEvent) - Method in class chemaxon.marvin.common.MAction

Sets the action state.

setActionStringTokens(String[]) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the action string token of the checker

setActionStringTokens(String[]) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the action string token of the fixer

setActionStringTokens(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the action string tokens of the action

setActive(boolean) - Method in class chemaxon.standardizer.AbstractStandardizerAction

setActive(boolean) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

setActive(boolean) - Method in interface chemaxon.standardizer.StandardizerAction

Sets whether the action is active, and can be used

setActiveAtomReference(MolAtom) - Method in class chemaxon.core.calculations.stereo.StereoActivePart

For internal use only.

setActiveGroups(String...) - Method in class chemaxon.standardizer.Standardizer

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

use StandardizerConfiguration.filterGroups(String...) on the configuration returned by the method Standardizer.getConfiguration()

setAdvancedSave(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets wether the user prefers advanced svae or not.

setAlias(String) - Method in class chemaxon.calculations.services.ServiceArgument

Sets the argument alias.

setAlias(String) - Method in class chemaxon.calculations.services.ServiceDescriptor

Sets the service alias.

setAliasstr(String) - Method in class chemaxon.struc.MolAtom

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

setAlign(boolean) - Method in class chemaxon.search.RgroupDecomposition

Sets alignment.

setAlignmentMode(int) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the alignment mode.

setAlignScaffold(boolean) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets the scaffold aligning mode.

setAllowExperimentalFeatures(boolean) - Method in class chemaxon.marvin.common.UserSettings

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

Not supported anymore

setAllowTraditionalNitrogen(boolean) - Method in class chemaxon.checkers.ValenceErrorChecker

Sets if the checker should allow traditional N representation

setAllowValenceError(boolean) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Sets replace should be applied even in case of invalid valence in the result

setAminoAcid(boolean) - Method in class chemaxon.standardizer.actions.GroupDefinition

Sets whether the group represents an amino-acid

setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets peptide bridge coloring enabled.

setAminoAcidBondColoringEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets wether the user uses peptide bridge coloring or not.

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

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

setAnimated(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Starts or stops animation in each cells of the table or in the simple viewer.

setAnimated(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets animation of a cell of the table.

setAnimDelay(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the repeat delay for animations.

setAnimFPS(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the frames per second for animations.

setAnimSync(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets the animation synchronization.

setAnnotatedOutput(File) - Method in class chemaxon.naming.document.DocumentAnnotator

Set the destination file where an annotated version of the source document should be written.

setAnnotatedOutput(OutputStream) - Method in class chemaxon.naming.document.DocumentAnnotator

Set the destination output stream where an annotated version of the source document should be written.

setAnnotatedOutputDirectory(File) - Method in class chemaxon.naming.document.DocumentAnnotator

Set the directory where the annotated document and associated resources will be placed.

setAnnotatedOutputDirectory(File, boolean) - Method in class chemaxon.naming.document.DocumentAnnotator

Set the directory where the annotated document and associated resources will be placed.

setAnyBondStyles(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the any bond style.

setArcAngle(double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the central angle of the arc.

setArcHeight(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

setArcWidth(double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

setArgument(int, ServiceArgument<?>) - Method in class chemaxon.calculations.services.ServiceDescriptor

Replaces the argument at specified index with specified argument

setAromaticityChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects aromaticity atom query properties or not.

setAromatizationMethod(int) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Sets the aromatization method.

setAromatizeMethod(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the aromatize method.

setArrow(boolean) - Method in class chemaxon.struc.graphics.MPolyline

Sets or unsets arrow mode.

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

Sets the flags.

setArrowLength(int, double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the arrow head length.

setArrowWidth(int, double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the arrow head width.

setAssigned(int, boolean) - Method in class chemaxon.alignment.AlignmentMolecule

setAsymmetryFactor(float) - Method in class chemaxon.descriptors.MDParameters

Sets the value of the asymmetry factor of the current parametrized metric.

setAtno(int) - Method in class chemaxon.struc.MolAtom

Sets the atomic number.

setAtom(int) - Method in class chemaxon.chemterms.AtomContext

Sets the input atom.

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

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(int) for atom removal and MoleculeGraph.add(MolAtom) for adding new atoms.

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

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RgMolecule.add(MolAtom) to modify the structure.

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

Deprecated.

As of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and RxnMolecule.add(MolAtom) to modify the structure.

setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the specified atom in the S-group graph.

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

Sets the specified atom in the S-group graph.

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

Sets the specified atom in the S-group graph.

setAtom0(int, MolAtom) - Method in class chemaxon.struc.Molecule

Sets the atom at the specified index.

setAtom0(int, MolAtom) - Method in class chemaxon.struc.MoleculeGraph

Sets the atom at the specified index.

setAtom0(int, MolAtom) - Method in class chemaxon.struc.SelectionMolecule

Sets the atom at the specified index.

setAtom1(int) - Method in class chemaxon.alignment.MinMaxDistance

setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom

Sets the first atom of a bond.

setAtom1(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom

Sets the first node of an edge.

setAtom2(int) - Method in class chemaxon.alignment.MinMaxDistance

setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.MolAtom

Sets the second atom of a bond.

setAtom2(MolBond, MolAtom) - Static method in class chemaxon.struc.sgroup.SgroupAtom

Sets the second node of an edge.

setAtomFont(Font) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom symbol font name.

setAtomIndex(int) - Method in class chemaxon.calculations.nmr.NMRShift

Sets the atom index.

setAtomIndex(int, int) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the index of the ith atom of this multiplet.

setAtomIndexMap(int[]) - Method in class chemaxon.calculations.CalculatorPlugin

setAtomIndices(int[]) - Method in class chemaxon.calculations.nmr.NMRMultiplet

sets the indices of the atoms of this multiplet.

setAtomMap(int) - Method in class chemaxon.struc.MolAtom

Sets the atom-atom mapping number.

setAtomMappingMethod(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom mapping method.

setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides the atom mapping.

setAtomMappingVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the atom mapping visibility.

setAtomNumberingType(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the atom numbering.

setAtomNumberingType(int) - Method in class chemaxon.marvin.beans.MolPrinter

sets atom numbering type.

setAtomNumberingType(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom numbering type.

setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Set the atom properties visibility

setAtomPropertiesVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets atom properties visibility.

setAtoms(MolAtom[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Sets the atoms.

setAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

setAtoms(List<MolAtom>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method sets the atoms property

setAtomSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the color of an atom set.

setAtomSetColorMode(int, int) - Method in class chemaxon.struc.MDocument

Sets the atom set coloring mode.

setAtomSetFont(int, MFont) - Method in class chemaxon.struc.MDocument

Sets the font of an atom set.

setAtomSetRGB(int, int) - Method in class chemaxon.struc.MDocument

Sets the color of an atom set.

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

Sets the set sequence number of the atom.

setAtomSetSeq(int, String, int, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets the atom set sequence number of an atom.

setAtomSetSeq(int, String, String, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets atom set sequence numbers.

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

Sets the set sequence number of all atoms.

setAtomSetSeqs(int, String, int[]) - Method in class chemaxon.marvin.common.MDocStorage

Sets atom set sequence numbers.

setAtomsize(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the atom size.

setAtomSize(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the size of displayed atoms in units of regular bond length.

setAtomSize(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the atom size in C-C bond length units.

setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides the atom symbols in 3D.

setAtomSymbolsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets atom symbol visibility in 3D mode.

setAttach(int) - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).

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

Deprecated.

as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).

setAttachedDataMatch(int) - Method in class chemaxon.search.api.options.SearchOptions

Sets whether attached data (in data sgroups) should be used when comparing structures.

setAttachedDataPrefixes(String) - Method in class chemaxon.search.api.options.SearchOptions

Sets the prefixes of the names of those data sgroups that will be used during structure comparison.

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

Sets a new order for the given attachment point.

setAttachmentPointsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the attachment points visibility.

setAttachmentType(int) - Method in class chemaxon.search.RgroupDecomposition

Sets the attachment point representation type in ligand molecules.

setAttachmentType(int) - Method in class chemaxon.search.RgroupDecompositionResults

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

Sets the attach parent s-group information to the extra atom properties

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MAnalysisBox

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MBracket

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MEFlow

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MElectron

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MElectronContainer

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MPolyline

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MReactionSign

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRectangle

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.graphics.MRoundedRectangle

Sets the value of an attribute.

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

Sets the value of an attribute.

setAttribute(String, String) - Method in class chemaxon.struc.MObject

Sets the value of an attribute.

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

Sets attributes of selected text.

setAutoAlign(boolean) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the alignment behavior of the text-box.

setAutoCheckStructure(boolean) - Method in class chemaxon.marvin.common.UserSettings

Turn on automatic Structure checking

setAutoHeight(boolean) - Method in class chemaxon.struc.graphics.MNameTextBox

Turns on/off automatic height calculation.

setAutoHeight(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Turns on/off automatic height calculation.

setAutomaticFogEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the fog to automatic calculation mode.

setAutomaticReactionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the calculation of reaction plus signs to automatic.

setAutoResize(boolean) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the resizing behavior of the text-box.

setAutoScale(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the autoscale property.

setAutoSize(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Turns on/off automatic size calculation.

setAutoTabScale(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Allows or disallows automatic changing of tab scale.

setBackground(Color) - Method in class chemaxon.struc.MObject

Sets the background color of the object.

setBackgroundColor(Color) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the background color.

setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer

Sets the background color for the current cell based on selection.

setBackgroundColor(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewCellRenderer

Sets the background color for the current cell based on selection.

setBackgroundColor(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewCellEditor

Sets the background color for the current cell based on selection.

setBallRadius(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the ball radius in units of covalent radius.

setBallRadius(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the ball radius for "ball and stick" mode.

setBallRadius(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the ball radius for ball and stick mode.

setBarrierLimit(double) - Method in class chemaxon.alignment.AtropIsomerDetector

Set the energy barrier limit.

setBaseElectronContainer(MolAtom, MDocument) - Method in class chemaxon.struc.graphics.MEFlow

setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlow

setBaseElectronContainerIndex(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlow

setBaseElectronIndexInContainer(int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

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

Sets the base font family.

setBaseFontStyle(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the base font style.

setBasicpKaLowerLimit(double) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setBasicPkaLowerLimit(double) instead. This method will be removed in a future version.

setBasicPkaLowerLimit(double) - Method in class chemaxon.calculations.PkaPlugin

Sets the minimum basic pKa (default: -10).

setBestLigandPosition(MolAtom, MolAtom) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Calculates and sets an optimal position for a ligand atom.

setBestLigandPosition(MolAtom, MolAtom, double) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Calculates and sets an optimal position for a ligand atom.

setBicycloStereo(BicycloStereoDescriptor[]) - Method in class chemaxon.struc.MolAtom

Registers the bicyclo stereo information for this atom.

setBitCount(int) - Method in class chemaxon.descriptors.CFParameters

Sets the bit count (number of fingerprint bits to be set to 1) parameter.

setBitCount(int) - Method in class chemaxon.descriptors.RFParameters

Sets the bit count (number of fingerprint bits to be set to 1) parameter.

setBoldBondWidth(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bold bond width.

setBoldBondWidth(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the bold bond with.

setBoldBondWidth(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bold bond width in pt.

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

Deprecated.

as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and MoleculeGraph.add(MolBond) for adding a new bond to the molecule.

setBond(int, MolBond) - Method in class chemaxon.struc.RgMolecule

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RgMolecule.add(MolBond) for adding a new bond to the molecule.

setBond(int, MolBond) - Method in class chemaxon.struc.RxnMolecule

Deprecated.

as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and RxnMolecule.add(MolBond) for adding a new bond to the molecule.

setBond(int, MolBond) - Method in class chemaxon.struc.SelectionMolecule

Deprecated.

as of Marvin 6.2. Use SelectionMolecule.removeBond(MolBond) for bond removal and SelectionMolecule.add(MolBond) for adding a new bond to the molecule.

setBondCorrespondence(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

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

setBondCount(int) - Method in class chemaxon.descriptors.CFParameters

Sets the path length (number of adjacent bonds) parameter.

setBondCount(int) - Method in class chemaxon.descriptors.RFParameters

Sets the path length (number of adjacent bonds) parameter.

setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the visibility of the currently used bond at the mouse cursor.

setBondDraggedAlong(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the visibility of the currently used bond at the mouse cursor.

setBondHashSpacing(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the bond hash spacing that is the distance the hashes in a hashed bond.

setBondHashSpacing(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond hash spacing.

setBondIndex(int, int, int) - Method in class chemaxon.struc.BondTable

Sets the index of the bond connecting two atoms.

setBondLength(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bond length.

setBondLength(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the bond length in pt.

setBondLength(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond length in pt.

setBondLengthVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bond length display option.

setBondLengthVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the bond length visibility

setBonds(List<MolBond>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

setBonds(List<MolBond>) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method sets the bonds property

setBondSetColor(int, Color) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the color of a bond set.

setBondSetColorMode(int, int) - Method in class chemaxon.struc.MDocument

Sets the bond set coloring mode.

setBondSetRGB(int, int) - Method in class chemaxon.struc.MDocument

Sets the color of a bond set.

setBondSetSeq(int, String, int, int, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets bond set sequence numbers.

setBondSetSeq(int, String, String, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets bond set sequence numbers.

setBondSetSeqAll(int, String, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets all bond set sequence numbers.

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

Sets the set sequence number of all bonds.

setBondSetSeqs(int, String, List<int[]>) - Method in class chemaxon.marvin.common.MDocStorage

Sets bond set sequence numbers.

setBondSetThickness(int, double) - Method in class chemaxon.struc.MDocument

Sets the thickness of a bond set.

setBondSpacing(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the bond spacing.

setBondSpacing(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the double bond spacing that is the distance of the two lines representing a double bond.

setBondSpacing(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the double bond spacing.

setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MolRenderer

Sets the border for the current cell based on selection.

setBorder(JTable, boolean, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewCellRenderer

Sets the border for the current cell based on selection.

setBorder(JTable, MViewPane, boolean, int, int) - Method in class chemaxon.marvin.beans.MViewCellEditor

Sets the border for the current cell based on selection.

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

Sets the width of the border between cells.

setBottomMargin(double) - Method in class chemaxon.struc.PageSettings

setBracketOrientation(int) - Method in class chemaxon.struc.graphics.MBracket

Sets the orientation of the bracket.

setBridgehead(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing bridgehead H

setBridgingRAllowed(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets whether different undefined R-atoms can match the same group of atoms.

setByteOrder(ByteBuffer) - Method in class chemaxon.formats.PositionedInputStream

setC(int, boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets the state of a checkbox in a GridBagView table.

setCacheCapacity(int) - Method in class chemaxon.marvin.common.MDocStorage

Sets the maximum number of cached documents.

setCalculateEnergy(boolean) - Method in class chemaxon.calculations.GeometryPlugin

Sets the calculation of dreiding energy.

setCalculateForLEConformer(String) - Method in class chemaxon.calculations.GeometryPlugin

Sets the condition for lowest energy conformer calculation before geometry calculations are processed.

setCalculateMMFF94Energy(boolean) - Method in class chemaxon.calculations.GeometryPlugin

Sets the calculation of MMFF94 energy.

setCalculateMoleculeProjections(boolean) - Method in class chemaxon.calculations.GeometryPlugin

Sets the calculation of molecule projections.

setCalculateVolume(boolean) - Method in class chemaxon.calculations.GeometryPlugin

setCarbonVisibility(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility style of the C labels on Carbon atoms.

setCellIndex(int) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the viewer cell index.

setCellSize(int) - Method in class chemaxon.descriptors.MDParameters

Sets the size (number of bits) of the bins (cells).

setCellSize(Dimension) - Method in class chemaxon.marvin.common.TableSupport

Sets the molecule cell size for GridBagView.

setCellwiseWeights(boolean) - Method in class chemaxon.descriptors.MDParameters

Sets boolean telling whether cell weights are to be generated for current parametrized metric.

setCenterMolecule(boolean) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Center the molecule before MD calculation (It is not set by default.)

setCentralAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MulticenterSgroup

Sets the central atom of this sgroup.

setCentralAtomReference(MolAtom) - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor

For internal use only.

setCharge(int) - Method in class chemaxon.struc.MolAtom

Sets the charge.

setChargeAngle(double) - Method in class chemaxon.struc.MolAtom

Sets the charge angle for the atom.

setCharged(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing charged H

setChargeLocation(int) - Method in class chemaxon.struc.Sgroup

Sets the charge location attribute of the S-group.

setChargeMatching(int) - Method in class chemaxon.search.api.options.SearchOptions

Set charge matching behavior.

setChargeWithCircle(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility of Charge with Circle

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

Sets the URL of the configuration for Checkers in marvin sketch.

setCheckSpHyb(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets whether the sp-hybridization state of the atoms should be considered.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.CalculatorPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.GeometryPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.LogDPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.PkaPlugin

Deprecated.

For internal use only.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.TautomerPlugin

Deprecated.

setChemicalTermsArgument(String) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Deprecated.

For internal use only.

setChemicalTermsParameters(Properties, String) - Method in class chemaxon.calculations.CalculatorPlugin

Deprecated.

For internal use only.

setChemTermsFilter(String) - Method in class chemaxon.search.api.options.SearchOptions

Sets the Chemical Terms filter expression.

setChemTermsFilterConfig(File) - Method in class chemaxon.search.api.options.SearchOptions

Sets the configuration file for Chemical Terms filter.

setChemTermsFilterConfig(String) - Method in class chemaxon.search.api.options.SearchOptions

Sets the configuration string for Chemical Terms filter.

setChirality(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction

Sets the chirality value of absolute stereo action

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

Set chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.

setChirality(Map<Integer, Integer>) - Method in class chemaxon.struc.MoleculeGraph

Sets the chiralities of atoms.

setChiralitySupport(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets chirality support to show or hide the R/S labels.

setChiralitySupport(int) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the chirality display mode.

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

Sets the chirality support parameter.

setChlorideIonConcentration(double) - Method in class chemaxon.calculations.LogDPlugin

Sets the Cl- concentration (default: 0.1).

setChlorideIonConcentration(double) - Method in class chemaxon.calculations.LogPPlugin

Sets the Cl- concentration (default: 0.1).

setClassification(NMRErrorClassification) - Method in class chemaxon.calculations.nmr.NMRShift

Sets the error classification of the stored chemical shift.

setClassName(String) - Method in class chemaxon.calculations.services.LocalServiceDescriptor

Sets the full class name of the service

setClassName(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the name of the standardizer class

setClassName(String) - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor

Sets the name of the checker class

setClean(int, String) - Method in class chemaxon.formats.MolExporter

Sets molecule cleaning in exporter.

setClean(int, String, MolFilter) - Method in class chemaxon.formats.MolExporter

Sets molecule cleaning in exporter.

setClean2dOpts(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the 2D cleaning options.

setClean3dOpts(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the 3D cleaning options.

setCleanDim(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the space dimensions for cleaning.

setCleanHOptionEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets to add an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.

setCleanResultStructures(boolean) - Method in class chemaxon.calculations.ResonancePlugin

Sets 2D cleaning of the result structures: if true then resonants returned by ResonancePlugin.getStructure(int) and ResonancePlugin.getStructures() methods are cleaned in 2D.

setCleanTemplates(Standardizer, Molecule[]) - Static method in class chemaxon.standardizer.StandardizerUtil

Sets the default clean templates.

setCloridIonConcentration(double) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setChlorideIonConcentration(double) instead. This method will be removed in a future version.

setCloridIonConcentration(double) - Method in class chemaxon.calculations.LogPPlugin

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

Use LogPPlugin.setChlorideIonConcentration(double) instead. This method will be removed in a future version.

setCloseEnabled(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Set the accessibility of the Close menu item in the File menu.

setColor(AlignmentProperties.ColoringScheme) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

sets which atomtypes to use.

setColor(Color) - Method in class chemaxon.struc.MObject

Sets the color of the object.

SETCOLOR_COLORLESS - Static variable in class chemaxon.struc.MDocument

The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.

SETCOLOR_DEFAULT - Static variable in class chemaxon.struc.MDocument

Default set colors are used for coloring the atom/bond set.

SETCOLOR_SPECIFIED - Static variable in class chemaxon.struc.MDocument

The user specified set colors are used for coloring the atom/bond set.

setColoring(int) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets hit coloring options.

setColoringEnabled(boolean) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets whether substructure hit coloring should be used.

setColoringScheme(AlignmentProperties.ColoringScheme) - Method in class chemaxon.alignment.Alignment

setColorScheme(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the color scheme.

setColorScheme(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the color scheme.

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

Sets the nuber of columns.

setColumnCount(int) - Method in class chemaxon.struc.PageSettings

setColumnWidth(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the default column width.

setColumnWidth(int, int) - Method in class chemaxon.marvin.common.TableOptions

Sets the default width of a specified column.

setCommandLineParameters(String[]) - Method in class chemaxon.calculations.api.CalculatorLogger

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

Sets the comment.

setComment(String) - Method in class chemaxon.struc.RgMolecule

Sets the comment of the root molecule.

setComponentIDPropertyNames(String[], String[]) - Method in class chemaxon.reaction.Reactor

Sets reactant/product ID property (SDF/MRV tag) names.

setComponentIDPropertyNames(String, String) - Method in class chemaxon.reaction.Reactor

Sets reactant/product ID property (SDF/MRV tag) names.

setConfigurationReader(StructureCheckerConfigurationReader) - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

setConfigurationReader(StructureCheckerConfigurationReader) - Method in interface chemaxon.structurechecker.CheckerRunner

Sets a new configuration for the Runner.

setConfirmExit(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Sets to drop confirmation dialog about exit or not.

setConformerCount(int) - Method in class chemaxon.alignment.Alignment

The dihedral angles of every flexible molecule should be randomized before alignment.

setConformerCount(int) - Method in class chemaxon.alignment.AlignOnPairedAtoms

setConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects connection count atom query properties or not.

setConnectivity(int) - Method in class chemaxon.struc.Sgroup

Sets S-group connectivity.

setConsiderHPLCEffect(boolean) - Method in class chemaxon.calculations.LogDPlugin

Sets to take into account the HPLC effect The default is the shake flask's logD

setConsiderTautomerization(boolean) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets to consider tautomerization.

setConsiderTautomerization(boolean) - Method in class chemaxon.calculations.LogDPlugin

Sets to consider tautomerization in calculation.

setConsiderTautomerization(boolean) - Method in class chemaxon.calculations.LogPPlugin

Sets to consider tautomerization.

setConsiderTautomerization(boolean) - Method in class chemaxon.calculations.PkaPlugin

Sets to consider tautomerization.

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

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

setContext(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the context of this data sgroup.

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

Sets the context of this data sgroup.

setConvergenceLimit(double) - Method in class chemaxon.alignment.AlignOnPairedAtoms

setCoordDependent(long) - Method in class chemaxon.struc.MProp

Sets the property as coordinate dependent.

setCoordinateBondStyle(String) - Method in class chemaxon.marvin.beans.MolPrinter

Set the coordinate bond line style when both atoms are single.

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

Sets the "coordinative" bond line style when both atoms are single.

setCoordinateBondStyleAtMulticenter(String) - Method in class chemaxon.marvin.beans.MolPrinter

Set the coordinate bond line style.

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

Sets the "coordinative" bond line style when one of the atoms is multicenter.

setCopolymerMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Adjusts copolymer matching mode.

setCopyAllReactantProperties(boolean) - Method in class chemaxon.reaction.Reactor

Sets to copy all reactant properties to output products/reactions.

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

Sets the selected format in the Copy As dialog.

setCopyReactantProperties(String[][]) - Method in class chemaxon.reaction.Reactor

Sets the reactant properties which should be copied to output products/reactions.

setCopyReactantProperties(String[][], String[][]) - Method in class chemaxon.reaction.Reactor

Sets the reactant properties which should be copied to output products/reactions.

setCopyReactantProperties(Map<String, String>) - Method in class chemaxon.reaction.Reactor

Sets the reactant properties which should created in output products/reactions, based on a pattern.

setCorners(double, double, double, double) - Method in class chemaxon.struc.MolAtom

Used internally by MolPainter.

setCorners(MPoint, MPoint) - Method in class chemaxon.struc.graphics.MRectangle

Sets the corners.

setCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle

setCorrectionData(PkaTrainingResult) - Method in class chemaxon.calculations.PkaPlugin

Sets correction data for calculation

setCorrectionLibrary(String) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets the correction library.

setCorrectionLibrary(String) - Method in class chemaxon.calculations.PkaPlugin

Sets the correction library.

setCorrectionLibraryPath(String) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets the correction library file directly.

setCorrectionLibraryPath(String) - Method in class chemaxon.calculations.PkaPlugin

Sets the correction library file directly.

setCount(int) - Method in class chemaxon.alignment.PairwiseAlignment

setCount(int) - Method in interface chemaxon.alignment.PairwiseComparison

setCount(int) - Method in class chemaxon.alignment.PairwiseSimilarity3D

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

Coupled/decoupled spectrum.

setCouplingConstants(double[][]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets coupling constants.

setCouplingNeeded(boolean) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets whether spin-spin couplings are taken into account.

setCouplingNeeded(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets whether spin-spin couplings are taken into account.

setCreateStatistics(boolean) - Method in class chemaxon.descriptors.MDGenerator

Toggles the create statistics flag.

setCreateStatistics(boolean) - Method in class chemaxon.descriptors.MDParameters

Toggles the create statistics flag of the MDGenerator object.

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

Change the crossing bond of an attachment point.

setCTCrossedBond(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Convert wiggly type double bonds to crossed.

setCTWigglyBond(MoleculeGraph) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Convert crossed double bonds to wiggly type.

setCTWigglyBond(MoleculeGraph, int) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Convert crossed double bond to wiggly type.

setCurrentDefaultFontMetrics(FontMetrics) - Method in class chemaxon.struc.graphics.MTextBox

Sets the current height of the text..

setCurrentFont(MFont, int) - Method in class chemaxon.struc.graphics.MTextBox

Sets font for selected text or the next character to be typed.

setCurrentForeground(Color) - Method in class chemaxon.struc.graphics.MTextBox

Sets color for selected text or the next character to be typed.

setCurrentFrameIndex(int) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Sets the current frame index.

setCurrentHeight(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the current height of the text..

setCurrentParametrizedMetric(int) - Method in class chemaxon.descriptors.MDParameters

Selects the specified parametrized metric to be the current.

setCurrentParametrizedMetric(int) - Method in class chemaxon.descriptors.PFParameters

Selects a metric to be used.

setCurrentTextAttributes(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextBox

Sets the attributes for the selected text or the next character to be typed.

setCurrentWidth(double) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the current height of the text..

setCurrentWidth(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the current height of the text..

setCursorPos(int, boolean) - Method in class chemaxon.struc.graphics.MTextBox

Sets the cursor position.

setCursorRow(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the cursor row number.

setCustomHtmlToXmlConverter(XmlToHtmlConverter) - Method in class chemaxon.naming.document.DocumentAnnotator

Provide a custom converter from XML to HTML, to be used instead of the default one.

setCustomName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the customName

setD2SOptions(String) - Method in class chemaxon.naming.document.DocumentAnnotator

Sets the options string to use for document annotation.

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

Sets the data value to be set.

setDataDetached(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets whether the data should be displayed close to the objects or separately (detached).

setDataLine(int, String) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets a line of data.

setDebug(int) - Method in class chemaxon.marvin.beans.MarvinPane

Switches on the debug messages.

setDefaultFont(MFont) - Method in class chemaxon.struc.graphics.MTextDocument

Sets the default font.

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

Sets the SWING default font in the JEditorPane.

setDefaultNodeWeightBehavior(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.alignment.Alignment

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

Sets the default molecule format in the "Save As" dialog.

setDehydrogenize(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set dehydrogenize parameter

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

Sets the dependent R-group definition (rgroupIndexThen) for the referenced R-group definition (rgroupIndexIf).

setDescription(String) - Method in class chemaxon.calculations.services.ServiceDescriptor

Sets the description (tooltip) of service descriptor

setDescription(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the description of the concerning checker

setDescription(String) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the description of the concerning fixer

setDescription(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the description of the action

setDescriptorURI(String) - Method in class chemaxon.calculations.services.JsonServiceDescriptor

Sets the URI of the JSON RPC descriptor file

setDesiredBufferSize(int) - Method in class chemaxon.formats.PositionedInputStream

Sets desired buffer size.

setDetachable(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Sets the detachable property.

setDetectCumulatedDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker

Sets the detectCumulatedDoubleBonds property

setDetectTransDoubleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker

Sets the detectTransDoubleBonds

setDetectTripleBonds(boolean) - Method in class chemaxon.checkers.RingStrainErrorChecker

Sets the detectTripleBonds property

setDiameter(int) - Method in class chemaxon.descriptors.ECFPParameters

Sets the diameter parameter.

setDiaStereoIsomerMixtureAllowedState(boolean) - Method in class chemaxon.calculations.TautomerPlugin

setDifLoc(double...) - Method in class chemaxon.struc.graphics.MElectron

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

Sets the dimension.

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

Sets the dimension.

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

Sets the dimension of the root structure and the R-groups.

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

Sets the dimension for all the structures.

setDirectory(File) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the working directory, if the Load/Save is in Last Opened Mode.

setDirty(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets or clears the dirty flag.

setDisabledGroupTypes(List<String>) - Method in class chemaxon.marvin.beans.MSketchPane

setDisplayChargeWithCircle(boolean) - Method in class chemaxon.marvin.common.UserSettings

setDisplayedChars(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the number of characters to be displayed (1...999 or 0 for no restriction)

setDisplayedLines(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the number of lines to be displayed (0: show all)

setDisplayLabelsAndBoxes(boolean) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Set the option to show labels and bounding boxes for the parts of the result: target, query, score.

setDisplayLonePairsAsLine(boolean) - Method in class chemaxon.marvin.common.UserSettings

setDispopts(int) - Method in class chemaxon.marvin.beans.MarvinPane

Sets display options.

setDispopts(int) - Method in class chemaxon.marvin.beans.MolPrinter

Modifies the display options in the advanced way of handling display options.

setDispopts(int, int) - Method in class chemaxon.marvin.beans.MolPrinter

Modifies the display options as in MolPrinter.setDispopts(int), but affects only limited display options using a mask.

setDispoptsExt(int) - Method in class chemaxon.marvin.beans.MolPrinter

Modifies the extended display options in the advanced way of handling display options.

setDispoptsExt(int, int) - Method in class chemaxon.marvin.beans.MolPrinter

Modifies the extended display options as in MolPrinter.setDispoptsExt(int), but affects only limited display options using a mask.

setDistinctFirstAtomMatching(boolean) - Method in class chemaxon.search.api.options.MolSearchOptions

Option ensuring that upon the findNext() call the first atom must be stepped as well.

setDiversity(double) - Method in class chemaxon.calculations.ConformerPlugin

Sets the diversity limit for the calculation.

setDoc(MDocument) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the current document and calculates its bounds.

setDocSource(MDocSource, int, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets the document source.

setDocument(int, MDocument) - Method in class chemaxon.marvin.beans.MViewPane

Sets the document

setDocument(int, MDocument) - Method in class chemaxon.marvin.common.TableSupport

Sets the k-th record directly.

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

setDocument(MDocument) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the document.

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

setDocumentStyleName(String, boolean) - Method in class chemaxon.marvin.common.UserSettings

setDomainMax(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the upper end of this multiplet.

setDomainMax(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the upper end of the spectrum.

setDomainMin(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the lower end of this multiplet.

setDomainMin(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the lower end of the spectrum.

setDominantTautomerDistributionCalculation(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets dominant tautomer distribution calculation: if true then dominant tautomer distribution is calculated.

setDontRemoveLastComponent(boolean) - Method in class chemaxon.standardizer.actions.StripSaltsAction

setDoubleBond(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction

Sets the double bond value of absolute stereo action

setDoubleBondStereoMatchingMode(int) - Method in class chemaxon.search.api.options.SearchOptions

Sets how double bond cis/trans stereo information should match during the search.

setDoublePrecision(int) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the double -> string conversion precision (maximal number of fraction digits) with zero-padding (12.56 -> 12.5600 if precision=4).

setDoublePrecision(int, boolean) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the double -> string conversion precision (maximal number of fraction digits).

setDoublePrecision(String) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the precision in the decimal format.

setDownWedge(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the wedge bond display convention.

setDownWedge(String) - Method in class chemaxon.marvin.beans.MolPrinter

Set the down wedge orientation.

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

Sets the convention to use for displaying a down wedge.

setDraggable(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Allows or denies mouse dragged events in cells.

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

Sets the dragged object.

setDuplicateFiltering(int) - Method in class chemaxon.reaction.Reactor

Sets duplicate product list filtering.

setEditable(boolean) - Method in class chemaxon.standardizer.actions.TransformAction

Sets if this action is editable.

setEditable(int) - Method in class chemaxon.marvin.beans.MViewCellEditor

Sets the mode that determines if the structure is editable.

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

Sets the mode that determines if the structure is editable.

setEditorClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the editorClassName

setEditorClassName(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the editorClassName

setEditorClassName(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the name of the editor of the standardizer class

setEditorClassName(String) - Method in class chemaxon.structurechecker.CheckerFixerFactory.CheckerClassDescriptor

Sets the name of the editor of the checker class

setElectronIndex(String, int) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

setElectronProp(int) - Method in class chemaxon.struc.MolAtom

Sets the number of lone pairs.

setElectronToAtomMapping(MolAtom, MElectronContainer) - Method in class chemaxon.struc.graphics.MChemicalStruct

setEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enables or disables this component, depending on the value of the parameter b.

setEnabled(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Enables or disables this component, depending on the value of the parameter b.

setEnabled(boolean) - Method in class chemaxon.struc.PageSettings

setEnabledT(int, int, boolean) - Method in class chemaxon.marvin.common.MDocStorage

Set the enabled state of a text field in a record.

setEnableStandardization(boolean) - Method in class chemaxon.descriptors.RFParameters

Sets if standardization is applied.

setEnableTranslateAndRotate(boolean) - Method in class chemaxon.alignment.AlignmentMolecule

setEncoding(Encoding) - Method in class chemaxon.formats.PositionedInputStream

Sets the encoding.

setEncoding(String) - Method in class chemaxon.formats.PositionedInputStream

Sets the encoding.

setEncoding(String, String) - Method in class chemaxon.formats.MolExportModule

Sets the output encoding using the export options.

setEncodings(String) - Method in class chemaxon.formats.converter.MolConverter.Builder

Sets the input and/or output encoding.

setEndgroupMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Adjusts polymer end group matching.

setEndPosition(long) - Method in class chemaxon.struc.MDocument

Sets the end position of this document in the input file.

setEndPosition(long) - Method in class chemaxon.struc.Molecule

Sets the end position of this molecule in the input file.

setEnforceAbsStereo(boolean) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

setEnumCodeNeeded(boolean) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Indicates whether unique Markush enumeration code should be generated.

setEnumerateHomology(boolean) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets if homology groups should be enumerated or not.

setEnumerateMarkush(boolean) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets whether markush structures should be hit enumerated according to the query structure.

setErrorProcessor(ErrorProcessor) - Method in class chemaxon.formats.MolExporter

Sets the error handler interface for concurrent mode.

setEuler(double, double, double) - Method in class chemaxon.struc.Transform3D

Sets the rotational component using the Euler angles provided.

setExact(boolean) - Method in class chemaxon.standardizer.actions.TransformAction

Sets the exact value of the action

setExactBondMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Specifies whether bond types should match exactly - looking for query bonds target.

setExactQueryAtomMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets whether exact query atom matching should be used or not.

setExactSpecialAtomMatching(String) - Method in class chemaxon.search.api.options.SearchOptions

Sets the identifiers of those special atoms that should match exactly during structure comparison.

setExcludeAntiAromaticCompounds(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets whether antiaromatic compounds should be generated.

setExcluded(AtomLabels) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Sets the abbreviations to be excluded

setExcluded(AtomLabels) - Method in class chemaxon.checkers.PseudoAtomChecker

setExcluded(AttachedDataChecker.DataExclusionList) - Method in class chemaxon.checkers.AttachedDataChecker

Sets the names of data S-groups to be excluded.

setExcludeHalogens(boolean) - Method in class chemaxon.calculations.HBDAPlugin

Sets if halogens should be excluded from hydrogen bond acceptors.

setExcludePhosphorus(boolean) - Method in class chemaxon.calculations.TPSAPlugin

Sets to exclude phosphorus from PSA calculation.
Default: true, phosphorus i excluded.

setExcludeString(String) - Method in class chemaxon.standardizer.AbstractSgroupAction

Sets the exclude string of action

setExcludeString(String) - Method in class chemaxon.standardizer.actions.ContractSgroupsAction

setExcludeString(String) - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction

setExcludeString(String) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

setExcludeSulfur(boolean) - Method in class chemaxon.calculations.HBDAPlugin

Sets if sulfur atom should be excluded from hydrogen bond acceptors.

setExcludeSulfur(boolean) - Method in class chemaxon.calculations.TPSAPlugin

Sets to exclude sulfur from PSA calculation.
Default: true, sulfur i excluded.

setExclusionRegexp(boolean) - Method in class chemaxon.checkers.AttachedDataChecker

Sets if the exclusion list should be treated as a regular expression.

setExhaustiveModeLimit(int) - Method in class chemaxon.search.api.options.SearchOptions

Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.

setExperimentalEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enable or disable experimental features.

setExplicitConnectionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects explicit connection count atom query properties or not.

setExpression(String) - Method in class chemaxon.calculations.services.DynamicArgument

Sets the expression

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

Sets the URL of the configuration file containing the list of external Checkers in marvin sketch.

setExtraLabel(String) - Method in class chemaxon.struc.MolAtom

Sets the extra atom label (also called atom value): "label" or "label1|label2".

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

Sets the extra label colors: lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

setExtraLabelColor(long) - Method in class chemaxon.struc.MolAtom

Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

setExtraLabelColorsForDocument(Molecule) - Method in class chemaxon.struc.MDocument

Sets the coloring mode sets and colors of extra labels

setExtraLabelSetColorMode(int, int) - Method in class chemaxon.struc.MDocument

setExtraLabelSetRGBs(int, int) - Method in class chemaxon.struc.MDocument

setExtraLabelSetRGBs(int, int, int) - Method in class chemaxon.struc.MDocument

setExtraLabelSetSeq(int) - Method in class chemaxon.struc.MolAtom

setEZLabelsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility state of absolute double bond stereo configuration labels.

setEzVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the E/Z display option.

setEZVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide E/Z labels

setFeature(int, int) - Method in class chemaxon.descriptors.pharmacophore.PMap

Sets a given feature of a given atom to true.

setFieldAccessor(MFieldAccessor) - Method in class chemaxon.marvin.common.MDocStorage

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

designed for MarvinView, do not use.

setFieldFont(String, Font) - Method in class chemaxon.marvin.beans.MViewPane

Sets the font for a named field in a table.

setFieldFontSize(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the field font size.

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

Sets the data field name.

setFields(String[]) - Method in class chemaxon.formats.converter.MolConverter.Builder

Sets the included fields to be shown in a table.

setFieldsShown(boolean) - Method in class chemaxon.marvin.common.TableOptions

Show or hide SDfile fields in the table

setFieldType(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the field type.

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

Sets the field type from string representation.

setFile(File) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the current molecule file but does not load it.

setFilter(MolFilter) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets the molecule filter.

setFinalStereoFix(boolean) - Method in class chemaxon.standardizer.Standardizer

Sets to perform final stereo fixes.

setFingerprint(int[]) - Method in class chemaxon.chemterms.MolContext

Sets the fingerprint of the input molecule.

setFingerprintGenerator(FingerprintGenerator) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Sets the fingerprint generator object (needed for query strings).

setFiveLongRings(List<List<MolAtom>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

This method sets the fiveLongRings property.

setFixed(int) - Method in class chemaxon.marvin.common.MDocStorage

Sets a document as fixed.

setFixerClassName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the fixerClassName

setFixMode(FixMode) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the fixMode

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

Sets the flags.

setFlags(int) - Method in class chemaxon.struc.MolAtom

Sets the flags.

setFlags(int) - Method in class chemaxon.struc.MolBond

Sets bond type (4 bit), stereo (2+2+1 bit), topology (2 bit) bond set (5 bit) and reacting center (7 bits) information.

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

Sets the flags of the molecule.

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

Sets the dimension and chiral flags.

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

Sets the flags.

setFlags(int, int) - Method in class chemaxon.struc.MolBond

Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit) information.

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

Sets specified bits in the flags.

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

Sets specified bits in the flags.

setFlexible(boolean) - Method in class chemaxon.descriptors.ShapeParameters

setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.alignment.AlignmentBase

Sets the maximum gradient component limit used for the optimization.

setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

setFlexibleRingRotatableBondCount(int) - Method in class chemaxon.alignment.AtropIsomerDetector

setFlexibleRingSize(int) - Method in class chemaxon.alignment.AlignmentBase

Sets the maximum gradient component limit used for the optimization.

setFlexibleRingSize(int) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

setFlexibleRingSize(int) - Method in class chemaxon.alignment.AtropIsomerDetector

setFlexibleRingSize(int) - Method in class chemaxon.alignment.PairwiseAlignment

setFlipped(boolean) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the flip property of this S-group.

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

Focus to the specified object.

setFogFactor(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the fog factor.

setFontScale(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the font scaling factor.

setForceField(String) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the force field type.

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

Sets the dipole export format.

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

Sets the spectrum export format.

setFormat(String) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set output format used by CalculatorPlugin.getResultAsString(int, Object)

setFormat(String) - Method in class chemaxon.formats.MolInputStream

Sets the molecule file format.

setFormat(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the default molecule file format.

setFormat(String) - Method in class chemaxon.standardizer.configuration.StandardizerActionStringWriter

Sets the string value of the format of molecule export used by the writer

setFormat(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfigurationXmlWriter

Sets the string value of the format of molecule export used by the writer

setFormat(String) - Method in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter

Sets the string value of the format of molecule export used by the writer

setFormulaRecognition(boolean) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Recognizes the molecular formulas in pseudo labels.

setForSpecIsotopeSymbol(String) - Method in class chemaxon.struc.MolAtom

Deprecated.

as of Marvin 6.3. use MolAtom.setSpecIsotopeSymbolPreferred(boolean) and MolAtom.setMassno(int) instead.

setFree(int) - Method in class chemaxon.struc.graphics.MElectronContainer

setFree(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

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

Sets NMR measurement frequency.

setFrequency(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the NMR measurement frequency.

setFromSgroupCopy(SgroupAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom

Make a copy of this S-group superatom.

setFunctionScale(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the scaling parameter for the function of this multiplet.

setFuzzinessFactor(float) - Method in class chemaxon.descriptors.PFParameters

Sets the value of the fuzziness factor, used in fuzzy bipolar pharmacophore autocorrelogram (FBPA) based convolution product in non-parametrized (generic) FBPA metric.

setFuzzyCutOff(float) - Method in class chemaxon.descriptors.PFParameters

setFuzzyLowerBound(int) - Method in class chemaxon.descriptors.PFParameters

setFuzzySmoothingFactor(float) - Method in class chemaxon.descriptors.PFParameters

Sets the value of the fuzzy smoothing factor used in the generation of fuzzy fingerprints.

setGenerateCASNumber(boolean) - Method in class chemaxon.calculations.ChemicalNamePlugin

Sets CAS number name generation.

setGenerateDistanceRanges(boolean) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

Generate intermolecular atomic distance ranges by tweaking conformation.

setGenerateMinorProducts(boolean) - Method in class chemaxon.reaction.Reactor

If set then products lists are not filtered out by the selectivity rule, but they are tagged as minor products.

setGeneratePreferredIUPACName(boolean) - Method in class chemaxon.calculations.ChemicalNamePlugin

Sets preferred IUPAC name generation.

setGenerateTraditionalIUPACName(boolean) - Method in class chemaxon.calculations.ChemicalNamePlugin

Sets traditional IUPAC name generation.

setGenNameFontSize(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the IUPAC name font size.

setGenNameShown(boolean) - Method in class chemaxon.marvin.common.TableOptions

Set visibility of IUPAC names.

setGeom3D(boolean) - Method in class chemaxon.calculations.PolarizabilityPlugin

Sets 3D geometry consideration.

setGlobalChecker(TaggedCalculatorInputChecker) - Static method in interface chemaxon.calculations.api.TaggedCalculator

Sets the global input checker that will be used by all calculators implementing this interface.

setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.formats.MolExportModule

Pass and set the global GUI properties container.

setGlobalGUIProperties(MPropertyContainer) - Method in class chemaxon.marvin.beans.MarvinPane

setGraphInvariantVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the graph invariant visibility

setGridVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

setGrinv(long) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the invariant the text box depends on.

setGrinvCC(long) - Method in class chemaxon.struc.MoleculeGraph

Sets the graph invariant change count.

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

Sets graph invariant calculation options passed to the module.

setGrinvVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides the graph invariants.

setGroupIndices(List<Integer>) - Method in class chemaxon.checkers.result.DataSgroupCheckerResult

setGroups(Map<String, Molecule>) - Method in class chemaxon.standardizer.actions.AliasToGroupAction

Sets the abbreviated groups of the action

setGUIContracted(boolean) - Method in class chemaxon.struc.Molecule

Deprecated.

as of Marvin 6.2, use Molecule.expandSgroups(int) or Molecule.contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED

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

Deprecated.

as of Marvin 6.2, use Molecule.expandSgroups(int) or Molecule.contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED

setGUIPropertyContainer(MPropertyContainer) - Method in class chemaxon.struc.MDocument

Sets the property container storing MarvinPane settings

setGUIStateRecursively(boolean) - Method in class chemaxon.struc.Sgroup

Deprecated.

as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality

setGUIStateRecursively(boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Deprecated.

setGUIStateRecursively(boolean, int) - Method in class chemaxon.struc.Sgroup

Deprecated.

as of Marvin 6.2, use Molecule.setGUIContracted(boolean) for such functionality

setHalfWidth(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the half-width of the NMR lines.

setHalfWidth(double) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets NMR half-width.

setHconnected(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing H connected H

setHCountMatching(int) - Method in class chemaxon.search.api.options.SearchOptions

Sets the H count matching mode.

setHeadCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the head crossing bonds of a ladder-type polymer.

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

Sets a logical cell extent by interpreting rows and columns as part of a sub-table.

setHeight(double) - Method in class chemaxon.struc.PageSettings

setHelpText(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the help text of the concerning checker

setHelpText(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the help text of the action

setHit(int[]) - Method in class chemaxon.chemterms.SearchContext

Sets the search hit, as a query atom index -> target atom index array, with negative target atom index denoting match on implicit H.

setHitColor(Color) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the color to be used when coloring the substructure hit.

setHitHomologyColor(Color) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Set the color of user defined homologies in a substructure hit.

setHitIndexType(int) - Method in class chemaxon.search.api.options.MolSearchOptions

Set the representation to use for hit indexes in case of Markush search.

setHitOrdering(int) - Method in class chemaxon.search.api.options.SearchOptions

Sets the hit ordering type.

setHomologyBroadTranslation(HomologyTranslationOption) - Method in class chemaxon.search.api.options.SearchOptions

Adjusts for which query atoms broad translation on target homology groups is allowed.

setHomologyNarrowTranslation(HomologyTranslationOption) - Method in class chemaxon.search.api.options.SearchOptions

Adjusts for which query homology atoms narrow translation on target specific atoms is allowed.

setHorizontalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the horizontal alignment.

setHybridizationState(int) - Method in class chemaxon.struc.MolAtom

Sets the hybridization state.

setHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects hydrogen count atom query properties or not.

SetHydrogenIsotopeSymbolAction - Class in chemaxon.standardizer.actions

Standardizer action that sets hydrogen isotope symbols to be used in the molecule (D/T or 2H/3H).

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

Initializes the action

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

Hydrogen isotope representation type

setHydrogenize(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set hydrogenize parameter

setHyperfine(boolean) - Method in class chemaxon.calculations.ConformerPlugin

Sets the hyperfine option for calculation.

setIconPath(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the icon path

setIconPath(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the path of icon associated to the action

setId(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the id of the action

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

setId(String) - Method in class chemaxon.struc.Sgroup

setID(String) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Sets the identifier string of the standardizer action

setID(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the id of the standardizer class

setID(String) - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor

Sets the id of the checker class

setIDBackgroundRGBA(int, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets the background color's RGBA value in a record.

setIdentifier(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the checker identifier

setIdentifier(String) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the fixer identifier

setIdentity() - Method in class chemaxon.struc.Transform3D

Makes identity transformation.

setIDForegroundRGBA(int, int) - Method in class chemaxon.marvin.common.MDocStorage

Sets the foreground color's RGBA value in a record.

setIgnoreAxialStereo(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets ignoring axial stereo information during serching.

setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.standardizer.Standardizer

Sets whether the configuration errors should be ignored by the standardization process.

setIgnoreConfigurationErrors(boolean) - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

setIgnoreConfigurationErrors(boolean) - Method in interface chemaxon.structurechecker.CheckerRunner

Sets whether configuration errors should be ignored on execution.

setIgnoreCumuleneOrRingCisTransStereo(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets ignoring cumulene cis-trans stereo information during serching.

setIgnoreDoubleBondStereo(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets ignoring double bond stereo information during serching.

setIgnoreError(boolean) - Method in class chemaxon.formats.converter.MolConverter

Sets the 'ignoreError' option.

setIgnoreReactionDefinedStandardizer(boolean) - Method in class chemaxon.reaction.Reactor

Sets to ignore the standardization defined in the STANDARDIZATION RDF/MRV tag of the reaction molecule.

setIgnoreRotatableBonds(boolean) - Method in class chemaxon.descriptors.PFParameters

setIgnoreRules(int) - Method in class chemaxon.reaction.Reactor

Ignore reaction rules: 0: apply both rules (default) Reactor.IGNORE_REACTIVITY: ignore reactivity (and exclude) rule Reactor.IGNORE_SELECTIVITY: ignore selectivity rule Reactor.IGNORE_TOLERANCE: ignore selectivity tolerance Reactor.IGNORE_REACTIVITY | Reactor.IGNORE_SELECTIVITY: ignore both rules Reactor.IGNORE_REACTIVITY | Reactor.IGNORE_TOLERANCE: ignore reactivity rule and selectivity tolerance

setIgnoreSynAntiStereo(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets ignoring syn-anti stereo information during serching.

setIgnoreTetrahedralStereo(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets ignoring tetrahedral stereo information during serching.

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

setImplicitH(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the display method of implicit hydrogens.

setImplicitH(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the display method of implicit hydrogens.

setImplicitHcount(int) - Method in class chemaxon.struc.MolAtom

Sets the number of implicit hydrogens.

setImplicitHMatching(int) - Method in class chemaxon.search.api.options.SearchOptions

Set option for matching implicit and explicit hydrogens.

setImplicitHydrogenCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects implicit hydrogen count atom query properties or not.

setImplicitHydrogenMode(boolean) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets implicit hydrogen mode.

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

Sets the tasks with the provided ID inactive.

setIndexOfOriginalLigand(int) - Method in class chemaxon.calculations.CalculatorPlugin.HydrogenData

setInitialTemperature(double) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the initial temperature.

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

Sets the input file format.

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

Sets the input file format.

setInputFormat(String) - Method in class chemaxon.struc.RgMolecule

Sets the input file format.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.AlignmentPlugin

setInputMolecule(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.ChargePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.ChemicalNamePlugin

setInputMolecule(Molecule) - Method in class chemaxon.calculations.ConformerPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.GeometryPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.HBDAPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.HLBPlugin

setInputMolecule(Molecule) - Method in class chemaxon.calculations.HuckelAnalysisPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.IonChargePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.LogDPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.LogPPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.MSAPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.PkaPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.PolarizabilityPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.RefractivityPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.ResonancePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set input molecule to process

setInputMolecule(Molecule) - Method in class chemaxon.calculations.TautomerPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.calculations.TPSAPlugin

Sets the input molecule.

setIntegrator(String) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the integrator used for calculations.

setIntensity(int, double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the intensity of the ith NMR line.

setInvisibleSets(long) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the visibility of the specified atom sets.

setIonicStrength(double) - Method in class chemaxon.calculations.PkaPlugin

Sets the ionic strength (default : 0.05).

setIsotopeMatching(int) - Method in class chemaxon.search.api.options.SearchOptions

Set the isotope matching mode.

setIsotopic(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing isotopic H

setIsValenceCheckNeeded(boolean) - Method in class chemaxon.struc.MolAtom

Sets the boolean value if MolAtom.isValenceCheckNeeded.

setJar(String) - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Sets the path of the jar containing the standardizer class

setJar(String) - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor

Sets the path of the jar containing the checker class

setKeepCounts(boolean) - Method in class chemaxon.descriptors.ECFPParameters

Sets the counts (multiplicity) parameter.

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets if result molecule keeps explicit hydrogens or not

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets if result molecule keeps explicit hydrogens or not

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.calculations.PkaPlugin

Sets if result molecule keeps explicit hydrogens or not

setKeepExplicitHydrogens(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets if any explicit hydrogen

setKeepHydrogens(Properties) - Method in class chemaxon.calculations.CalculatorPlugin

setKeepMapping(boolean) - Method in class chemaxon.reaction.mapper.AutoMapper.Options

Default value true

setKeepMapping(boolean) - Method in class chemaxon.reaction.mapper.AutoMapper

setKeepMapping(boolean) - Method in interface chemaxon.reaction.mapper.ReactionMapper

Sets if the initial mapping of the atoms should be kept or not.

setKeepMapping(boolean) - Method in class chemaxon.standardizer.actions.MapAction

Sets keep mapping for the underlying mapper.

setKeepMapping(boolean) - Method in class chemaxon.standardizer.actions.MapReactionAction

Sets keep mapping for the underlying mapper.

setKeepQueryOrder(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Set option for rearranging query atoms to increase search performance.

setKeepSingleAtom(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set behavior on acyclic input

setL(int, int, String) - Method in class chemaxon.marvin.common.MDocStorage

Sets a text label in a record.

setL(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets a label in a GridBagView table.

setLabelCenter(int) - Method in class chemaxon.struc.sgroup.SgroupAtom

Sets the index of the character in the label the bonds should point to.

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

Defines properties for cells containing label components.

setLastLine() - Method in class chemaxon.formats.Recognizer

Sets last line flag.

setLastSketchFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings

setLastViewFrameSize(Dimension) - Method in class chemaxon.marvin.common.UserSettings

setLeftMargin(double) - Method in class chemaxon.struc.PageSettings

setLeftName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom

Set the string that will be shown at the left side of the molecule.

setLegendImages(Molecule[]) - Method in class chemaxon.calculations.gui.MChart

setLegendLabels(String[]) - Method in class chemaxon.calculations.gui.MChart

setLegendTexts(String[]) - Method in class chemaxon.calculations.gui.MChart

setLength(int) - Method in class chemaxon.descriptors.CDParameters

setLength(int) - Method in class chemaxon.descriptors.CFParameters

setLength(int) - Method in class chemaxon.descriptors.ECFPParameters

setLength(int) - Method in class chemaxon.descriptors.MDParameters

Sets the length (number of cells) of the descriptor.

setLength(int) - Method in class chemaxon.descriptors.RFParameters

Sets the length (number of bits) of the reaction fingerprint.

setLength(int) - Method in class chemaxon.descriptors.SDParameters

setLfin(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set handling option for multi fragment (disconnected) inputs

setLfout(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set handling option for multi fragment (disconnected) results.

setLicenseEnvironment(String) - Method in class chemaxon.alignment.AlignmentBase

setLicenseEnvironment(String) - Method in class chemaxon.alignment.AlignRigidEasy

setLicenseEnvironment(String) - Method in class chemaxon.alignment.AtropIsomerDetector

setLicenseEnvironment(String) - Method in class chemaxon.alignment.PairwiseAlignment

setLicenseEnvironment(String) - Method in interface chemaxon.alignment.PairwiseComparison

setLicenseEnvironment(String) - Method in class chemaxon.alignment.PairwiseSimilarity3D

setLicenseEnvironment(String) - Method in class chemaxon.calculations.api.ProgressableCalculator

setLicenseEnvironment(String) - Method in class chemaxon.calculations.CalculatorPlugin

Sets license environment to be stored.

setLicenseEnvironment(String) - Method in class chemaxon.calculations.GeometryPlugin

setLicenseEnvironment(String) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

setLicenseEnvironment(String) - Method in class chemaxon.calculations.stereo.StereoisomerEnumeration

setLicenseEnvironment(String) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

setLicenseEnvironment(String) - Method in class chemaxon.checkers.AbstractStructureChecker

setLicenseEnvironment(String) - Method in class chemaxon.chemterms.ChemTermsEvaluator

For internal usage only.

setLicenseEnvironment(String) - Method in class chemaxon.core.calculations.Ring

This method is for internal use only.

setLicenseEnvironment(String) - Method in class chemaxon.core.calculations.TopologyAnalyzer

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

Sets the license environment.

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

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.ECFPGenerator

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.descriptors.pharmacophore.PMapper

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

Sets the license environment.

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

setLicenseEnvironment(String) - Method in interface chemaxon.license.api.Licensable

Sets the current license environment identifier.

setLicenseEnvironment(String) - Method in class chemaxon.reaction.Reactor

For internal use only.

setLicenseEnvironment(String) - Method in class chemaxon.search.hitdisplay.HitDisplayTool

setLicenseEnvironment(String) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the license environment.

setLicenseEnvironment(String) - Method in class chemaxon.search.MolSearch

setLicenseEnvironment(String) - Method in class chemaxon.search.RgroupDecomposition

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.AbstractStandardizerAction

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

setLicenseEnvironment(String) - Method in class chemaxon.standardizer.Standardizer

Sets the license environment.

setLicenseEnvironment(String) - Method in interface chemaxon.standardizer.StandardizerAction

Sets the license environment of the action

setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the bond's ligand error visibility

setLigandErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide ligand errors

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

Sets the order of a specified ligand.

setLigandOrderVisibility(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the ligand order visibility.

setLineColor(Color) - Method in class chemaxon.struc.MObject

Sets the color of the object.

setLineNumberInFile(int) - Method in exception class chemaxon.formats.MolFormatException

Sets the line number relative to the first line of the file.

setLineNumberInRecord(int) - Method in exception class chemaxon.formats.MolFormatException

Sets the line number relative to the first line of the record.

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

Sets link node outer atoms to default values, if they are not set yet.

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

Sets link node outer atoms to default values if they are not set yet; making sure that the resulting link node configuration is valid.

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

Sets one of the link node's outer neighbor atoms.

setList(int[]) - Method in class chemaxon.struc.MolAtom

Sets the list elements.

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

Sets the list elements.

setListener(DocumentAnnotator.Listener) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder

setListeners(MDocStorage.Listener[]) - Method in class chemaxon.marvin.common.MDocStorage

setListFont(Font) - Method in class chemaxon.marvin.common.TableOptions

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

Sets the load/save filechooser working directory selection method names, based on the preferences dialog.

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

Sets the filechooser's default working directory, if the filechooser working directory selection method is saveCustomLocation.

setLocalAromaticChecking(boolean) - Method in class chemaxon.struc.ValenceCheckOptions.Builder

Sets local aromatic checking option.

setLocalMenuName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the local menu name of the concerning checker

setLocalParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

In case of 2D molecule change the bonds flag (UP/DOWN), in case of 0D molecule set the atom flags to achieve the specified parity array.

setLocalParity(int[], int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

Set the given local parity for the given atomic indexes.

setLocation(Point3D) - Method in class chemaxon.struc.MolAtom

Sets the coordinates.

setLocation(Point3D) - Method in class chemaxon.struc.MoleculeGraph

Set the origin of the molecule.

setLocation(Point3D) - Method in class chemaxon.struc.RgMolecule

Set the origin of the molecule.

setLocation(Point3D) - Method in class chemaxon.struc.RxnMolecule

Set the origin of the molecule.

setLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Sets the atom coordinates.

setLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Sets the atom coordinates.

setLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MMidPoint

Sets the location

setLocation(Point3D, Transform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint

Sets the coordinates.

setLocation(Point3D, Transform3D) - Method in class chemaxon.struc.MPoint

Sets the point's location.

setLogger(CalculatorLogger) - Method in interface chemaxon.calculations.api.CalculatorBuilder

Sets the logger object to be used.

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

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

setLogLevel(CalculatorLogger.Level) - Method in class chemaxon.calculations.api.CalculatorLogger

setLogLevel(String) - Method in class chemaxon.calculations.api.CalculatorLogger

setlogPMethod(LogPMethod) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setLogPMethod(LogPMethod) instead. This method will be removed in a future version.

setlogPMethod(LogPMethod) - Method in class chemaxon.calculations.LogPPlugin

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

Use LogPPlugin.setLogPMethod(LogPMethod) instead. This method will be removed in a future version.

setLogPMethod(LogPMethod) - Method in class chemaxon.calculations.LogDPlugin

Sets the logP calculation method.

setLogPMethod(LogPMethod) - Method in class chemaxon.calculations.LogPPlugin

Sets the logP calculation method.

setLogPTraining(InputStream) - Method in class chemaxon.calculations.LogDPlugin

Sets the user defined logP training from a stream of parameters.

setLogPTrainingId(String) - Method in class chemaxon.calculations.LogDPlugin

Sets the user defined logP training.

setLonely(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing lonely H

setLonePairAsLine(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility of Lone Pairs

setLonePairAutoCalc(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets the state of the automatic lone pair calculation.

setLonePairsAsLines(boolean) - Method in class chemaxon.struc.graphics.MElectronContainer

setLonePairsAutoCalculated(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the state of the automatic calculation of lone pairs.

setLonePairsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides (implicit) lone pairs.

setLonePairsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility state of lone pairs.

setLowestEnergyConformerCalculation(boolean) - Method in class chemaxon.calculations.ConformerPlugin

Switchs the lowest energy conformer calculation on/off.

setM(int, Molecule...) - Method in class chemaxon.marvin.beans.MViewPane

Sets the nth animation or structure.

setMainMoleculeGraph(MoleculeGraph) - Method in class chemaxon.struc.MDocument

Sets the main molecule graph.

setMapped(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing mapped H

setMappingStyle(ReactionMapper.MappingStyle) - Method in class chemaxon.reaction.mapper.AutoMapper.Options

Default value ReactionMapper.MappingStyle.COMPLETE

setMappingStyle(ReactionMapper.MappingStyle) - Method in class chemaxon.reaction.mapper.AutoMapper

Sets the mapping style

setMappingStyle(ReactionMapper.MappingStyle) - Method in interface chemaxon.reaction.mapper.ReactionMapper

Sets the mapping style.

setMappingStyle(ReactionMapper.MappingStyle) - Method in class chemaxon.standardizer.actions.MapAction

Sets Mapping Style for the underlying mapper.

setMappingStyle(ReactionMapper.MappingStyle) - Method in class chemaxon.standardizer.actions.MapReactionAction

Sets Mapping Style for the underlying mapper.

setMarginInPt(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the Margin of the painted molecule.

setMarginSize(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the documents margin size.

setMarginSize(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the documents margin size.

setMarkBonds(boolean) - Method in class chemaxon.reaction.mapper.AutoMapper.Options

Default value false

setMarkBonds(boolean) - Method in class chemaxon.reaction.mapper.AutoMapper

setMarkBonds(boolean) - Method in interface chemaxon.reaction.mapper.ReactionMapper

Sets if the changing bonds should be marked or not.

setMarkBonds(boolean) - Method in class chemaxon.standardizer.actions.MapAction

Sets mark bonds for the underlying mapper.

setMarkBonds(boolean) - Method in class chemaxon.standardizer.actions.MapReactionAction

Sets mark bonds for the underlying mapper.

setMarkushAromHandling(MarkushAromaticityHandlingOption) - Method in class chemaxon.search.api.options.SearchOptions

Set handling of Markush aromatization information (ambiguous aromatic rings) during Markush search

setMarkushDisplayMode(int) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the Markush display mode.

setMarkushEnabled(boolean) - Method in class chemaxon.search.api.options.MolSearchOptions

Sets whether targets containing Markush features should be treated as Markush libraries

setMassno(int) - Method in class chemaxon.struc.MolAtom

Sets the mass number.

setMaxCols(int) - Method in class chemaxon.marvin.common.TableOptions

Set maximum value of columns in the table

setMaximum(int) - Method in interface chemaxon.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setMaximum(int) - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

Gets the maximum value.

setMaximumTautomerizationPathLength(int) - Method in class chemaxon.calculations.TautomerPlugin

Sets the maximum allowed length of the tautomerization path in chemical bonds.

setMaxIons(int) - Method in class chemaxon.calculations.PkaPlugin

In case of PkaPlugin.MODEL_SMALL model, it sets the maximum number of ionizable atoms to be considered and uses simple calculation method to compute pKa values.

setMaxNumberOfConformers(int) - Method in class chemaxon.calculations.ConformerPlugin

Sets the maximum number of conformers to be calculated.

setMaxNumberOfProductSets(int) - Method in class chemaxon.reaction.Reactor

Sets the maximum number of products sets to be returned for one reactant set.

setMaxRepetitions(int) - Method in class chemaxon.struc.MolAtom

Sets the maximum number of repetitions for a link atom.

setMaxRows(int) - Method in class chemaxon.marvin.common.TableOptions

Set maximum value of rows in the table

setMaxSize(int) - Method in class chemaxon.marvin.common.TableOptions

Set the maximum number of molecules displayed in the table.

setMaxStereoisomerCount(int) - Method in class chemaxon.calculations.stereo.StereoisomerSettings

Sets the maxinum number of stereoisomers to be generated.

setMaxStructureCount(int) - Method in class chemaxon.calculations.ResonancePlugin

Sets the maximum number of structures to be generated.

setMaxStructureCount(int) - Method in class chemaxon.calculations.TautomerPlugin

Sets the maximum number of structures to be generated.

setMaxStructureCount(long) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets the maximum number of structures to be generated.

setMaxThreadCount(int) - Method in class chemaxon.reaction.mapper.AutoMapper.Options

Default value Integer.MAX_VALUE
The number of threads used for mapping will be the minimum of maxThreadCount and the number of available processors.

setMeasure(RemoveFragmentAction.Measurement) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

Sets the measurement of the action

setMElectrons(MElectron[]) - Method in class chemaxon.struc.graphics.MElectronContainer

setMenuItem(JMenuItem, int) - Method in class chemaxon.marvin.common.MAction

For internal use only.

setMergedst(double) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the merge distance.

setMessage(String) - Method in interface chemaxon.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setMetalAtoms(List<MolAtom>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult

This method sets the metalAtoms property

setMetalconnected(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing metal connected H

setMethod(RemoveFragmentAction.Method) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

Sets the method of the action

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

setMethodName(String) - Method in class chemaxon.calculations.services.ServiceDescriptor

Sets the method name to call

setMethylsRotatable(boolean) - Method in class chemaxon.alignment.AtropIsomerDetector

This is a speedup heuristics.

setMicropKaCalc(boolean) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setMicroPkaCalc(boolean) instead. This method will be removed in a future version.

setMicroPkaCalc(boolean) - Method in class chemaxon.calculations.PkaPlugin

Sets micro pKa calculation.

setMinDistTryCount(int) - Method in class chemaxon.alignment.MinMaxDistance

setMinimum(int) - Method in interface chemaxon.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setMinimumHeight(double) - Method in class chemaxon.struc.graphics.MTextBox

Sets the minimum height of the text..

setMinimumHeightSet(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Turns on/off minimum height calculation.

setMinRepetitions(int) - Method in class chemaxon.struc.MolAtom

Sets the minimum number of repetitions for a link node.

setMixSgroupMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Set options for mixed S-group matching.

setMMFF94(boolean) - Method in class chemaxon.calculations.ConformerPlugin

Sets the forcefield to MMFF94.

setMMFF94Optimization(boolean) - Method in class chemaxon.calculations.GeometryPlugin

Sets MMFF94 optimization.

setMode(AlignmentAccuracyMode) - Method in class chemaxon.alignment.Alignment

setMode(AlignmentAccuracyMode) - Method in class chemaxon.alignment.PairwiseAlignment

setModel(int) - Method in class chemaxon.calculations.PkaPlugin

Sets the calculation model.

setModified(boolean) - Method in class chemaxon.standardizer.Changes

Sets whether any modifications were applied on the molecule.

setMol(Molecule) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the current molecule and calculate its bounds.

setMol(Molecule) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the molecule.

setMol(File, String) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the molecule.

setMol(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the current molecule and calculate its bounds.

setMol(String) - Method in class chemaxon.marvin.beans.MSketchPane

Starts loading a molecule into the sketcher.

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

Starts loading a molecule into the sketcher.

setMolbg(Color) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the molecule background color.

setMolCenter(int, String, Point3D) - Method in class chemaxon.marvin.common.MDocStorage

Sets a molecule center.

setMolconvert(File) - Method in class chemaxon.naming.document.DocumentAnnotator

setMolecule(int, Molecule) - Method in class chemaxon.standardizer.actions.CreateGroupAction

Sets the molecule of the group at the provided index

setMolecule(int, Molecule) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction

Sets the molecule of the solvent at the provided index

setMolecule(int, Molecule) - Method in class chemaxon.standardizer.actions.StripSaltsAction

Sets the molecule of the salt at the provided index

setMolecule(Molecule) - Method in class chemaxon.alignment.MinMaxDistance

setMolecule(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the input molecule after standardization.

setMolecule(Molecule) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult

setMolecule(Molecule) - Method in interface chemaxon.checkers.result.StructureCheckerResult

This method sets the molecule

setMolecule(Molecule) - Method in class chemaxon.chemterms.MolContext

Sets the input molecule.

setMolecule(Molecule) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable

Sets the Molecule which will be represented by the MTransferable.

setMolecule(Molecule) - Method in interface chemaxon.marvin.datatransfer.MTransferable

Sets the Molecule which will be represented by the transferable.

setMolecule(Molecule) - Method in class chemaxon.structurechecker.AdvancedCheckerRunner

setMolecule(Molecule) - Method in class chemaxon.structurechecker.BasicCheckerRunner

Deprecated.

setMolecule(Molecule) - Method in interface chemaxon.structurechecker.CheckerRunner

Sets the molecule to be checked by the checkers

setMolecule(MoleculeGraph) - Method in class chemaxon.core.calculations.ElementalAnalyzer

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph) - Method in class chemaxon.core.calculations.Ring

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph) - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph, int) - Method in class chemaxon.core.calculations.Ring

Specifies a molecule to calculate with.

setMolecule(MoleculeGraph, int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Specifies a molecule to calculate with.

setMolecule(Molecule, boolean) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the input molecule after an optional standardization.

setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the input molecule after an optional standardization and/or modification.

setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.calculations.ChargePlugin

setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.calculations.CalculatorPlugin

setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

setMolecule(Molecule, boolean, boolean, boolean) - Method in class chemaxon.calculations.TautomerPlugin

setMolecule(String) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Specifies a molecule to calculate with.

setMolecule(String) - Method in class chemaxon.core.calculations.ElementalAnalyzer

Specifies a molecule to calculate with.

setMoleculeAndMarkushTarget(Molecule, Molecule) - Method in class chemaxon.search.hitdisplay.HitDisplayTool

Sets the target structure.

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

Sets the preferred size of the cells containing molecules.

setMoleculeIterator(MoleculeIterator) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the molecule iterator.

setMoleculeMovie(MMoleculeMovie) - Method in class chemaxon.struc.MDocument

Sets the molecule movie.

setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.alignment.Alignment

setMolecules(AlignmentMolecule, AlignmentMolecule) - Method in class chemaxon.alignment.AlignOnPairedAtoms

setMolecules(Molecule, Molecule) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the two molecular structures to be matched.

setMoleculeToAlign(Molecule, boolean) - Method in class chemaxon.alignment.AlignOnPairedAtoms

Sets the molecule to align to the reference.

setMolID(int) - Method in class chemaxon.alignment.AlignmentMolecule

setMolIndex(int) - Method in exception class chemaxon.formats.MolExportException

Sets the molecule index.

setMolNameFontSize(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the molecule name font size.

setMolNameShown(boolean) - Method in class chemaxon.marvin.common.TableOptions

Sets visibility of molecule names.

setMolPainter(int, String, MolPainter) - Method in class chemaxon.marvin.common.MDocStorage

Sets a molecule painter.

setMolTemplate(Molecule) - Method in class chemaxon.marvin.beans.MolPrinter

setMonitor(StructureCheckerMonitor) - Method in class chemaxon.structurechecker.AdvancedCheckerRunner

Sets the monitor.

setMonomerTransform(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.

setMoreErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the more error message of the concerning checker

setMPLabelsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility state of M/P labels.

setMPVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the M/P display option.

setMPVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

setMsCalc(boolean) - Method in class chemaxon.calculations.HBDAPlugin

Sets microspecies calculation.

setMsCalc(boolean) - Method in class chemaxon.calculations.PkaPlugin

Sets calculation of microspecies distributions.

setMultiplets(NMRMultiplet[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets NMRMultiplet array of the spectrum.

setMultiplier(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the multiplier.

setNaKIonConcentration(double) - Method in class chemaxon.calculations.LogDPlugin

Sets the Na+, K+ concentration (default: 0.1).

setNaKIonConcentration(double) - Method in class chemaxon.calculations.LogPPlugin

Sets the Na+, K+ concentration (default: 0.1).

setName(String) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the name of the NMR spectrum

setName(String) - Method in class chemaxon.calculations.PkaTrainingResult

Sets the name

setName(String) - Method in class chemaxon.calculations.services.ServiceArgument

Sets the name of the argument

setName(String) - Method in class chemaxon.calculations.services.ServiceDescriptor

Sets the name of the service

setName(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the checker name

setName(String) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the fixer name

setName(String) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the name of the action

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

Sets the molecule name/title.

setName(String) - Method in class chemaxon.struc.RgMolecule

Sets the name of the root molecule.

setNameAndMnemonic(String) - Method in class chemaxon.marvin.common.MAction

Sets the label and the mnemonic character.

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

setNavmode(String) - Method in class chemaxon.marvin.beans.MViewPane

Sets the mouse drag action.

setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.alignment.AlignmentBase

setNodeType(AlignmentProperties.NodeType) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

setNoErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the no error message of the concerning checker

setNonHitColor(Color) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the color to be used when coloring the part of the target which is not matching to the query.

setNonHitColor3D(Color) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the color to be used when coloring the part of the 3D target which is not matching to the query.

setNonQueryImplicitHcount(int) - Method in class chemaxon.struc.MolAtom

Sets the number of non-query implicit hydrogens attached.

setNormalized(boolean) - Method in class chemaxon.descriptors.MDParameters

Toggles the normalized flag of the current parametrized metric.

setNormalTautomerGenerationMode(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Generates only normal tautomers.

setNotSpec(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.alignment.NodeColor

Sets the behavior for cases where the color of a node is not specified.

setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

setNucleus(NMRSpectrum.Nucleus) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Sets the NMR active nucleus.

setNumberOfAtomsAcceptToRotate(int) - Method in class chemaxon.alignment.AtropIsomerDetector

If only a given number of atoms (or less) can be found at one of the side of the dihedral skip this.

setNumberOfNMRActiveNuclei(int) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets number of the NMR active nuclei.

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

Sets an object

setObject(MObject, int) - Method in class chemaxon.struc.MSelectionDocument

Sets an object

setObject(String, Object) - Method in class chemaxon.struc.MPropertyContainer

Sets a property object.

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

Sets the object that contains the selection.

setOccupied(int) - Method in class chemaxon.struc.graphics.MElectronContainer

setOccupied(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer

setOeqcheck(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set oeqcheck parameter

SetOfSmallestRingsOption - Enum Class in chemaxon.search.api.options

Option type describing the supported smallest set of rings used for property calculations.

setOKActionListener(ActionListener) - Method in class chemaxon.calculations.gui.PluginFactory

Sets the "OK" button pressed action listener.

setOneErrorMessage(String) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the one error message of the concerning checker

setOneLetterName(String) - Method in class chemaxon.struc.sgroup.AminoAcidSgroup

Sets the one letter name of the amino acid.

setOnlyExpanded(boolean) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

setOptimization(int) - Method in class chemaxon.calculations.ConformerPlugin

Sets the optimization criteria for the calculation.

setOptimization(int) - Method in class chemaxon.calculations.GeometryPlugin

Sets the optimization criteria for lowest energy conformer calculation.

setOptimizeProjection(boolean) - Method in class chemaxon.calculations.GeometryPlugin

setOption(String, String) - Method in class chemaxon.search.api.options.SearchOptions

Sets search options.

setOptions(DocumentAnnotatorOptions) - Method in class chemaxon.naming.document.DocumentAnnotator

Sets the options used for document annotation.

setOptions(HitDisplayOptions, String) - Static method in class chemaxon.search.hitdisplay.HitDisplayOptions

Parses the option list given while updating a HitDisplayOptions object.

setOptions(String) - Method in class chemaxon.formats.MolImportModule

Sets the import options.

setOptions(String) - Method in class chemaxon.search.api.options.SearchOptions

Sets search options.

setOrder(int) - Method in class chemaxon.struc.graphics.MAssigner

Sets the order of an assigner.

setOrderSensitiveSearch(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Specifies whether the same set of target atoms found in a different order should be considered as a different hit.

setOrientationType(AlignmentProperties.OrientationType) - Method in class chemaxon.alignment.Alignment

setOriginal(Molecule) - Method in class chemaxon.standardizer.actions.GroupDefinition

Sets the original molecule of the group.

setOriginalIds(int[]) - Method in class chemaxon.search.RgroupDecompositionResults

setOrigTargetMayBeMarkush(boolean) - Method in class chemaxon.search.MolSearch

Only for internal use!

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

Sets the output file.

setOutput(OutputStream, String) - Method in class chemaxon.formats.converter.MolConverter.Builder

Sets the output stream.

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

Sets the output file.

setOutputFlags(int) - Method in class chemaxon.formats.converter.MolConverter.Builder

Sets output flags.

setOutputIn3d(boolean) - Method in class chemaxon.calculations.stereo.StereoisomerSettings

3D structures are generated (invalid 3D structure are filtered)

setOutputParameters(Object[]) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Prepares the output based on the result type string.

setOutputPrecision(int) - Method in class chemaxon.descriptors.MDParameters

Specifies the output precision for floating point values.

setOutputReactionMappingStyle(int) - Method in class chemaxon.reaction.Reactor

Sets the output reaction's mapping style.

setOutputStream(OutputStream) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Sets the output stream.

setPageFormat(PageFormat, String) - Method in class chemaxon.marvin.common.UserSettings

setPageSettings(PageSettings) - Method in class chemaxon.struc.MDocument

Sets the page settings of multipage molecular document.

setParameter(String, String) - Method in class chemaxon.descriptors.DescriptorGenerator

Sets a parameter of the current descriptor configuration.

setParameters() - Method in class chemaxon.search.MolSearch

setParameters() - Method in class chemaxon.search.RgroupDecomposition

setParameters(CDParameters) - Method in class chemaxon.descriptors.CustomDescriptor

Sets parameters, allocates internal storage if needed and clears the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.BCUT

Sets the parameters of an already created BCUT object.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ChemicalFingerprint

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ECFP

Sets the parameters of an already created ECFP object.

setParameters(MDParameters) - Method in class chemaxon.descriptors.MolecularDescriptor

Sets the parameters for an already created MolecularDescriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.PharmacophoreFingerprint

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ReactionFingerprint

Sets parameters, allocates internal storage if needed and cleans the descriptor.

setParameters(MDParameters) - Method in class chemaxon.descriptors.ScalarDescriptor

Sets parameters, allocates internal storage if needed and cleans the descriptor.

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

Sets parameters from an XML file representation overwriting all previous settings with the new ones.

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

Sets parameters from an XML file representation overwriting all previous settings with the new ones.

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

Sets the parameters of an already created BCUT object.

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

Sets the parameters of an already created ChemicalFingerprint object.

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

Sets the parameters of an already created CustomDescriptor object.

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

Sets the parameters of an already created ECFP object.

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

Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.

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

Sets the parameters for an already created MolecularDescriptor.

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

Sets parameters from an XML string representation overwriting all previous parameters settings with the new ones.

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

Sets the parameters of an already created PharmacophoreFingerprint object.

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

Sets the parameters of an already created ReactionFingerprint object.

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

Sets the parameters of an already created ScalarDescriptor object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.HAcc

Sets the parameters of an already created HAcc object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.HDon

Sets the parameters of an already created HDon object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.Heavy

Sets the parameters of an already created HeavyAtomCount object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.LogD

Sets the parameters of an already created LogD object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.LogP

Sets the parameters of an already created LogP object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.Mass

Sets the parameters of an already created Mass object.

setParameters(String) - Method in class chemaxon.descriptors.scalars.TPSA

Sets the parameters of an already created TPSA object.

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

Sets the parameters of an already created ShapeDescriptor object.

setParameters(Properties) - Method in class chemaxon.calculations.AlignmentPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.CalculatorPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.ChargePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.ChemicalNamePlugin

setParameters(Properties) - Method in class chemaxon.calculations.ConformerPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.GeometryPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Sets parameters.

setParameters(Properties) - Method in class chemaxon.calculations.HBDAPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.HLBPlugin

setParameters(Properties) - Method in class chemaxon.calculations.HuckelAnalysisPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.IonChargePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.LogDPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.LogPPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.MSAPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Sets the parameter table.

setParameters(Properties) - Method in class chemaxon.calculations.PkaPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.PolarizabilityPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.RefractivityPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.ResonancePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Sets the input parameters for the plugin Accepted parameters: type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem| largestring|keep] Framework calculation type bmf: Bemis-Murcko framework bmfl: Bemis-Murcko loose framework mcs: Pairwise Maximum Common Substructure sssr: SSSR cssr: CSSR allringsystems: all fused ring systems largestringsystem: largest fused ring system largestring: largest ring keep: no framework reduction; useful for testing pre/post process keepsingleatom: [true|false] If set true then a single atom will be assigned to acyclic fragments.

setParameters(Properties) - Method in class chemaxon.calculations.TautomerPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.calculations.TPSAPlugin

Sets the input parameters for the plugin.

setParams(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the parameter string.

setParent(Component) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the parent component.

setParentComponent(Component) - Method in class chemaxon.calculations.gui.PluginFactory

Sets the parent component - this is used to set options panes positions.

setParentMolecule(Molecule) - Method in class chemaxon.struc.Sgroup

Sets the parent molecule.

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

Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.

setParity(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph

Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.

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

Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity.

setPath(String) - Method in class chemaxon.standardizer.configuration.StandardizerActionStringReader

setPath(String) - Method in interface chemaxon.standardizer.configuration.StandardizerConfigurationReader

Sets the base path of the configuration.

setPath(String) - Method in class chemaxon.standardizer.configuration.StandardizerConfigurationXmlReader

setPatternMolecule(Molecule) - Method in class chemaxon.alignment.MolAligner

Sets pattern molecule and calculates its dimension

setPeakDomainMax(double[]) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the array of peak upper ends.

setPeakDomainMax(int, double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the upper end of the ith peak.

setPeakDomainMin(double[]) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the array of peak lower ends.

setPeakDomainMin(int, double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the lower end of the ith peak.

setPeptideDisplay(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the Peptide display settings.

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

Sets the peptide displaying tpye.

setpH(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

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

Use IsoelectricPointPlugin.setPh(double) instead. This method will be removed in a future version.

setpH(double) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setPh(double) instead. This method will be removed in a future version.

setpH(double) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

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

Use MajorMicrospeciesAccessorPlugin.setPh(double) instead. This method will be removed in a future version.

setpH(double) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

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

Use MajorMicrospeciesPlugin.setPh(double) instead. This method will be removed in a future version.

setpH(double) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setPh(double) instead. This method will be removed in a future version.

setpH(double) - Method in class chemaxon.calculations.TautomerPlugin

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

Use TautomerPlugin.setPh(double) instead. This method will be removed in a future version.

setPh(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets a single pH value for the calculation of charge distribution.

setPh(double) - Method in class chemaxon.calculations.LogDPlugin

Sets a single pH value for the logD calculation.

setPh(double) - Method in class chemaxon.calculations.LogPPlugin

Sets the pH for logP calculation

setPh(double) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.

setPh(double) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.

setPh(double) - Method in class chemaxon.calculations.PkaPlugin

Sets the pH value for the calculation of microspecies distributions.

setPh(double) - Method in class chemaxon.calculations.TautomerPlugin

Sets the pH to be considered in dominant tautomer generation.

setPhaseShiftedMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Adjusts if the phase shifted polymer should match on the original.

setpHLower(double) - Method in class chemaxon.calculations.HBDAPlugin

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

Use HBDAPlugin.setPhLower(double) instead. This method will be removed in a future version.

setpHLower(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

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

Use IsoelectricPointPlugin.setPhLower(double) instead. This method will be removed in a future version.

setpHLower(double) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setPhLower(double) instead. This method will be removed in a future version.

setpHLower(double) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setPhLower(double) instead. This method will be removed in a future version.

setPhLower(double) - Method in class chemaxon.calculations.HBDAPlugin

Sets pH lower limit for the calculation of microspecies distributions.

setPhLower(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets pH lower limit for the calculation of charge distribution (default: 0.0).

setPhLower(double) - Method in class chemaxon.calculations.LogDPlugin

Sets pH lower limit (default: 0.0).

setPhLower(double) - Method in class chemaxon.calculations.PkaPlugin

Sets pH lower limit for the calculation of microspecies distributions.

setpHStep(double) - Method in class chemaxon.calculations.HBDAPlugin

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

Use HBDAPlugin.setPhStep(double) instead. This method will be removed in a future version.

setpHStep(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

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

Use IsoelectricPointPlugin.setPhStep(double) instead. This method will be removed in a future version.

setpHStep(double) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setPhStep(double) instead. This method will be removed in a future version.

setpHStep(double) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setPhStep(double) instead. This method will be removed in a future version.

setPhStep(double) - Method in class chemaxon.calculations.HBDAPlugin

Sets pH step for the calculation of microspecies distributions.

setPhStep(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets pH step for the calculation of charge distribution.

setPhStep(double) - Method in class chemaxon.calculations.LogDPlugin

Sets pH step to be taken between the pH lower and upper limits (default: 1.0).

setPhStep(double) - Method in class chemaxon.calculations.PkaPlugin

Sets pH step for the calculation of microspecies distributions.

setpHUpper(double) - Method in class chemaxon.calculations.HBDAPlugin

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

Use HBDAPlugin.setPhUpper(double) instead. This method will be removed in a future version.

setpHUpper(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

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

Use IsoelectricPointPlugin.setPhUpper(double) instead. This method will be removed in a future version.

setpHUpper(double) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setPhUpper(double) instead. This method will be removed in a future version.

setpHUpper(double) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setPhUpper(double) instead. This method will be removed in a future version.

setPhUpper(double) - Method in class chemaxon.calculations.HBDAPlugin

Sets pH upper limit for the calculation of microspecies distributions.

setPhUpper(double) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets pH upper limit for the calculation of charge distribution (default: 14.0).

setPhUpper(double) - Method in class chemaxon.calculations.LogDPlugin

Sets pH upper limit (default: 14.0).

setPhUpper(double) - Method in class chemaxon.calculations.PkaPlugin

Sets pH upper limit for the calculation of microspecies distributions.

setPiece(String) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the molecule piece.

setpKaCorrectionLibrary(InputStream) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setPkaCorrectionLibrary(InputStream) instead. This method will be removed in a future version.

setpKaCorrectionLibrary(String) - Method in class chemaxon.calculations.LogDPlugin

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

Use LogDPlugin.setPkaCorrectionLibrary(String) instead. This method will be removed in a future version.

setPkaCorrectionLibrary(InputStream) - Method in class chemaxon.calculations.LogDPlugin

Sets the pKa correction library from a stream.

setPkaCorrectionLibrary(String) - Method in class chemaxon.calculations.LogDPlugin

Sets the pKa correction library.

setpKaPrefixType(int) - Method in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.setPkaPrefixType(int) instead. This method will be removed in a future version.

setPkaPrefixType(int) - Method in class chemaxon.calculations.PkaPlugin

Sets pKa prefix type (default: PkaPlugin.STATIC_PKA_PREFIX) STATIC pKa prefix: pKa's prefix does not depend on the submitted microstate DYNAMIC pKa prefix: pKa's prefix does depend on the submitted microstate

setPlainText(String) - Method in class chemaxon.struc.graphics.MTextDocument

Sets the document as plain text.

setPluginChecked(P) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the plugin.

setPluginChecked(P) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Sets the calculator plugin object.

setPluginUnchecked(CalculatorPlugin) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Sets the calculator plugin object without compile-time type check.

setPMAPTagName(String) - Method in class chemaxon.descriptors.PFGenerator

Sets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.

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

Sets the name of the pharmacophore map tag to be considered in the input SDfile.

setPointed(boolean) - Method in class chemaxon.struc.graphics.MElectron

setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the points.

setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MPolyline

Sets the points.

setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MTextBox

Sets the points.

setPolymerendgroup(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing polymer end group H

setPolymerMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Adjust polymer matching.

setPopupMenusEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Allows popup menus.

setPos(int) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the data display DASP position (0...9).

setPosition(int, double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the position of the ith NMR line.

setPreferredSize(Dimension) - Method in class chemaxon.marvin.beans.MViewPane

Sets the preferred size of the component.

setPreferredWidth(double) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the preferred width of the text-box.

setPrehydrogenize(boolean) - Method in class chemaxon.calculations.ConformerPlugin

Turns the prehydrogenization on/off.

setPreprocessor(ConcurrentStandardizerProcessor.MolTransformer) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the preprocessor.

setPrintEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Set the accessibility of the Print menu item in the File menu.

setPriority(int) - Method in class chemaxon.fixers.StructureFixerDescriptor

Sets the fixer priority.

setProductAtomsByMap(MolAtom[]) - Method in class chemaxon.chemterms.ReactionContext

Deprecated.

use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> product atom array.

setProductIndexes(int[]) - Method in class chemaxon.reaction.Reactor

Sets the product indexes (1-based) to be returned (default: null - all products).

setProducts(Molecule[]) - Method in class chemaxon.chemterms.ReactionContext

Deprecated.

Use ReactionContext.setReaction(RxnMolecule) instead. Sets the products.

setProgress(int) - Method in interface chemaxon.alignment.AlignmentMoleculeFactory.ProgressBarInterface

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.alignment.PairwiseAlignment

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in interface chemaxon.alignment.PairwiseComparison

setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface) - Method in class chemaxon.alignment.PairwiseSimilarity3D

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.alignment.AlignmentBase

Sets the progress monitor for the alignment.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.alignment.PairwiseAlignment

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.AlignmentPlugin

Sets a progress observer to be used in AlignmentPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.CalculatorPlugin

Sets a progress observer to be used in CalculatorPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.ConformerPlugin

Sets a progress observer to be used in ConformerPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.GeometryPlugin

Sets a progress observer to be used to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Sets a progress observer to be used in IsoelectricPointPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets a progress observer to be used in MolecularDynamicsPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.PkaPlugin

Sets a progress observer to be used in PkaPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.ResonancePlugin

Sets a progress observer to be used in ResonancePlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Sets a progress monitor to be used in StereoisomerPlugin.run() to display progress status.

setProgressMonitor(ProgressMonitor) - Method in class chemaxon.calculations.TautomerPlugin

Sets a progress observer to be used in TautomerPlugin.run() to display progress status.

setProgressValue(int) - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

Set progress.

setProperties(Properties) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable

Sets display properties of the Molecule.

setProperties(Properties) - Method in interface chemaxon.marvin.datatransfer.MTransferable

Sets display properties of the Molecule.

setProperty(AlignmentProperties) - Method in class chemaxon.alignment.Alignment

setProperty(AlignmentProperties) - Method in class chemaxon.alignment.AlignmentBase

Sets the properties for the alignment.

setProperty(String, String) - Method in class chemaxon.calculations.services.ServiceDescriptor

Sets a descriptor property

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

Sets a property for the given key with the given value.

setProperty(String, String) - Method in class chemaxon.struc.Molecule

Sets an RDfile/SDfile property.

setProperty(String, String, boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets a property for the given key with the given value.

setPropertyObject(String, Object) - Method in class chemaxon.struc.Molecule

Sets an RDfile/SDfile property object.

setProtectAllTetrahedralStereoCenters(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets the protection of all tetrahedral stereo centers: if true then all tetrahedral stereo information is preserved by the tautomer generator.

setProtectAromaticity(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets aromaticity protection: if true then aromatic bonds are not modified by the tautomer generator.

setProtectCharge(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets charge protection: if true then the charge of charged atoms are not modified by the tautomer generator.

setProtectDoubleBondStereo(boolean) - Method in class chemaxon.calculations.stereo.StereoisomerSettings

Sets double bond stereo protection.

setProtectDoubleBondStereo(boolean) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Sets double bond stereo protection: if true then the stereo configuration of double bonds with preset stereo information will not be changed.

setProtectDoubleBondStereo(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets double bond stereo protection: if true then double bonds stereo information is preserved by the tautomer generator.

setProtectEsterGroups(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets the protection of ester groups: if true then ester groups are excluded from the tautomerization.

setProtectLabeledTetrahedralStereoCenters(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets the protection of labeled tetrahedral stereo centers: if true then labeled tetrahedral stereo centers are protected by the tautomer generator.

setProtectTetrahedralStereo(boolean) - Method in class chemaxon.calculations.stereo.StereoisomerSettings

Sets the protection of tetrahedral stereo centers.

setProtectTetrahedralStereo(boolean) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Sets the protection of tetrahedral stereo centers: if true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed.

setProximity(AlignmentProperties.ProximityPotentialType) - Method in class chemaxon.alignment.AlignmentBase

Sets the proximity potential type used for the alignment.

setPruneIn(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set prunein parameter

setPruneOut(boolean) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set pruneout parameter

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

Sets a query property as an integer.

setQProp(String, Object) - Method in class chemaxon.struc.MolAtom

Sets a query property.

setQuery(AlignmentMolecule) - Method in class chemaxon.alignment.PairwiseAlignment

setQuery(AlignmentMolecule) - Method in interface chemaxon.alignment.PairwiseComparison

setQuery(AlignmentMolecule) - Method in class chemaxon.alignment.PairwiseSimilarity3D

setQuery(Molecule) - Method in class chemaxon.alignment.PairwiseAlignment

setQuery(Molecule) - Method in interface chemaxon.alignment.PairwiseComparison

setQuery(Molecule) - Method in class chemaxon.alignment.PairwiseSimilarity3D

setQuery(Molecule) - Method in class chemaxon.chemterms.SearchContext

Sets the query molecule and the map array.

setQuery(Molecule) - Method in class chemaxon.search.AbstractSearch

Specifies the query structure to search for.

setQuery(Molecule) - Method in class chemaxon.search.api.MolComparator

Loads the query molecule into this comparator.

setQuery(Molecule) - Method in class chemaxon.search.MarkushGenerator

Sets the query.

setQuery(Molecule) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the query structure.

setQuery(Molecule) - Method in class chemaxon.search.MolSearch

setQuery(Molecule) - Method in class chemaxon.search.RgroupDecomposition

Specifies the query structure to search for.

setQuery(Molecule) - Method in class chemaxon.search.RgroupDecompositionResults

setQuery(Molecule, int[]) - Method in class chemaxon.search.AbstractSearch

Specifies the query structure to search for.

setQuery(Molecule, int[]) - Method in class chemaxon.search.MolSearch

setQuery(String) - Method in class chemaxon.search.FormulaSearch

Sets the chemical formula query string used for searching

setQuery(String) - Method in class chemaxon.search.MolSearch

Specifies the query structure to search for in String format.

setQueryAbsoluteStereo(boolean) - Method in class chemaxon.search.api.options.MolSearchOptions

Sets whether the chiral flag should be ignored or not for the query molecule.

setQueryAromaticity(int) - Method in class chemaxon.struc.MolAtom

Sets the aromatic/aliphatic query property.

setQueryAtom(MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Sets the atom to be searched for by the action (the query atom)

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

Sets the program code for the query option.

setQueryDisplay(boolean) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Set query display option

setQueryFingerprint(int[]) - Method in class chemaxon.chemterms.SearchContext

Sets the fingerprint of the query molecule.

setQueryFingerprint(T) - Method in class chemaxon.descriptors.SimilarityCalculator

Sets the query fingerprint

setQueryMode(boolean) - Method in class chemaxon.formats.MolImporter

Sets query mode.

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

Sets the data query operator.

setQueryRigidForced(boolean) - Method in class chemaxon.alignment.PairwiseAlignment

setQueryRigidForced(boolean) - Method in interface chemaxon.alignment.PairwiseComparison

Set this molecule to be rigid in the input conformation even if it contains rotatable bonds

setQueryRigidForced(boolean) - Method in class chemaxon.alignment.PairwiseSimilarity3D

setQuerystr(String) - Method in class chemaxon.struc.QueryBond

Sets the query string.

setQueryString(String) - Method in class chemaxon.struc.MolAtom

Assigns the query string to this atom.

setRadical(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing radical H

setRadicalMatching(int) - Method in class chemaxon.search.api.options.SearchOptions

Set the radical matching mode.

setRadicalValue(Radical) - Method in class chemaxon.struc.MolAtom

Sets the radical value of the atom.

setRadius(double) - Method in class chemaxon.struc.graphics.MElectron

setRadius(double) - Method in class chemaxon.struc.graphics.MElectronContainer

Sets Radius for all MElectrons

setRandomEnumeration() - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets random enumeration.

setRandomSeed(long) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets the random seed to be used in case of random enumeration.

setRandomSeed(long) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the random seed value.

setRange(double, double) - Method in class chemaxon.calculations.gui.MChart

setRangeDecimalCount(int) - Method in class chemaxon.calculations.gui.MChart

setRatio(int[]) - Method in class chemaxon.reaction.Reactor

Sets the ratio of the reactants.

setReactantAtomsByMap(MolAtom[]) - Method in class chemaxon.chemterms.ReactionContext

Deprecated.

use ReactionContext.setReaction(RxnMolecule) instead. Sets the map -> reactant atom array.

setReactantIterators(MoleculeIterator[], int) - Method in class chemaxon.reaction.ConcurrentReactorProcessor

Sets the reactant iterators.

setReactants(Molecule[]) - Method in class chemaxon.chemterms.ReactionContext

Deprecated.

Use ReactionContext.setReaction(RxnMolecule) instead. Sets the reactants.

setReactants(Molecule[]) - Method in class chemaxon.reaction.Reactor

Sets the reactants.

setReaction(Molecule) - Method in class chemaxon.reaction.Reactor

Sets the reaction with reaction rules set in RDF/MRV tags REACTIVITY, EXCLUDE, SELECTIVITY, TOLERANCE.

setReaction(Molecule, String) - Method in class chemaxon.reaction.Reactor

Sets the reaction with reaction rules set in RDF/MRV tags REACTIVITY, EXCLUDE, SELECTIVITY, TOLERANCE.

setReaction(Molecule, String, String, String, double[]) - Method in class chemaxon.reaction.Reactor

Sets the reaction and the reaction rules.

setReaction(Molecule, String, String, String, String) - Method in class chemaxon.reaction.Reactor

Sets the reaction and the reaction rules.

setReaction(RxnMolecule) - Method in class chemaxon.chemterms.ReactionContext

Sets the reaction.

setReactionArrow(MRArrow) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow.

setReactionArrow(Point3D[]) - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Sets the reaction arrow.

setReactionArrow(Point3D...) - Method in class chemaxon.struc.RxnMolecule

Sets the endpoint coordinates of the reaction arrow.

setReactionArrow0(Point3D...) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow.

setReactionArrowEndPoints(Point3D[]) - Method in class chemaxon.struc.RxnMolecule

Sets the endpoints of the reaction arrow in this reaction.

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

Sets the reaction arrow type.

setReactionArrowType(String) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow type from type name.

setReactionCenterMarkEnabled(boolean) - Method in class chemaxon.reaction.Reactor

Sets whether the bonds of the reaction center on the output should be marked with the following bond marks: MolBond.RC_MAKE_OR_BREAK for bonds that are created or broken during the reaction MolBond.RC_CHANGE for bonds that are changed (type and/or one ligand change)

setReactionIDPropertyName(String) - Method in class chemaxon.reaction.Reactor

Sets the reaction ID property (RDF/MRV tag) name.

setReactionSchemaMap(int) - Method in class chemaxon.reaction.AtomIdentifier

Sets the map of the identified atom (the mapping in the reaction schema)

setReactionSmarts(String) - Method in class chemaxon.checkers.SubstructureChecker

Sets the reactionSmarts

setReactionStereo(int) - Method in class chemaxon.struc.MolAtom

Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.

setReactionString(String) - Method in class chemaxon.reaction.Reactor

Sets the reaction and optionally the reaction rules specified in a string.

setReactionString(String, String) - Method in class chemaxon.reaction.Reactor

Sets the reaction and optionally the reaction rules specified in a string.

setReactionSupport(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Allows or disallows reaction drawing.

setReactionUnpairedMapMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Set option for matching unpaired(orphan or widow) atom maps to any atom.

setReactor(Reactor) - Method in class chemaxon.reaction.ConcurrentReactorProcessor

Sets the Reactor object that will be used for reaction processing.

setRecordIDBackground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane

Highlights a record by setting the background of its identifier field.

setRecordIDForeground(int, Color) - Method in class chemaxon.marvin.beans.MViewPane

Highlights a record by setting the foreground of its identifier field.

setReference(double[][]) - Method in class chemaxon.alignment.AlignRigidEasy

sets the coordinates of the reference molecule directly If this used the AlignRigidEasy.getReferenceAndRotatedFused() cannot be applied

setReference(Molecule) - Method in class chemaxon.alignment.AlignRigidEasy

sets the reference molecule which remains intact

setReferenceMolecule(Molecule, boolean) - Method in class chemaxon.alignment.AlignOnPairedAtoms

Sets the reference molecule to align to.

setRemoveUnusedDefinitions(boolean) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the remove unused definitions option.

setRendering(String) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the rendering style.

setRendering(String) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the rendering style of atoms and bonds.

setRepeatingUnitAtom(MolAtom, boolean) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Adds or removes an atom to/from the list of paradigmatic repeating unit atoms.

setReplaceAtom(MolAtom) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

Sets the atom to replaced with by the action

setRequestMethod(JsonServiceDescriptor.Method) - Method in class chemaxon.calculations.services.JsonServiceDescriptor

Sets the HTTP method of the request.

setResidueAtomId(int) - Method in class chemaxon.struc.MolAtom

Sets the residue atom identifier.

setResidueSeq(int) - Method in class chemaxon.struc.MolAtom

Sets the residue sequence number.

setResidueType(int) - Method in class chemaxon.struc.MolAtom

Sets the residue type.

setResourceDirectory(File) - Method in class chemaxon.naming.document.DocumentAnnotator

Set the directory where resources will be stored.

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

Sets the restH condition on an R-group definition.

setResultType(int) - Method in class chemaxon.reaction.Reactor

Sets the result type.

setReverse(boolean) - Method in class chemaxon.reaction.Reactor

Sets the "reverse" property: true if the reaction is to be processed in reversed direction, that is, the product and reactant sides are swapped.

setRgroup(int) - Method in class chemaxon.struc.MolAtom

Sets the R-group ID.

setRgroupAttachmentPointOrder(int) - Method in class chemaxon.struc.MolAtom

Sets the attachment point order of an R-group attachment point.

setRgroupsVisible(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Shows or hides R-group definitions.

setRgroupsVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets whether the R-group definitions are visible.

setRHLB(boolean) - Method in class chemaxon.calculations.HLBPlugin

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

Deprecated, use HLBPlugin.enableRequiredHLBValue(boolean) instead.

setRightMargin(double) - Method in class chemaxon.struc.PageSettings

setRightName(String) - Method in class chemaxon.struc.sgroup.SgroupAtom

Set the string that will be shown at the right side of the molecule.

setRingBondCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects ring bond count atom query properties or not.

setRingChainTautomerizationAllowed(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets if ring tautomers are allowed or not.
Default true

setRingCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects ring count atom query properties or not.

setRingFlexibility(int, int) - Method in class chemaxon.calculations.AlignmentPlugin

If BOTH the two parameters is true for the ring then the ring is treated flexible.

setRLigandEqualityCheck(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets whether undefined R-atoms with the same R-group ID should match the same structure.

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

Sets R-logic flags.

setRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule

Sets R-logic occurrence range.

setRLogicVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Set R-logic visibility.

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

Sets R-logic visibility

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

Sets the root structure.

setRotatable(double[][]) - Method in class chemaxon.alignment.AlignRigidEasy

sets the coordinates of the rotatable molecule directly If this used the AlignRigidEasy.getReferenceAndRotatedFused() and AlignRigidEasy.getRotatedMolecule() cannot be applied

setRotatable(Molecule) - Method in class chemaxon.alignment.AlignRigidEasy

sets the molecule to translate and rotate during the alignment

setRotation(double, double, double, double) - Method in class chemaxon.struc.Transform3D

Sets the rotation components.

setRotationCenter(Point3D) - Method in class chemaxon.struc.Transform3D

Sets the rotation center.

setRowAndColumn0(int) - Method in class chemaxon.struc.graphics.MTextBox

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

Sets the total nuber of rows.

setRowCount(int) - Method in class chemaxon.struc.PageSettings

setRowHeight(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the row height.

setRxnMoleculeTautomerizationAllowed(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Rxn molecule (chemical reaction)tautomerization is allowed in case of all tautomer generation.

setSaltID(int, String) - Method in class chemaxon.standardizer.actions.StripSaltsAction

Sets the name of the salt at the provided index

setSampleHighlightOn(boolean) - Method in class chemaxon.calculations.gui.MChart

setSampleLabels(String[]) - Method in class chemaxon.calculations.gui.MChart

setSampleValues(double[][]) - Method in class chemaxon.calculations.gui.MChart

setSamplingAccuracy(int) - Method in class chemaxon.alignment.AtropIsomerDetector

Set sampling accuracy.

setSamplingAccuracy(AtropIsomerDetector.Accuracy) - Method in class chemaxon.alignment.AtropIsomerDetector

Set sampling accuracy.

setSamplingInterval(double) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Number of trajectory frames to be stored from the sampling start time to the end of calculation.

setSamplingStart(double) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the beginning of trajectory sampling.

setSaveBOM(boolean) - Method in class chemaxon.marvin.common.UserSettings

setSaveGUIPropertiesInMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets whether the GUI properties should be saved when saving as a Marvin file

setSaveIniEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enables or disables automatic preference saving.

setSaveLoadZoomFactorToMRV(boolean) - Method in class chemaxon.marvin.common.UserSettings

Tells wether to save the zoom factor information to mrv files or not.

setScale(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the scale factor in units of regular bond length.

setScale(double) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the scale factor and changes magnification of the canvas.

setScale(double) - Method in class chemaxon.struc.Transform3D

Sets the scale factor.

setScaleFactor(float) - Method in class chemaxon.descriptors.MDParameters

Sets scaleFactor used with the current parametrized metrics.

setScalingHypothesis(MolecularDescriptor) - Method in class chemaxon.descriptors.MDParameters

Sets (stores) the specified scaling hypothesis.

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

Sets the screening configuration.

setSDFColoring(String, Properties) - Method in class chemaxon.marvin.common.TableSupport

Sets SDF coloring.

setSearchAll(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects all R-atoms or not.

setSearchBridgehead(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for bridgehead explicit hydrogens

setSearchCharged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for charged explicit hydrogens

setSearchContracted(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Sets the checker should search for contracted abbreviated groups or not

setSearchDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker

Sets checker to detect valence properties with the default valence of the current atom type.

setSearchDisconnected(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms not connected to any other atoms or not.

setSearchExpanded(boolean) - Method in class chemaxon.checkers.AbbreviatedGroupChecker

Sets the checker should search for expanded abbreviated groups or not

setSearchGeneric(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms without identifier numbers or not.

setSearchHConnected(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for H connected explicit hydrogens

setSearchIsotopic(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for isotopic explicit hydrogens

setSearchLinker(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms with more than one connection or not.

setSearchLonely(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for lonely explicit hydrogens

setSearchMapped(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for mapped explicit hydrogens

setSearchMode(McsSearchMode) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the search mode that controls the running time and the accuracy of the algorithm.

setSearchNested(boolean) - Method in class chemaxon.checkers.RatomChecker

Sets the option determining if the checker detects R-atoms within R-groups or not.

setSearchNonDefaultValence(boolean) - Method in class chemaxon.checkers.ValencePropertyChecker

Sets checker to detect valence properties with non-default valence of the current atom type.

setSearchOptions(MolSearchOptions) - Method in class chemaxon.search.api.MolComparator

Loads the search options into this comparator.

setSearchOptions(MolSearchOptions) - Method in class chemaxon.search.MolSearch

Sets search options.

setSearchOptions(MolSearchOptions) - Method in class chemaxon.search.RgroupDecomposition

setSearchOptions(SearchOptions) - Method in class chemaxon.search.AbstractSearch

Sets search options.

setSearchOptions(SearchOptions) - Method in class chemaxon.search.MarkushGenerator

Copies all search parameters from options.

setSearchOptions(SearchOptions) - Method in class chemaxon.search.RgroupDecompositionResults

setSearchOptions(String) - Method in class chemaxon.reaction.Reactor

Modifies the default search options used by the Reactor engine.

setSearchOptions(String) - Method in class chemaxon.standardizer.actions.TransformAction

Sets the search options of the action

setSearchPolymerEndGroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for polymer end group explicit hydrogens

setSearchRadical(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for radical explicit hydrogens

setSearchSgroup(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for S-group explicit hydrogens

setSearchSgroupEnd(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for S-group end explicit hydrogens

setSearchType(int) - Method in class chemaxon.search.FormulaSearch

Sets the type of the formula search.

setSearchValenceError(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for valence errored explicit hydrogens

setSearchWedged(boolean) - Method in class chemaxon.checkers.ExplicitHydrogenChecker

Sets whether the checker search for wedged explicit hydrogens

setSelectable(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Enables the user to select a cell by clicking on it or using the cursor movement keys.

setSelected(boolean) - Method in class chemaxon.struc.graphics.MChemicalStruct

Selects or unselects the object.

setSelected(boolean) - Method in class chemaxon.struc.graphics.MMoleculeMovie

Selects or unselects the object.

setSelected(boolean) - Method in class chemaxon.struc.graphics.MTextBox

Selects or unselects the text box.

setSelected(boolean) - Method in class chemaxon.struc.MObject

Selects or unselects the object.

setSelected(boolean) - Method in class chemaxon.struc.MolAtom

Selects or unselects this atom.

setSelected(boolean) - Method in class chemaxon.struc.NoStructure

Sets whether this NoStructure is selected.

setSelected(MoleculeGraph, boolean) - Static method in class chemaxon.struc.graphics.MChemicalStruct

Selects or unselects atoms in a molecule graph.

setSelectedAtoms(int, String, int[]) - Method in class chemaxon.marvin.common.MDocStorage

Sets the selected atom indices.

setSelectedAtoms(int, String, String) - Method in class chemaxon.marvin.common.MDocStorage

Sets the selected atom indices.

setSelectedFields(String[]) - Method in class chemaxon.marvin.common.TableOptions

Set selected fields array in Table Options dialog box

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

Selects a molecule.

setSelectedPage(int) - Method in class chemaxon.struc.PageSettings

setSeparator(String) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Sets the separator string.

SETSEQ_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom set sequence number is currently 63.

SETSEQ_MAX - Static variable in class chemaxon.struc.MolBond

Maximum bond set sequence number.

SETSEQ_OFF - Static variable in class chemaxon.struc.MolBond

Bond set sequence number offset in flags.

setSeriesColors(Color[]) - Method in class chemaxon.calculations.gui.MChart

setServicesConfigurationPath(String) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Sets the custom services configuration path.

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

Sets the URL of the configuration for Services in marvin

setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Enable or disable atom/bond set coloring.

setSetColoringEnabled(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Colors atoms and bonds according to the color of the pre-defined set they belong to.

setSetSeq(int) - Method in class chemaxon.struc.MolAtom

Sets the atom set sequence number.

setSetSeq(int) - Method in class chemaxon.struc.MolBond

Sets the bond set.

setSeverity(CheckerSeverity) - Method in class chemaxon.checkers.StructureCheckerDescriptor

Sets the severity of the concerning checker

setSgroup(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing s-group H

setSgroupDataFormatted(boolean) - Method in class chemaxon.marvin.beans.MarvinPane

Sets if the Sgroup data to be formatted.

setSgroupDataFormatted(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets if the Sgroup data to be formatted.

setSgroupend(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing s-group end H

setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.Sgroup

Sets the molecule graph.

setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Sets the molecule graph.

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

Sets or unsets an S-group as a parent of an atom.

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

Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.

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

Sets or unsets an S-group as a parent of an atom in reactants, products or agents.

setShapeData(ShapeData) - Method in class chemaxon.descriptors.ShapeDescriptor

setShift(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the chemical shift.

setShift(double) - Method in class chemaxon.calculations.nmr.NMRShift

Sets the chemical shift.

setShiftError(double) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets the estimated error of the chemical shift.

setShiftError(double) - Method in class chemaxon.calculations.nmr.NMRShift

Sets the error (confidence interval radius) of the shift.

setShiftErrorClassification(NMRErrorClassification) - Method in class chemaxon.calculations.nmr.NMRMultiplet

Sets error classification of the chemical shift.

setShifts(NMRShift[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets chemical shifts.

setShowMultiMoleculeOnEditSource(boolean) - Method in class chemaxon.marvin.common.UserSettings

setShowUnsuccessfulReactions(boolean) - Method in class chemaxon.reaction.Reactor

Sets if unsuccessful reactions (reactions which do not result products) should be shown in output.

setSimilarityScoreDisplay(int) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions

Sets the mode of similarity score display.

setSingle(boolean) - Method in class chemaxon.reaction.Reactor

Process unambiguous reactions only, where each reactant has a single reaction site.

setSingleCellLabelShown(boolean) - Method in class chemaxon.marvin.common.TableOptions

Tests whether label should be shown for a single cell.

setSingleUpOrDownBond(boolean) - Method in class chemaxon.standardizer.actions.ClearStereoAction

Sets the single wedge value of absolute stereo action

setSize(int) - Method in class chemaxon.marvin.common.MDocStorage

Sets the total number of entries.

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

Sets the default any bond drawing style in the sketcher.

setSketchArrowHeadLength(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow head length.

setSketchArrowHeadWidth(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow head width.

setSketchArrowTailLength(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow tail length.

setSketchArrowTailWidth(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the arrow tail width.

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

Sets the default carbon visibility style in the sketcher.

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

Sets the sketcher's default color scheme.

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

Sets the display method of implicit hydrogens for the sketcher.

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

Sets the default ligand order visibility style in the sketcher.

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

Sets the load working directory for MarvinSketch load filechooser.

setSketchMode(int) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the sketching mode.

setSketchMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the sketcher's default 2D molecule background color.

setSketchMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the sketcher's default 3D molecule background color.

setSketchRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than UserSettings.MAX_RECENT_FILE_LIST_SIZE then the size will be the value of UserSettings.MAX_RECENT_FILE_LIST_SIZE

setSketchRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 2D sketcher.

setSketchRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 3D sketcher.

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

Not implemented yet, don't use it.

setSkip(int, double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the distance of the (visible) head or tail from the corresponding line end point.

setSkipsToEndPoints() - Method in class chemaxon.struc.graphics.MEFlow

setSmallestRingSizeChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects smallest ring size atom query properties or not.

setSmartsQueryChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects SMARTS query properties or not.

setSMILESFontSize(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the SMILES font size.

setSMILESShown(boolean) - Method in class chemaxon.marvin.common.TableOptions

Set visibility of SMILES strings.

setSolventID(int, String) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction

Sets the name of the solvent at the provided index

setSolventRadius(double) - Method in class chemaxon.calculations.MSAPlugin

Sets solvent radius.

setSpecIsotopeSymbolPreferred(boolean) - Method in class chemaxon.struc.MolAtom

Sets special isotope symbol usage preference.

setSrgoups(List<Sgroup>) - Method in class chemaxon.checkers.result.SgroupCheckerResult

This method sets the groups property

setSSRType(SetOfSmallestRingsOption) - Method in class chemaxon.search.api.options.SearchOptions

Sets which type of set of smallest rings to use for property calculations

setStandardizer(Standardizer) - Method in class chemaxon.descriptors.DescriptorGenerator

Sets the standardizer object to be used during descriptor generation.

setStandardizer(Standardizer) - Method in class chemaxon.reaction.Reactor

Sets the reactant standardizer object.

setStandardizer(Standardizer) - Method in class chemaxon.search.MarkushGenerator

Sets standardizer object of this MolSearch class, to be used for the query and target molecules, Chemical Terms configuration and re-standardization of query tautomers at tautomer searching.

setStandardizer(Standardizer) - Method in class chemaxon.search.MolSearch

Sets the standardizer to be used for query and target molecules and re-standardization of query tautomers in case of tautomer substructure search.

setStandardizer(Standardizer) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the standardizer that will be used for performing standardizations.

setStartAt(int) - Method in class chemaxon.marvin.common.TableOptions

Set the index number of the molecule that is the first to be displayed.

setStartEnd(MolAtom, MPoint) - Method in class chemaxon.struc.graphics.MEFlowBasePoint

Sets the atoms.

setStartPosition(long) - Method in class chemaxon.struc.MDocument

Sets the starting position of this document in the input file.

setStartPosition(long) - Method in class chemaxon.struc.Molecule

Sets the starting position of this molecule in the input file.

setStartupSelectorShown(boolean) - Method in class chemaxon.marvin.common.UserSettings

setStepLimit(int) - Method in class chemaxon.alignment.AlignmentBase

setStepNumber(int) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the number of simulation steps.

setStepTime(double) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Sets the simulation timestep.

setStereo2Flags(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond

Sets double bond stereo information.

setStereoFontRatio(float) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the ratio of the font size of the stereo label compared to the normal atom label size.

setStereoGroupNumber(int) - Method in class chemaxon.struc.MolAtom

Sets the stereochemical group number for AND and OR groups of the enhanced stereo representation.

setStereoGroupType(int) - Method in class chemaxon.struc.MolAtom

Sets the stereochemical group type for enhanced stereo representation.

setStereoisomerismType(int) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Sets which type of stereoiseomers should be generated.

setStereoisomerType(EnumSet<StereoisomerSettings.StereoisomerType>) - Method in class chemaxon.calculations.stereo.StereoisomerSettings

Sets which types of stereoisomers should be generated.

setStereoModel(int) - Method in class chemaxon.search.api.options.SearchOptions

Set stereo model option.

setStereoSearchType(int) - Method in class chemaxon.search.api.options.SearchOptions

Specifies the way stereo information is considered during searching.

setStickdst(double) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the sticking distance.

setStickThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the stick thickness.

setStickThickness(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the 3D stick's diameter.

setStickThickness(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the stick diameter for ball and stick mode.

setStoichiometry(String) - Method in class chemaxon.standardizer.actions.ExpandAction

Sets the stoichiometry value of the action

setStoreAppliedTaskData(boolean) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

If set, then applied task data is stored and can be retrieved with methods ConcurrentStandardizerProcessor.getAppliedTaskIDs(), ConcurrentStandardizerProcessor.getAppliedTaskIndexes(), ConcurrentStandardizerProcessor.getInputMolecule().

setString(String, String) - Method in class chemaxon.struc.MPropertyContainer

Sets a property.

setStructureID(String) - Method in class chemaxon.calculations.MarkushEnumerationPlugin

Sets structure ID to be used in Markush code generation.

setSubscript(String) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the subscript.

setSubscript(String) - Method in class chemaxon.struc.Sgroup

Sets the subscript for non-superatom S-groups.

setSubsetChangable(boolean) - Method in class chemaxon.marvin.common.TableOptions

Sets whether startAt and maxSize can be changed.

setSubstitutionCountChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects substitution count atom query properties or not.

setSubType(int) - Method in class chemaxon.struc.Sgroup

Sets polymer S-group subtype.

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

Sets the given molecule as the supergraph of this graph.

setSupergraph(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule

Sets the given molecule as the supergraph of this graph and its components.

setSupplier(Supplier<Molecule>) - Method in class chemaxon.chemterms.MolContext

setSurfaceAreaType(int) - Method in class chemaxon.calculations.MSAPlugin

Sets surface area calculation type: MSAPlugin.VAN_DER_WAALS or MSAPlugin.SOLVENT.

setSymmetricalFuzzy(boolean) - Method in class chemaxon.descriptors.PFParameters

setSymmetryFiltering(boolean) - Method in class chemaxon.calculations.ResonancePlugin

Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.

setSymmetryFiltering(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.

setT(int, int, String) - Method in class chemaxon.marvin.common.MDocStorage

Sets a text field in a record.

setT(int, String) - Method in class chemaxon.marvin.beans.MViewPane

Sets a text field in a GridBagView table.

setTabScale(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the magnification in the molecule cells.

setTag(char) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the tag character for the footnote display.

setTag(String) - Method in class chemaxon.struc.MolAtom

Sets the tag of the atom.

setTag(String) - Method in class chemaxon.struc.MolBond

Sets the tag of the bond.

setTags(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the tags of the action

setTailCrossingBonds(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup

Sets the tail crossing bonds of a ladder-type polymer.

setTakeCanonicalForm(boolean) - Method in class chemaxon.calculations.ResonancePlugin

Sets whether canonical form should be taken.

setTakeCanonicalForm(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets whether canonical form should be generated.

setTakeDominantTautomers(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets whether dominant tautomers should be generated.

setTakeFullTautomerizationSpectrum(boolean) - Method in class chemaxon.calculations.PkaPlugin

Sets to consider the full tautomer distribution upon the macro pka calculation.

setTakeGenericTautomer(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets whether generic tautomer should be generated.

setTakeGenericTautomer(boolean, boolean) - Method in class chemaxon.calculations.TautomerPlugin

setTakeMajorContributors(boolean) - Method in class chemaxon.calculations.ResonancePlugin

Sets whether major contributors should be taken.

setTakeMajorTatomericForm(boolean) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Sets to use major tautomeric form in calculation.

setTakeMajorTautomer(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets whether major tautomer should be generated.

setTakePartialNeutralization(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets if partial neutralization prior to canonical tauotmer generation is allowed or not.

setTakeResonantStructures(boolean) - Method in class chemaxon.calculations.ChargePlugin

Sets calculation with resonant structures.

setTakeResonantStructures(boolean) - Method in class chemaxon.calculations.OrbitalElectronegativityPlugin

Sets calculation with resonant structures.

setTakeStandardForm(boolean) - Method in class chemaxon.calculations.TautomerPlugin

For internal use only.

setTarget(Molecule) - Method in class chemaxon.chemterms.SearchContext

Sets the target molecule.

setTarget(Molecule) - Method in class chemaxon.search.AbstractSearch

Specifies the target molecule.

setTarget(Molecule) - Method in class chemaxon.search.api.MolComparator

Loads the target molecule into this comparator.

setTarget(Molecule) - Method in class chemaxon.search.hitdisplay.HitDisplayTool

Sets the target structure.

setTarget(Molecule) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the target structure.

setTarget(Molecule) - Method in class chemaxon.search.MolSearch

setTarget(Molecule) - Method in class chemaxon.search.RgroupDecomposition

Specifies the target molecule to search in.

setTarget(Molecule, int[]) - Method in class chemaxon.search.AbstractSearch

Specifies the target molecule with excluded atoms.

setTarget(Molecule, int[]) - Method in class chemaxon.search.MolSearch

setTarget(String) - Method in class chemaxon.search.FormulaSearch

Sets the chemical formula target string used to search in

setTargetAbsoluteStereo(boolean) - Method in class chemaxon.search.api.options.MolSearchOptions

Sets whether the chiral flag should be ignored or not for the target molecule.

setTargetFingerprint(int[]) - Method in class chemaxon.chemterms.SearchContext

Sets the fingerprint of the target molecule.

setTargetHomologyMatchingMode(TargetHomologyMatchingMode) - Method in class chemaxon.search.api.options.SearchOptions

Sets the target homology matching mode option.

setTargetMolecule(Molecule) - Method in class chemaxon.alignment.MolAligner

Sets target molecule and calculates its dimension

setTargetRigidForced(boolean) - Method in class chemaxon.alignment.PairwiseAlignment

setTargetRigidForced(boolean) - Method in interface chemaxon.alignment.PairwiseComparison

Set this molecule to be rigid in the input conformation even if it contains rotatable bonds

setTargetRigidForced(boolean) - Method in class chemaxon.alignment.PairwiseSimilarity3D

setTargets(Molecule[]) - Method in class chemaxon.search.MarkushGenerator

Sets the targets.

setTargets(Molecule[]) - Method in class chemaxon.search.RgroupDecompositionResults

setTautomerEqualityMode(TautomerEqualityMode) - Method in class chemaxon.search.api.options.MolSearchOptions

Internal use only.

setTautomerSearch(int) - Method in class chemaxon.search.api.options.SearchOptions

Sets if tautomers of the query should be enumerated for search.

setTautomerSubstructureMode(TautomerSubstructureMode) - Method in class chemaxon.search.api.options.MolSearchOptions

Internal use only.

setTCenter(int) - Method in class chemaxon.struc.graphics.MRectangle

Sets the transformed point.

setTemperature(double) - Method in class chemaxon.calculations.PkaPlugin

Sets the temperature (default: 298 Kelvin).

setTemplates(Molecule[]) - Method in class chemaxon.standardizer.actions.Clean2DAction

Sets the clean templates of the action

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

Sets the bond deletion style.

setTerms(List<MAnalysisBoxTerm>) - Method in class chemaxon.struc.graphics.MAnalysisBox

Sets the terms of this analysis box.

setText(String) - Method in class chemaxon.struc.graphics.MNameTextBox

Sets the text.

setText(String) - Method in class chemaxon.struc.graphics.MReactionSign

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

Sets the text.

setThickness(double) - Method in class chemaxon.struc.graphics.MPolyline

Sets the line thickness.

setThreadCount(int) - Method in class chemaxon.formats.converter.MolConverter

Sets the number of threads for concurrent processing.

setThreadCount(int) - Method in class chemaxon.formats.MolExporter

Sets the number of threads for concurrent processing.

setThreadCount(int) - Method in class chemaxon.formats.MolImporter

Sets the number of threads for concurrent processing.

setThreeLetterName(String) - Method in class chemaxon.struc.sgroup.AminoAcidSgroup

Sets the three letter name of the amino acid.

setThreshold(float) - Method in class chemaxon.descriptors.MDParameters

Sets the value of the threshold of the current parametrized metric.

setThrowable(Throwable) - Method in class chemaxon.calculations.output.CalculatorPluginOutput

Sets the throwable object.

setThrowExceptionOnTimeout(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Sets if search should throw exception upon timeout.

setTimelimit(int) - Method in class chemaxon.calculations.ConformerPlugin

Sets the timelimit for the calculation.

setTimeLimit(double) - Method in class chemaxon.calculations.api.CalculatorLogger

setTimeLimit(double) - Method in class chemaxon.calculations.TautomerPlugin

Sets an upper time limit for the canonical tautomer generation.

setTimeLimit(int) - Method in class chemaxon.alignment.AlignmentBase

Sets the maximum time used for the alignment.

setTimeLimit(long) - Method in class chemaxon.reaction.mapper.AutoMapper

setTimeLimit(long) - Method in interface chemaxon.reaction.mapper.ReactionMapper

Sets time limit for the calculation.

setTimeLimit(long) - Method in class chemaxon.search.mcs.MaxCommonSubstructure

Sets the maximum allowed time for MCS search.

setTimeLogging(boolean) - Method in class chemaxon.calculations.api.CalculatorLogger

setTimeoutInSeconds(int) - Method in class chemaxon.alignment.AtropIsomerDetector

Set time out.

setTimeoutLimitMilliseconds(int) - Method in class chemaxon.search.api.options.SearchOptions

The search on a single target timeouts reaching this amount of time.

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

Sets the frame title.

setTitle(String) - Method in class chemaxon.calculations.gui.MChart

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

Scrolls to the specified cell.

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

Sets the top level container (JFrame, JDialog, etc) of the pane.

setTopMargin(double) - Method in class chemaxon.struc.PageSettings

setTopologyConstraint(int) - Method in class chemaxon.search.mcs.BuildupMcs

Sets the maximum difference in topology the mapped part of the molecules can have.

setTOption(int) - Method in class chemaxon.struc.graphics.MRectangle

Sets the transformation options.

setTraditionalNitrogenAllowed(boolean) - Method in class chemaxon.struc.ValenceCheckOptions.Builder

Sets the traditional way of checking ylidene and nitro groups.

setTraining(String) - Method in class chemaxon.calculations.LogPPlugin

Sets the user defined training.

setTrainingResults(InputStream) - Method in class chemaxon.calculations.LogPPlugin

Sets the user defined training from a stream.

setTransfer(Transferable) - Method in class chemaxon.marvin.datatransfer.MarvinTransferable

Sets the Transferable which contains the Molecule that should be retrieved.

setTransfer(Transferable) - Method in interface chemaxon.marvin.datatransfer.MTransferable

Sets the Transferable for importing Molecule from that.

setTransform(RxnMolecule) - Method in class chemaxon.standardizer.actions.TransformAction

Sets the transformation

setTransformationEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Enable/disable transformation

setTranslation(double, double, double) - Method in class chemaxon.struc.Transform3D

Sets the translation components (Transform3D.m03, Transform3D.m13 and Transform3D.m23).

setTranslation(Point3D) - Method in class chemaxon.struc.Transform3D

Sets the translation components (Transform3D.m03, Transform3D.m13 and Transform3D.m23).

setTransparent(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the transparency state of the painting.

setType(int) - Method in class chemaxon.checkers.AromaticityErrorChecker

setType(int) - Method in class chemaxon.struc.graphics.MBracket

Sets the bracket type.

setType(int) - Method in class chemaxon.struc.graphics.MRArrow

Sets the type of this arrow.

setType(int) - Method in class chemaxon.struc.MolBond

Sets bond type and does valence checking for the endpoints.

setType(StructuralFrameworksPlugin.FrameworkTypes) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Set framework type to calculate.

setType(AromatizeAction.Type) - Method in class chemaxon.standardizer.actions.AromatizeAction

Sets the type of aromatization

setType(Clean2DAction.Type) - Method in class chemaxon.standardizer.actions.Clean2DAction

Sets the type of action

setType(ConvertDoubleBondsAction.Type) - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

Sets the type of action

setType(SetHydrogenIsotopeSymbolAction.Type) - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

Sets the type of action

setType(Class<T>) - Method in class chemaxon.calculations.services.ServiceArgument

Sets the class of the argument

setType(String) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

Sets the type value of the action

setTypes(List<String>) - Method in class chemaxon.checkers.AtomTypeChecker

Sets the checked atom types

setUndefinedRAtom(int) - Method in class chemaxon.search.api.options.SearchOptions

Sets the matching behavior of an undefined R atom in the query.

setUndefinedRAtom(int, boolean) - Method in class chemaxon.search.api.options.SearchOptions

For internal use only! Sets the undefined R-atom matching behavior with a flag denoting whether the value comes from the user (outside) or else from the default R-atom matching setting in

invalid reference

RgroupDecomposition#setQuery(chemaxon.struc.Molecule)

setUndefinedRAtomUserDefined(boolean) - Method in class chemaxon.search.api.options.SearchOptions

For internal use only!

setUndo(int) - Method in class chemaxon.marvin.beans.MSketchPane

Sets the maximum undo depth.

setUnit(DipoleResult.Unit) - Method in class chemaxon.calculations.dipole.DipoleResult

Sets the dipole moment unit, see DipoleResult.Unit.

setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder

Sets NMR spectrum unit.

setUnit(NMRSpectrum.Unit) - Method in class chemaxon.calculations.nmr.NMRSpectrum

Sets the unit type.

setUnitDisplayed(boolean) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets whether the units string should be displayed.

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

Sets the unit of this data field.

setUnsaturationChecking(boolean) - Method in class chemaxon.checkers.AtomQueryPropertyChecker

Sets the option determining if the checker detects unsaturation atom query properties or not.

setUpperLeftPoint(Point3D) - Method in class chemaxon.struc.PageSettings

setURL(String) - Method in class chemaxon.calculations.services.ServiceDescriptor

Sets the service URL

setUseAllAtoms(boolean) - Method in class chemaxon.alignment.AlignmentMoleculeFactory

setUseDefaultSalts(boolean) - Method in class chemaxon.standardizer.actions.StripSaltsAction

Sets whether default salt dictionary should be used

setUseDefaultSolvents(boolean) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction

Sets whether default solvent dictionary should be used

setUsePMAP(boolean) - Method in class chemaxon.descriptors.PFGenerator

Omit or use pharmacophore map data optionally available in molecular structure.

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

Pharmacophore map data in imported Molecule-s should be used.

setUserSettings(UserSettings) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the user settings object.

setUserTypes(String) - Method in class chemaxon.calculations.LogPPlugin

Sets user types.

setVagueBondLevel(int) - Method in class chemaxon.search.api.options.SearchOptions

Option for less strict evaluation of query bonds (e.g.

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

Enables or disables valence check on this molecule graph, depending on the value of the parameter b.

setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.MoleculeGraph

Sets the options for valence checking.

setValenceCheckOptions(ValenceCheckOptions) - Method in class chemaxon.struc.RgMolecule

setValenceerror(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing valence error H

setValenceError(boolean) - Method in class chemaxon.struc.MolAtom

Sets or clears the valence error flag.

setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the visibility state of valence errors.

setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.beans.MSketchPane

Shows or hides valence errors

setValenceErrorVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide valence errors

setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.beans.MViewPane

Shows or hides valence errors

setValenceErrorVisibleInView(boolean) - Method in class chemaxon.marvin.common.UserSettings

Show or hide valence errors in MarvinView

setValenceMatching(boolean) - Method in class chemaxon.search.api.options.SearchOptions

Set valence check option.

setValenceProp(int) - Method in class chemaxon.struc.MolAtom

Sets the valence property.

setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the atom valence propertiy visibility

setValencePropertyVisible(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets atom valence property visibility.

setValid(boolean) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Sets the validity of the standardizer action.

setvalidateSgroupsAtCreation(boolean) - Method in class chemaxon.marvin.common.UserSettings

Set the validation of the possible sgroups and allow only the chemically correct ones on sgroups creation and edit dialog.

setValue(int) - Method in interface chemaxon.core.util.MProgressMonitor

Deprecated.

setValue(int) - Method in interface chemaxon.core.util.ProgressMonitor

Sets the current progress value.

setValue(T) - Method in class chemaxon.calculations.services.ServiceArgument

Sets the service argument value

setVerbose(boolean) - Method in class chemaxon.chemterms.ChemTermsEvaluator

Sets verbose mode.

setVerbose(boolean) - Method in class chemaxon.descriptors.pharmacophore.PMapper

Sets verbose output.

setVerbose(boolean) - Method in class chemaxon.search.AbstractSearch

For debugging purposes only.

setVerbose(boolean) - Method in class chemaxon.search.api.options.SearchOptions

For debugging purposes only.

setVerify3d(boolean) - Method in class chemaxon.calculations.stereo.StereoisomerSettings

Invalid 3D structures of generated stereoisomers are filtered.

setVerticalAlignment(int) - Method in class chemaxon.struc.graphics.MTextBox

Sets the vertical alignment.

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

Sets the default any bond drawing style in the viewer.

setViewAtomMarkEnabled(boolean) - Method in class chemaxon.marvin.common.UserSettings

Sets atom mark and highlight visibility in Marvin View.

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

Sets the default carbon visibility style in the viewer.

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

Sets the viewer's default color scheme.

setViewHandlerType(int) - Method in class chemaxon.marvin.common.TableOptions

Sets the view handler type.

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

Sets the display method of implicit hydrogens for the viewer.

setViewLayout(int) - Method in class chemaxon.marvin.common.UserSettings

Set the layout of MarvinView.

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

Sets the default ligand order visibility style in the viewer.

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

Sets the load working directory for MarvinView load filechooser.

setViewMolbg2d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the default molecule background color for the 2D viewer.

setViewMolbg3d(Color) - Method in class chemaxon.marvin.common.UserSettings

Sets the default molecule background color for the 3D viewer.

setViewNavmode2d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the navigation mode for the 2D viewer.

setViewNavmode3d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the navigation mode for the 3D viewer.

setViewRecentFileListSize(int) - Method in class chemaxon.marvin.common.UserSettings

Sets the recent file list requested size, if it is smaller than zero, then the size will be zero, if it is more than 10 then the size will be 10.

setViewRendering2d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 2D viewer.

setViewRendering3d(String) - Method in class chemaxon.marvin.common.UserSettings

Sets the rendering style for the 3D viewer.

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

Not implemented, don't use it.

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

Sets the nuber of visible rows.

setWedged(boolean) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

Sets the value of property for removing wedged H

setWeights(double[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint

Sets the atom weights for location calculation.

setWeights(float[]) - Method in class chemaxon.descriptors.MDParameters

Sets the cell-wise weight factors for the current parametrized metric.

setWeights(float[], float[]) - Method in class chemaxon.descriptors.PFParameters

Sets the cell-wise weight factors for the current parametrized metric.

setWidth(double) - Method in class chemaxon.struc.PageSettings

setWigglyBondVisibility(boolean) - Method in class chemaxon.calculations.TautomerPlugin

Sets how wiggly bonds connected to double bonds are displayed.
For internal use only.

setWinScale(double) - Method in class chemaxon.marvin.beans.MViewPane

Sets the magnification in the zoom windows.

setWireThickness(double) - Method in class chemaxon.marvin.beans.MarvinPane

Sets the line thickness for wireframe mode.

setWireThickness(double) - Method in class chemaxon.marvin.beans.MolPrinter

Sets the line thickness for wireframe mode.

setWireThickness(double) - Method in class chemaxon.marvin.common.UserSettings

Sets the bond thickness in wireframe mode.

setWord(ByteBuffer, int, int) - Method in class chemaxon.formats.PositionedInputStream

setWorkerThreadCount(int) - Method in class chemaxon.reaction.ConcurrentReactorProcessor

Sets the number of worker threads.

setWorkerThreadCount(int) - Method in class chemaxon.standardizer.ConcurrentStandardizerProcessor

Sets the number of worker threads.

setX(double) - Method in class chemaxon.struc.MolAtom

Sets the X coordinate.

setX(double) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the X coordinate.

setXMLTokens(String...) - Method in class chemaxon.standardizer.StandardizerActionDescriptor

Sets the XML tokens of the action

setXState(int) - Method in class chemaxon.struc.Sgroup

Sets the expanded/contracted state.

setXState(int, int) - Method in class chemaxon.struc.Sgroup

Deprecated.

as of Marvin 6.2, use Sgroup.setXState(int) instead

setXState0(int) - Method in class chemaxon.struc.Sgroup

setXY(double, double) - Method in class chemaxon.struc.MolAtom

Sets the x and y coordinates.

setXYZ(double, double, double) - Method in class chemaxon.struc.MolAtom

Sets the coordinates.

setY(double) - Method in class chemaxon.struc.MolAtom

Sets the Y coordinate.

setY(double) - Method in class chemaxon.struc.sgroup.DataSgroup

Sets the Y coordinate.

setZ(double) - Method in class chemaxon.struc.MolAtom

Sets the Z coordinate.

setZero() - Method in class chemaxon.struc.Transform3D

Sets all components to zero.

setZoomToScaffoldOnLoad(boolean) - Method in class chemaxon.marvin.common.UserSettings

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

Returns the severity of the checker

SEVERITY - Static variable in class chemaxon.checkers.StructureCheckerDescriptor

severity of checker

Sg - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Sg.

Sgroup - Class in chemaxon.struc

Represents a structural group (S-group) in a molecule.

Sgroup(Molecule, int) - Constructor for class chemaxon.struc.Sgroup

Deprecated.

As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType).

Sgroup(Molecule, int, int) - Constructor for class chemaxon.struc.Sgroup

Deprecated.

As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType) and Sgroup.setXState(int).

Sgroup(Molecule, SgroupType) - Constructor for class chemaxon.struc.Sgroup

Sgroup(Molecule, SgroupType, int) - Constructor for class chemaxon.struc.Sgroup

Sgroup(Sgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.Sgroup

Copy constructor.

Sgroup(Sgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.Sgroup

Copy constructor.

SGROUP - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of an Sgroup.

SGROUP_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which is the only atom in an Sgroup.

SGROUP_SGROUP_MAP - Static variable in class chemaxon.checkers.result.ConversionConstants

The key of the map from cloned S-groups to original S-groups.

SGROUP_TYPE_COUNT - Static variable in class chemaxon.struc.Sgroup

Number of S-group types.

SgroupAtom - Class in chemaxon.struc.sgroup

Superatom of SuperatomSgroup.

SgroupAtom(SuperatomSgroup) - Constructor for class chemaxon.struc.sgroup.SgroupAtom

Constructs a superatom for a superatom type S-group.

SgroupCheckerResult - Class in chemaxon.checkers.result

A descendant of DefaultStructureCheckerResult for identifying Sgroup problems.

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

Constructor which initialize all the properties.

SGROUPEND_H - Static variable in class chemaxon.struc.MolAtom

Hydrogen atom which have a neighbor that is in a SuperatomSgroup.

SgroupFactory - Class in chemaxon.struc

A factory class to create different types of S-groups.

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

sgroupGraph - Variable in class chemaxon.struc.Sgroup

The S-group's internal structure.

SgroupIterator() - Constructor for class chemaxon.struc.IteratorFactory.SgroupIterator

Deprecated.

Constructs an s-group iterator for the specified molecule of the factory.

sgroupType - Variable in class chemaxon.struc.Sgroup

The S-group type.

SgroupType - Enum Class in chemaxon.struc

Enum of possible S-group types.

SHAc - Enum constant in enum class chemaxon.calculations.PkaTrainingResult.PkaType

ShapeData - Class in chemaxon.alignment

Holds the shape representation data of a molecule used for shape-based alignment and similarity calculations.

ShapeDescriptor - Class in chemaxon.descriptors

Shape descriptor implements a 3D alignment based similarity calculation.

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

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

Copy constructor.

ShapeDescriptor(ShapeParameters) - Constructor for class chemaxon.descriptors.ShapeDescriptor

Creates a new instance of ShapeDescriptor according to the parameters given.

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

Creates a new instance of ShapeDescriptor according to the parameters given.s

ShapeGenerator - Class in chemaxon.descriptors

Generates ShapeDescriptor data from a molecule using 3D shape analysis.

ShapeGenerator(AlignmentProperties.ColoringScheme) - Constructor for class chemaxon.descriptors.ShapeGenerator

SHAPELY_SCHEME - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Shapely color scheme in display option flags.

SHAPELY_SCHEME_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts

Shapely color scheme.

ShapeParameters - Class in chemaxon.descriptors

Configuration parameters for shape-based molecular descriptor generation and comparison.

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

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

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

Creates a new object based on a given configuration string.

SHORTCUTS - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "shortcuts".

shortestPath(int, int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Calculates the shortest topological path (number of bonds) between two atoms.

shortName() - Method in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory

shortName() - Method in class chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory

shortName() - Method in interface chemaxon.calculations.solubility.SolubilityCategory

Returns the name of category.

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

Identifier of parameter: "showSets".

showDialog() - Method in class chemaxon.marvin.common.TableOptions

Bring up Table Options dialog box

showErrorDialog(String, Throwable) - Method in class chemaxon.marvin.beans.MarvinPane

Show error dialog.

showFileDialog(String, Molecule) - Method in class chemaxon.marvin.beans.MarvinPane

Shows an Open or Save file dialog.

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

Shows file open dialog.

showFormalCharge(Set<FormulaGenerationRule>) - Static method in enum class chemaxon.calculations.elemental.FormulaGenerationRule

Returns true if the formal charge should be shown at the end of the formula based on the given rules.

showSelectedNodes() - Method in class chemaxon.alignment.AlignmentMolecule

showStartupSelector() - Method in class chemaxon.marvin.beans.MSketchPane

This method is used in startup time to throw up a skin selector dialog.

Si - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Si.

similarity(AlignmentMolecule) - Method in class chemaxon.alignment.PairwiseAlignment

similarity(AlignmentMolecule) - Method in interface chemaxon.alignment.PairwiseComparison

similarity(AlignmentMolecule) - Method in class chemaxon.alignment.PairwiseSimilarity3D

similarity(Molecule) - Method in class chemaxon.alignment.PairwiseAlignment

similarity(Molecule) - Method in interface chemaxon.alignment.PairwiseComparison

Calculates the 3D similarity between the previously set query and the target.

similarity(Molecule) - Method in class chemaxon.alignment.PairwiseSimilarity3D

SIMILARITY - Static variable in interface chemaxon.search.api.SearchConstants

Similarity search.

SIMILARITY - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions

The similarity score is shown and stored in the MPropertyContainer of the Molecule.

SIMILARITY_LABEL - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions

Label for the similarity score part of the hit.

SIMILARITY_OFF - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions

The similarity score is neither shown nor stored in the MPropertyContainer of the Molecule.

Descriptor similarity calculation can be performed using SimilarityCalculator.

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

This factory creates a similarity calculator object according to the user defined parameters.

SimilarityException - Exception Class in chemaxon.descriptors

Exception class for similarity calculator tools.

similarityNode - Variable in class chemaxon.descriptors.MDParameters

node holding the similarity calculations related parameters

Calculates the similarity of two bit strings.

SimilarityUtil() - Constructor for class chemaxon.search.util.SimilarityUtil

SIMPLE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.OrientationType

SIMPLE_VIEW - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "simpView".

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

Simplify a reaction to a molecule if possible.

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

Simplifies the main molecule object if possible.

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

Simplifies this RxnMolecule by moving the atoms and bonds from the reactants, products, and agents to a Molecule.

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

Single bond type.

SINGLE - Static variable in class chemaxon.struc.MolBond

Single bond type.

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

Single or aromatic query bond type.

SINGLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond

Single or aromatic query bond type.

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

Single or double query bond type.

SINGLE_OR_DOUBLE - Static variable in class chemaxon.struc.MolBond

Single or double query bond type.

sinkIsAtom() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's sink is an atom.

sinkIsBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's sink is a bond.

sinkIsIncipBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's sink is an incipient bond.

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

Gets the total number of properties.

size() - Method in class chemaxon.struc.prop.MHashProp

Gets the table size.,

size() - Method in class chemaxon.struc.prop.MListProp

Gets the array size.

sizeToString(double) - Static method in class chemaxon.struc.graphics.MFont

Converts an integer or fractional size to a string.

SKC - Static variable in class chemaxon.formats.MFileFormat

SKC file format

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

Identifier of parameter: "sketchAnyBond".

SKETCH_ARROW_HEAD_LENGTH - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "sketchArrowHeadLength".

SKETCH_ARROW_HEAD_WIDTH - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "sketchArrowHeadWidth".

SKETCH_ARROW_TAIL_LENGTH - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "sketchArrowTailLength".

SKETCH_ARROW_TAIL_WIDTH - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "sketchArrowTailWidth".

SKETCH_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "sketchCarbonVisibility".

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

Identifier of parameter: "sketchHelp".

SKETCH_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "sketchLigandOrderVisibility".

SKETCH_STARTUP_SHOWN - Static variable in class chemaxon.marvin.common.SketchParameterConstants

SKETCHABLE - Static variable in class chemaxon.marvin.beans.MViewPane

Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinSketch in a new window.

SKETCHPANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.common.SketchParameterConstants

SKETCHPANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.common.SketchParameterConstants

SketchParameterConstants - Class in chemaxon.marvin.common

Parameters of MSketchPane.

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

Identifier of parameter: "skin".

skip(long) - Method in class chemaxon.formats.PositionedInputStream

Skips over and discards n bytes of data.

SKIP_COORDINATE_BONDS - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Exclude coordinate bonds from bond iteration.

SKIP_COVALENT_BONDS - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Exclude covalent bonds from bond iteration.

SKIP_EXPLICIT_H - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Exclude explicit hydrogens from atom iteration.

SKIP_LONE_PAIR - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Exclude lone pairs from atom iteration.

SKIP_MULTICENTER - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Exclude multicenters from atom iteration.

SKIP_PSEUDO_ATOM - Static variable in class chemaxon.struc.IteratorFactory

Deprecated.

Exclude pseudo atoms from atom iteration.

skipLine() - Method in class chemaxon.formats.PositionedInputStream

Skips the next line.

skipRecord() - Method in class chemaxon.calculations.CalculatorPluginMDocSource

Skips the next document.

skipRecord() - Method in class chemaxon.formats.MDocSource

Skips the next document.

skipRecord() - Method in class chemaxon.formats.MolImporter

Skips the next molecule or document instead of reading it into memory.

skipRecords(int, int, ProgressMonitor, int, Runnable) - Method in class chemaxon.formats.MDocSource

Sm - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Sm.

SM_ATOM - Static variable in class chemaxon.marvin.beans.MSketchPane

Atom mode.

SM_BOND - Static variable in class chemaxon.marvin.beans.MSketchPane

Bond mode.

SM_DELETE - Static variable in class chemaxon.marvin.beans.MSketchPane

Delete mode.

SM_FLAGS_OFF - Static variable in class chemaxon.marvin.beans.MSketchPane

Offset of flags in sketch mode.

SM_MASK - Static variable in class chemaxon.marvin.beans.MSketchPane

Sketch mode mask.

SM_SELECT - Static variable in class chemaxon.marvin.beans.MSketchPane

Select mode.

SM_SELECT_LASSO - Static variable in class chemaxon.marvin.beans.MSketchPane

Lasso select mode.

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

Represents that small ring errors have been found in the molecule

smallestRing() - Method in class chemaxon.core.calculations.Ring

Identifies the smallest ring (number of atoms) in the molecule.

smallestRingSize() - Method in class chemaxon.core.calculations.Ring

Calculates the size of the smallest ring in the molecule.

smallestRingSizeOfAtom(int) - Method in class chemaxon.core.calculations.Ring

Calculates the size of the smallest ring an atom is a member of.

smallestRingSystem() - Method in class chemaxon.core.calculations.Ring

Identifies the smallest ring system (number of rings) in the molecule.

smallestRingSystemSize() - Method in class chemaxon.core.calculations.Ring

Calculates the size of the smallest ring system (number of rings) in the molecule.

SMARTS - Static variable in class chemaxon.formats.MFileFormat

SMARTS.

SMARTS_H_DAYLIGHT_COMP_MODE - Static variable in class chemaxon.struc.MolAtom

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

Not used anymore, will be removed in future releases.

SMARTS_H_MARVIN_COMP_MODE - Static variable in class chemaxon.struc.MolAtom

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

Not used anymore, will be removed in future releases.

SMILES - Static variable in class chemaxon.formats.MFileFormat

SMILES.

Sn - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Sn.

SOLID - Enum constant in enum class chemaxon.rendering.constants.AnyBondStyle

Solid line is used when rendering Any bonds.

SOLID - Enum constant in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle

Solid line is used when rendering Coordinate bonds.

SOLID - Enum constant in enum class chemaxon.rendering.constants.CoordinateBondStyle

Solid line is used when rendering Coordinate bonds.

SolubilityCalculator - Class in chemaxon.calculations.solubility

Solubility calculator.

SolubilityCalculator() - Constructor for class chemaxon.calculations.solubility.SolubilityCalculator

Default constructor.

SolubilityCalculator(String) - Constructor for class chemaxon.calculations.solubility.SolubilityCalculator

Constructor for internal use only.

SolubilityCategories - Class in chemaxon.calculations.solubility

Stores the array of solubility categories.

SolubilityCategories(SolubilityCategory[], SolubilityUnit) - Constructor for class chemaxon.calculations.solubility.SolubilityCategories

Constructor.

SolubilityCategories.UndefinedSolubilityCategory - Class in chemaxon.calculations.solubility

Undefined category.

SolubilityCategory - Interface in chemaxon.calculations.solubility

Interface for solubility categories.

SolubilityResult - Class in chemaxon.calculations.solubility

Solubility prediction result.

SolubilityResult(Molecule, double) - Constructor for class chemaxon.calculations.solubility.SolubilityResult

SolubilityUnit - Enum Class in chemaxon.calculations.solubility

Solubility unit.

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

Represents that solvents have been found in the molecule

SOLVENT - Static variable in class chemaxon.calculations.MSAPlugin

Surface area type: 3D solvent accessible surface area.

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

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

StructureCheckerErrorType.SOLVENT_AMBIGUOUS is used instead

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

Represents that more than one type of solvents have been found in the molecule

SOLVENT_ID_PROPERTY - Static variable in class chemaxon.standardizer.actions.RemoveSolventsAction

Property key for solvent ID

SOLVENT_LIST_KEY - Static variable in class chemaxon.standardizer.actions.RemoveSolventsAction

Property key for solvent list modification

SolventChecker - Class in chemaxon.checkers

SolventChecker detects common solvents in multi-fragment molecules.

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

Default constructor

sort(Sgroup[], int) - Static method in class chemaxon.struc.Sgroup

Sorts S-groups in parent-child or child-parent order.

SORT_CHILD_PARENT - Static variable in class chemaxon.struc.Sgroup

Child-parent sort order.

SORT_PARENT_CHILD - Static variable in class chemaxon.struc.Sgroup

Parent-child sort order.

sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.MoleculeGraph

Sorts bonds in the same order as they appear in another chemical graph.

sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RgMolecule

Sort edges in the same order as they appear in the specified array.

sortBondsAccordingTo(MolBond[]) - Method in class chemaxon.struc.RxnMolecule

Sort edges in the same order as they appear in the specified array.

SOURCE_TEXT - Static variable in class chemaxon.naming.document.DocumentToStructure

Molecule property key on results: the source text, as it appears in the original document.

sourceIsAtom() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's source is an atom.

sourceIsBond() - Method in class chemaxon.struc.graphics.MEFlow

Gets whether this arrow's source is a bond.

SPACEFILL - Enum constant in enum class chemaxon.rendering.constants.RenderingStyle

Spacefill rendering style.

Special matching atom indexes: - Search tag in chemaxon.search.api.SearchHit.getSingleHit()

Section

SPHERIC - Enum constant in enum class chemaxon.alignment.AlignmentProperties.NodeType

SPIN - Static variable in class chemaxon.marvin.common.ViewParameterConstants

Identifier of parameter: "spin".

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

Identifier of parameter: "splashScreenImage".

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

Replaces all disconnected reaction components by its connected fragments in the structure array.

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

Finds those component parts that are contained in the molecule graph m and creates separate components from the fragments contained in m, splitting them from the previous merges.

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

Replaces a disconnected reaction component by its connected fragments in the structure array.

splitDisconnectedComponent(long) - Method in class chemaxon.struc.RxnMolecule

Replaces a disconnected reaction component by its connected fragments in the structure array.

splitFileAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil

Parses "file{options}" strings used in molecule file import.

splitFormatAndOptions(String) - Static method in class chemaxon.formats.MFileFormatUtil

Parses "format:options" strings used in molecule file import and export.

Sr - Static variable in class chemaxon.struc.PeriodicTable

Atomic number of the element Sr.

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

Calculate the size of smallest ring containing this atom.

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

sssr - Enum constant in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes

SSSR - Enum constant in enum class chemaxon.search.api.options.SetOfSmallestRingsOption

Smallest set of smallest rings.

SST_ALTERNATING - Static variable in class chemaxon.struc.Sgroup

Alternating polymer S-group subtype.

SST_BLOCK - Static variable in class chemaxon.struc.Sgroup

Block polymer S-group subtype.

SST_RANDOM - Static variable in class chemaxon.struc.Sgroup

Random polymer S-group subtype.

ST_AMINOACID - Static variable in class chemaxon.struc.Sgroup

Amino acid S-group type.

ST_ANY - Static variable in class chemaxon.struc.Sgroup

Any polymer S-group type.

ST_COMPONENT - Static variable in class chemaxon.struc.Sgroup

Component S-group type.

ST_COPOLYMER - Static variable in class chemaxon.struc.Sgroup

Copolymer S-group type.

ST_CROSSLINK - Static variable in class chemaxon.struc.Sgroup

Crosslink S-group type.

ST_DATA - Static variable in class chemaxon.struc.Sgroup

Data S-group type.

ST_FORMULATION - Static variable in class chemaxon.struc.Sgroup

Formulation S-group type.

ST_GENERIC - Static variable in class chemaxon.struc.Sgroup

Generic S-group type.

ST_GRAFT - Static variable in class chemaxon.struc.Sgroup

Graft S-group type.

ST_MER - Static variable in class chemaxon.struc.Sgroup

Mer S-group type.

ST_MIXTURE - Static variable in class chemaxon.struc.Sgroup

Mixture S-group type.

ST_MODIFICATION - Static variable in class chemaxon.struc.Sgroup

Modification S-group type.

ST_MONOMER - Static variable in class chemaxon.struc.Sgroup

Monomer S-group type.

ST_MULTICENTER - Static variable in class chemaxon.struc.Sgroup

Multicenter S-group type.

ST_MULTIPLE - Static variable in class chemaxon.struc.Sgroup

Multiple group S-group type.

ST_SRU - Static variable in class chemaxon.struc.Sgroup

SRU (Structural Repeating Unit: polymers and repeating units with repetition ranges) S-group type.

ST_SUPERATOM - Static variable in class chemaxon.struc.Sgroup

Superatom S-group type.

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

Performs the standardization of the next input molecule, and returns the standardized molecule.

standardize(Molecule) - Method in class chemaxon.calculations.AlignmentPlugin

standardize(Molecule) - Method in class chemaxon.calculations.CalculatorPlugin

Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).

standardize(Molecule) - Method in class chemaxon.calculations.ChemicalNamePlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.ConformerPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.calculations.ElementalAnalysisPlugin

Prevents default standardization: does nothing.

standardize(Molecule) - Method in class chemaxon.calculations.GeometryPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.calculations.HLBPlugin

standardize(Molecule) - Method in class chemaxon.calculations.IonChargePlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.IsoelectricPointPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.LogDPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.LogPPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesAccessorPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.MajorMicrospeciesPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.MolecularDynamicsPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.calculations.PkaPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.RefractivityPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.ResonancePlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.StereoisomerPlugin

Deprecated.

Clears enhanced stereo information.

standardize(Molecule) - Method in class chemaxon.calculations.StructuralFrameworksPlugin

Standardize input molecule
Standardization currently ungroups SGroups

standardize(Molecule) - Method in class chemaxon.calculations.TautomerPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.calculations.TopologyAnalysisPlugin

Expands sgroups.

standardize(Molecule) - Method in class chemaxon.descriptors.MDParameters

Standardizes the Molecule and returns the standardized form.

standardize(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction

Calls AbstractStandardizerAction.standardize1(Molecule).

standardize(Molecule) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction

standardize(Molecule) - Method in class chemaxon.standardizer.Standardizer

Standardization for one input molecule: performs the standardization actions according to the XML configuration.

standardize(Molecule) - Method in interface chemaxon.standardizer.StandardizerAction

Standardizes the provided molecule.

standardize1(Molecule) - Method in class chemaxon.standardizer.AbstractStandardizerAction

This method contains the current standardization mechanism.

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AddExplicitHydrogensAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AliasToAtomAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AliasToGroupAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.AromatizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.Clean2DAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.Clean3DAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ClearIsotopesAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ClearStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ContractSgroupsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertPiMetalBondsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.CreateGroupAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.DearomatizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.DisconnectMetalAtomsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ExpandAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ExpandSgroupsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MapAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MapReactionAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.MesomerizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.NeutralizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RearrangeReactionAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAbsoluteStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAtomValuesAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveAttachedDataAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveFragmentAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveRGroupDefinitionsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveSolventsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.RemoveStereoCareBoxAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.SetAbsoluteStereoAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.StripSaltsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.TautomerizeAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.TransformAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.UngroupSgroupsAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.UnmapAction

standardize1(Molecule) - Method in class chemaxon.standardizer.actions.WedgeCleanAction

StandardizedMolSearch - Class in chemaxon.search

MolSearch subclass that standardizes query and target structures by default before searching.

StandardizedMolSearch() - Constructor for class chemaxon.search.StandardizedMolSearch

Constructs a StandardizedMolSearch object.

standardizeIonicGroups(Molecule) - Static method in class chemaxon.calculations.CalculatorPlugin

Default standardization: nitro groups: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1] sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]

standardizer - Variable in class chemaxon.descriptors.MDParameters

transform molecules into standard form before descriptor generation

Standardizer - Class in chemaxon.standardizer

Performs the standardization determined by the XML configuration file, or simple action string configuration.

Standardizer(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with XML configuration

Standardizer(Standardizer) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer based on an existing standardizer

Standardizer(File) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with XML configuration

Standardizer(InputStream) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with XML configuration

Standardizer(String) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with auto-recognized XML or action string configuration

Standardizer(String, String) - Constructor for class chemaxon.standardizer.Standardizer

Initializes a new standardizer with auto-recognized XML or action string configuration

StandardizerAction - Interface in chemaxon.standardizer

Interface of standardizer actions.

StandardizerActionDescriptor - Class in chemaxon.standardizer

Descriptor of StandardizerAction objects.

StandardizerActionDescriptor(Class<? extends StandardizerAction>) - Constructor for class chemaxon.standardizer.StandardizerActionDescriptor

Constructs a descriptor based on standardizer action class.

StandardizerActionFactory - Class in chemaxon.standardizer

Factory of StandardizerAction objects.

StandardizerActionFactory() - Constructor for class chemaxon.standardizer.StandardizerActionFactory

Default constructor.

StandardizerActionFactory(String, String) - Constructor for class chemaxon.standardizer.StandardizerActionFactory

With this constructor inner and external configuration location can be defined.

StandardizerActionFactory.Builder - Class in chemaxon.standardizer

Builder class for StandardizerActionFactory.

StandardizerActionFactory.StandardizerClassDescriptor - Class in chemaxon.standardizer

Descriptor of a standardizer class

StandardizerActionInfo - Annotation Interface in chemaxon.standardizer

Standardizer action info annotation.

StandardizerActionStringReader - Class in chemaxon.standardizer.configuration

Standardizer configuration reader for parsing action strings.

StandardizerActionStringReader(String) - Constructor for class chemaxon.standardizer.configuration.StandardizerActionStringReader

Default constructor of the reader.

StandardizerActionStringReader(String, StandardizerActionFactory) - Constructor for class chemaxon.standardizer.configuration.StandardizerActionStringReader

Constructor with custom standardizer action factory

StandardizerActionStringWriter - Class in chemaxon.standardizer.configuration

Standardizer configuration writer for action strings.

StandardizerActionStringWriter() - Constructor for class chemaxon.standardizer.configuration.StandardizerActionStringWriter

StandardizerClassDescriptor() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Initializes an empty standardizer class descriptor

StandardizerClassDescriptor(String, String, String, String) - Constructor for class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor

Initializes a standardizer class descriptor

StandardizerConfiguration - Class in chemaxon.standardizer.configuration

Standardizer configuration class.

StandardizerConfiguration() - Constructor for class chemaxon.standardizer.configuration.StandardizerConfiguration

standardizerConfigurationNode - Variable in class chemaxon.descriptors.MDParameters

node defining the Standardizer configuration

StandardizerConfigurationReader - Interface in chemaxon.standardizer.configuration

Configuration reader interface of Standardizer.

StandardizerConfigurationWriter - Interface in chemaxon.standardizer.configuration

Configuration writer interface of Standardizer.

StandardizerConfigurationXmlReader - Class in chemaxon.standardizer.configuration

Standardizer configuration reader for parsing XML configuration files.

StandardizerConfigurationXmlReader(InputStream) - Constructor for class chemaxon.standardizer.configuration.StandardizerConfigurationXmlReader

Initiate an StandardizerConfigurationXmlReader instance with the given inputSteam with the configuration

StandardizerConfigurationXmlReader(InputStream, StandardizerActionFactory) - Constructor for class chemaxon.standardizer.configuration.StandardizerConfigurationXmlReader

Initiate an StandardizerConfigurationXmlReader instance with the given inputSteam with the configuration

StandardizerConfigurationXmlWriter - Class in chemaxon.standardizer.configuration

Standardizer configuration writer for XML configuration files.

StandardizerConfigurationXmlWriter() - Constructor for class chemaxon.standardizer.configuration.StandardizerConfigurationXmlWriter

StandardizerUtil - Class in chemaxon.standardizer

Utility class for standardizer.

StandardizerUtil() - Constructor for class chemaxon.standardizer.StandardizerUtil

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

Represents that star atoms have been found in the molecule

STAR - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the star atom.

StarAtomChecker - Class in chemaxon.checkers

A descendant of AtomChecker detecting so called star atoms having "*" as atomic symbol.

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

Default constructor

start() - Method in interface chemaxon.alignment.AlignmentMoleculeFactory.ProgressBarInterface

start(MDocSource, String) - Method in class chemaxon.marvin.common.TableSupport

Starts loading molecules.

startCalculation() - Method in class chemaxon.calculations.api.ProgressableCalculator

startElement(String, String, String, Attributes) - Method in class chemaxon.naming.document.XmlToHtmlConverter

startEMFGenerator() - Static method in class chemaxon.marvin.util.ImageExportUtil

Starts the initialization of the .NET based EMF generator on a background thread.

startGrabLines() - Method in class chemaxon.formats.PositionedInputStream

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

startNow(MDocSource, String) - Method in class chemaxon.marvin.common.TableSupport

Starts loading molecules immediately.

STATIC_PKA_PREFIX - Static variable in class chemaxon.calculations.PkaPlugin

pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)

STATICpKaPREFIX - Static variable in class chemaxon.calculations.PkaPlugin

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

Use PkaPlugin.STATIC_PKA_PREFIX instead. This constant will be removed in a future release.

STATUS_BAR - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "statusBar".

STEP_DEFAULT - Static variable in class chemaxon.calculations.AlignmentPlugin

stepWedge() - Method in class chemaxon.struc.MolBond

Set the bond from 0 to MolBond.UP or UP to MolBond.DOWN.

stereo(int) - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Calculates absolute stereo configuration of the given atom.

stereo(int, int) - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Calculates absolute stereo configuration of the given double bond.

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

Represents that stereo-care boxes (search markers) have been found in the molecule

STEREO_DIASTEREOMER - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for "diastereomer" stereo search type.

STEREO_ENANTIOMER - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for "enantiomer" stereo search type.

STEREO_EXACT - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for "exact" stereo search type.

STEREO_IGNORE - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for "ignore" stereo search type.

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

Represents that stereo inversion/retention marks have been found in the molecule/reaction

STEREO_MASK - Static variable in class chemaxon.struc.MolBond

Single and double bond stereo mask.

STEREO_MODEL_COMPREHENSIVE - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant of the comprehensive stereo search model, which combines the advantages of local and global models.

STEREO_MODEL_DEFAULT - Static variable in interface chemaxon.search.api.SearchConstants

For markush search in all cases and for non-markush duplicate search in query tables SearchConstants.STEREO_MODEL_LOCAL, for non-markush duplicate search (with the exception of query tables) SearchConstants.STEREO_MODEL_GLOBAL.

STEREO_MODEL_GLOBAL - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant of the global stereo search model, which considers global stereo information (global parity, global double bond stereo configuration, etc.).

STEREO_MODEL_LOCAL - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for the local stereo search model, which only considers local stereo information (local parity, local double bond stereo configuration, etc.).

STEREO_SPECIFIC - Static variable in interface chemaxon.search.api.SearchConstants

Option value constant for "specific" stereo search type.

STEREO1_MASK - Static variable in class chemaxon.struc.MolBond

Single bond stereo mask.

STEREO2_CARE - Static variable in class chemaxon.struc.MolBond

Cis/trans info of this bond is taken care of during the SSS process if this flag is set - used only for query bonds.

StereoActivePart - Class in chemaxon.core.calculations.stereo

Stereo active molecule part with stereo active atom index and its ligands which takes part in the stereo description.

StereoActivePart(int, int[]) - Constructor for class chemaxon.core.calculations.stereo.StereoActivePart

Creates a new stereo active part.

StereoAnalysis - Class in chemaxon.calculations.stereo

The stereo analysis module is able to calculate stereochemical descriptors for a molecule, giving an analysis in terms of the stereochemical properties.

StereoAnalysis(Molecule) - Constructor for class chemaxon.calculations.stereo.StereoAnalysis

Creates an analysis.

StereoAnalysis(Molecule, String) - Constructor for class chemaxon.calculations.stereo.StereoAnalysis

Creates an analysis.

StereoCareBoxChecker - Class in chemaxon.checkers

Checker to find molecules containing Stereo-Care Boxes.

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

Creates a stereo-care box checker.

StereoCenter - Interface in chemaxon.calculations.stereo.stereocenters

Interface for stereo centers.

StereoCenterVisitor - Interface in chemaxon.calculations.stereo.stereocenters

Visitor interface for stereo centers.

Stereochemistry - Class in chemaxon.core.calculations.stereo

Central class for accessing functions analyzing the topology of a molecule.

Stereochemistry() - Constructor for class chemaxon.core.calculations.stereo.Stereochemistry

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

Reset the wedges of the molecule, based on the actual parity information in 2D, remove wedges in 3D.

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

Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.

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

Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.

StereoConstants - Interface in chemaxon.struc

Constants for atom parity and double bond stereo.

stereoDoubleBondCount() - Method in class chemaxon.core.calculations.stereo.Stereochemistry

Calculates the number of stereo double bonds.

StereoInversionRetentionMarkChecker - Class in chemaxon.checkers

Detects reaction inversion/retention marks on atoms.

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

Default constructor

STEREOISOMER_DOUBLEBOND - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

STEREOISOMER_TETRAHEDRAL - Enum constant in enum class chemaxon.calculations.api.CalculatorTag

StereoisomerEnumeration - Class in chemaxon.calculations.stereo

Enumerates stereoisomers of a molecule considering all tetrahedral and cis-trans stereocenters.

StereoisomerEnumeration(Molecule) - Constructor for class chemaxon.calculations.stereo.StereoisomerEnumeration

Constructs a StereoisomerEnumeration object with default settings.

StereoisomerEnumeration(Molecule, StereoisomerSettings) - Constructor for class chemaxon.calculations.stereo.StereoisomerEnumeration

Construct new StereoisomerEnumeration object.

StereoisomerEnumeration(Molecule, StereoisomerSettings, String) - Constructor for class chemaxon.calculations.stereo.StereoisomerEnumeration

Construct new StereoisomerEnumeration object.

StereoisomerPlugin - Class in chemaxon.calculations

Deprecated.

Use StereoisomerEnumeration instead.

StereoisomerPlugin() - Constructor for class chemaxon.calculations.StereoisomerPlugin

Deprecated.

StereoisomerSettings - Class in chemaxon.calculations.stereo

Settings class for StereoisomerEnumeration.

StereoisomerSettings.StereoisomerType - Enum Class in chemaxon.calculations.stereo

Types of stereoisomers.

stereoisomerTypes() - Method in class chemaxon.calculations.stereo.StereoisomerSettings

Returns the type of generated stereoisomers.

StereoType - Enum Class in chemaxon.calculations.stereo.stereocenters

Stereo center type.

stereoValue - Variable in class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor

stereoValue - Variable in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor

stereoValue - Variable in class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor

stereoValue - Variable in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor

stericEffectIndex(int) - Method in class chemaxon.core.calculations.TopologyAnalyzer

Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.

STGRP_ABS - Static variable in interface chemaxon.struc.StereoConstants

Absolute stereo group type for enhanced stereo representation.

STGRP_AND - Static variable in interface chemaxon.struc.StereoConstants

AND stereo group type for enhanced stereo representation.

STGRP_NONE - Static variable in interface chemaxon.struc.StereoConstants

Empty stereo group type setting meaning no enhanced stereo label.

STGRP_OR - Static variable in interface chemaxon.struc.StereoConstants

OR stereo group type for enhanced stereo representation.

STICK_DISTANCE - Static variable in class chemaxon.marvin.common.SketchParameterConstants

Identifier of parameter: "stickdst".

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

Identifier of parameter: "stickThickness".

STICKS - Enum constant in enum class chemaxon.rendering.constants.RenderingStyle

Stick rendering style.

Sticky(MMidPoint) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky

Copy constructor.

Sticky(MPolyline, int) - Constructor for class chemaxon.struc.graphics.MMidPoint.Sticky

Constructor.

Sticky(MRectangle, int) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky

Constructor.

Sticky(MRectanglePoint) - Constructor for class chemaxon.struc.graphics.MRectanglePoint.Sticky

Copy constructor.

STOICHIOMETRY_KEY - Static variable in class chemaxon.standardizer.actions.ExpandAction

Key of type for parsing and property changes

stop() - Method in interface chemaxon.alignment.AlignmentMoleculeFactory.ProgressBarInterface

stop() - Method in class chemaxon.search.AbstractSearch

Tries to stop the running search as fast as possible.

stop() - Method in class chemaxon.search.MolSearch

storageSizeChanged(MDocStorage, int, int) - Method in interface chemaxon.marvin.common.MDocStorage.Listener

Storage size changed.

storageSizeFinalized(MDocStorage) - Method in interface chemaxon.marvin.common.MDocStorage.Listener

Final storage size determined.

store() - Method in class chemaxon.calculations.gui.CalculatorPluginDisplay

Stores a new result item.

storeDoc(MDocument, int, String) - Method in class chemaxon.marvin.common.MDocStorage

Store new document and free the oldest accessed if the number of documents is too much to fit in memory.

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

Puts the given NoStructe into the document.

storeMainDoc(MDocument, int) - Method in class chemaxon.marvin.common.MDocStorage

Store new document and free the oldest accessed if the number of documents is too much to fit in memory.

storeTemporaryObject(String, Object) - Method in class chemaxon.struc.MolAtom

Stores an object temporarily.

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

Represents that straight double bonds have been found in the molecule

StraightDoubleBondChecker - Class in chemaxon.checkers

A descendant of AbstractStructureChecker detecting double bonds in molecule which can be either "E" or "Z".

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

Constructs EitherDoubleBondChecker instance

stringBuffer - Variable in class chemaxon.formats.MolExportModule

This buffer can contain the molecule file contents, in case of a text format.

stringToArray(String, String, int, int) - Static method in class chemaxon.formats.MPropHandler

stringToScalar(String, String) - Static method in class chemaxon.formats.MPropHandler

stringValue() - Method in class chemaxon.struc.prop.MStringProp

Gets the string value.

StripSaltsAction - Class in chemaxon.standardizer.actions

Standardizer action that strips salts from the molecule.

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

Initializes strip salts action

StructuralFrameworksPlugin - Class in chemaxon.calculations

Plugin class to calculate Bemis-Murcko and other structural scaffolds of input molecules.

StructuralFrameworksPlugin() - Constructor for class chemaxon.calculations.StructuralFrameworksPlugin

StructuralFrameworksPlugin.FrameworkTypes - Enum Class in chemaxon.calculations

FrameworkTypes represents the available calculations

StructuralFrameworksPlugin.VerbosePrinter - Interface in chemaxon.calculations

Verbose printer specification

STRUCTURE_KEY - Static variable in class chemaxon.standardizer.actions.TransformAction

Key of query molecule for parsing and property change

StructureChecker - Interface in chemaxon.checkers

General interface describing functions that are available for a chemical structure checker.

StructureCheckerActionStringReader - Class in chemaxon.structurechecker.configuration

Structure Checker configuration reader for parsing action strings.

StructureCheckerActionStringReader(String) - Constructor for class chemaxon.structurechecker.configuration.StructureCheckerActionStringReader

Default constructor

StructureCheckerActionStringReader(String, CheckerFixerFactory) - Constructor for class chemaxon.structurechecker.configuration.StructureCheckerActionStringReader

Constructor with custom checker factory

StructureCheckerActionStringWriter - Class in chemaxon.structurechecker.configuration

Structure Checker configuration writer for action strings.

StructureCheckerActionStringWriter() - Constructor for class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter

StructureCheckerConfigurationReader - Interface in chemaxon.structurechecker.configuration

Configuration reader interface for Structure Checker.

StructureCheckerConfigurationWriter - Interface in chemaxon.structurechecker.configuration

Configuration writer interface for Structure Checker.

StructureCheckerConfigurationXmlReader - Class in chemaxon.structurechecker.configuration

Structure Checker configuration reader for parsing XML configuration files.

StructureCheckerConfigurationXmlReader(InputStream) - Constructor for class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlReader

Initiate an StructureCheckerConfigurationXmlReader instance with the given inputSteam with the configuration

StructureCheckerConfigurationXmlReader(InputStream, CheckerFixerFactory) - Constructor for class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlReader

Initiate an StructureCheckerConfigurationXmlReader instance with the given inputSteam with the configuration

StructureCheckerConfigurationXmlWriter - Class in chemaxon.structurechecker.configuration

Structure Checker configuration writer for XML configuration files.

StructureCheckerConfigurationXmlWriter() - Constructor for class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlWriter

StructureCheckerDescriptor - Class in chemaxon.checkers

Descriptor for StructureChecker

StructureCheckerDescriptor(Class<? extends StructureChecker>) - Constructor for class chemaxon.checkers.StructureCheckerDescriptor

Constructs a descriptor based on checker class.

StructureCheckerErrorType - Enum Class in chemaxon.checkers

Enum containing possible error types for structure checkers.

StructureCheckerMonitor - Interface in chemaxon.structurechecker

Monitor for CheckerRunner.

StructureCheckerResult - Interface in chemaxon.checkers.result

An instance of StructureCheckerResult identifies a molecule problem

StructureFixer - Interface in chemaxon.fixers

A StructureFixer can fix a Molecule problem identified by a StructureCheckerResult

StructureFixerDescriptor - Class in chemaxon.fixers

Descriptor class for StructureFixer classes.

StructureFixerDescriptor(Class<? extends StructureFixer>) - Constructor for class chemaxon.fixers.StructureFixerDescriptor

Constructs a descriptor based on fixer class.

structureFormat - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions

The structure format used to represent hits converted from other sources than names (OSR, embedded structures, ...).

structureFormat(String) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder

styles() - Static method in enum class chemaxon.rendering.constants.AnyBondStyle

Return the rendering style names as string values.

styles() - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle

Return the rendering style names as string values.

styles() - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle

Return the rendering style names as string values.

styles() - Static method in enum class chemaxon.rendering.constants.RenderingStyle

Return the rendering style names as string values.

SUBFORMULA - Static variable in class chemaxon.search.FormulaSearch

Constant value specifying the sub formula search type.

SubjectToRemoval - Annotation Interface in chemaxon.common.annotations

Denotes that an entity has been deprecated and is subject to removal in a release following the specified date.

substring(int) - Method in class chemaxon.struc.graphics.MTextDocument.Section

Gets a substring.

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

Gets a substring of the document.

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

Gets a substring.

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

Gets a substring of the document.

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

Represents that the specified substructure has been found in the molecule

SUBSTRUCTURE - Enum constant in enum class chemaxon.descriptors.MetricsType

SUBSTRUCTURE - Static variable in interface chemaxon.search.api.SearchConstants

Substructure search that applies both screening and atom-by-atom search.

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

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

This error type is not used, will be removed

SubstructureChecker - Class in chemaxon.checkers

This descendant of AbstractStructureChecker is responsible for detecting substructures in a Molecule instance.

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

Default constructor.

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

Parameterized constructor.

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

Parameterized constructor.

SubstructureCheckerResult - Class in chemaxon.checkers.result

Structure checker result for substructure-based checks.

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

Constructor which initialize all the properties.

SubstructureFixer - Class in chemaxon.fixers

Fixer to fix substructure issues.

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

subtract(Point3D) - Method in class chemaxon.struc.Point3D

Subtract the given v2 vector from this one.

subtract(Point3D, Point3D) - Static method in class chemaxon.struc.Point3D

Calculates the difference of the two vectors

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

For internal use only.

sumConservedQuantities(MolAtom, int[], int) - Method in class chemaxon.struc.RgMolecule

For internal use only.

sumDistanceSquare(MoleculeGraph, Point3D) - Static method in class chemaxon.core.calculations.clean.CleanUtil

Calculates the sum of the distance square for each atom from a point.

sumNonEmptyPercent - Variable in class chemaxon.descriptors.MDGenerator

sumOfRadicals() - Method in class chemaxon.calculations.elemental.ElementalAnalysis

Calculates the sum of the radicals of all atoms of the molecule.

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

SuperatomSgroup - Class in chemaxon.struc.sgroup

Superatom S-group.

SuperatomSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Constructs a superatom S-group in expanded state.

SuperatomSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Constructs a superatom S-group.

SuperatomSgroup(SuperatomSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Copy constructor.

superGraph - Variable in class chemaxon.struc.MoleculeGraph

Parent of all parents.

SUPERSTRUCTURE - Enum constant in enum class chemaxon.descriptors.MetricsType

SUPERSTRUCTURE - Static variable in interface chemaxon.search.api.SearchConstants

Superstructure search (Value=6)

support - Variable in class chemaxon.standardizer.AbstractStandardizerAction

SVG - Enum constant in enum class chemaxon.naming.document.DocumentAnnotatorOptions.ImageFormat

SVG - Static variable in class chemaxon.formats.MFileFormat

Scalable Vector Graphics.

swap() - Method in class chemaxon.struc.MolBond

Change orientation.

swapAtoms(int, int) - Method in class chemaxon.struc.SelectionMolecule

Swap two atoms.

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

Swaps the head and tail bonds of a ladder-type polymer if both are set.

SwingUtil - Class in chemaxon.marvin.util

Swing utility functions.

SYBYLMOL - Static variable in class chemaxon.formats.MFileFormat

Tripos SYBYL molfiles.

SYM_CX - Static variable in class chemaxon.struc.MolAtom

Atom symbol string for CxSMILES export.

SYM_EXPLH - Static variable in class chemaxon.struc.MolAtom

Atom symbol string contains explicit H count if this flag is set.

SYM_IMPLH - Static variable in class chemaxon.struc.MolAtom

Atom symbol string contains implicit H count is shown flag is set.

SYM_MOLEX - Static variable in class chemaxon.struc.MolAtom

Atom symbol string for Molfile export.

SYM_NEUTRAL - Static variable in class chemaxon.struc.MolAtom

Atom symbol string does not contain the charge if this flag is set.

SYM_SMARTS - Static variable in class chemaxon.struc.MolAtom

Atom symbol string for SMILES export.

SYM_SQBRACKETS - Static variable in class chemaxon.struc.MolAtom

Atom symbol is shown in square brackets if this flag is set.

symbol() - Method in record class chemaxon.calculations.elemental.FormulaAtom

Returns the value of the symbol record component.

symbolOf(int) - Static method in class chemaxon.struc.MolAtom

Gets the element symbol for the specified atomic number.

symbolOf(int, int) - Static method in class chemaxon.struc.MolAtom

Gets the special element symbol for the specified atomic and mass numbers.

SYN - Static variable in interface chemaxon.struc.StereoConstants

Non-CIP stereodescriptor, syn (relative configuration).

szegedIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer

Calculates the Szeged index of the molecule.

T

T_BRACES - Static variable in class chemaxon.struc.graphics.MBracket: Braces.
T_CHEVRONS - Static variable in class chemaxon.struc.graphics.MBracket: Chevrons.
T_DOUBLE - Static variable in class chemaxon.struc.graphics.MBracket: The bracket has two sides.
T_NOROT - Static variable in class chemaxon.struc.graphics.MRectangle: Disable rotation.
T_ROUND - Static variable in class chemaxon.struc.graphics.MBracket: Round bracket type (parenthesis).
T_SINGLE - Static variable in class chemaxon.struc.graphics.MBracket: The bracket has one side.
T_SQUARE - Static variable in class chemaxon.struc.graphics.MBracket: Square bracket type.
Ta - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ta.
TAB_SCALE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "tabScale".
TableOptions - Class in chemaxon.marvin.common: SDF table options for MarvinView.
TableSupport - Class in chemaxon.marvin.common: Viewer table support class.
TableSupport(ViewPanel) - Constructor for class chemaxon.marvin.common.TableSupport: For internal use only.
TaggedCalculator - Interface in chemaxon.calculations.api: Base interface for calculator objects that can report a set of optional tags, which are used primarily to identify the calculator in configuration files.
TaggedCalculatorInputChecker - Interface in chemaxon.calculations.api: General interface of classes that are used by calculators to check if they can process an input molecule.
tags() - Method in interface chemaxon.calculations.api.TaggedCalculator: Returns the set of tags reported by this calculator.
tags() - Method in class chemaxon.calculations.ConformerPlugin
tags() - Method in class chemaxon.calculations.dipole.DipoleCalculator
tags() - Method in class chemaxon.calculations.GeometryPlugin
tags() - Method in class chemaxon.calculations.HBDAPlugin
tags() - Method in class chemaxon.calculations.IsoelectricPointPlugin
tags() - Method in class chemaxon.calculations.MSAPlugin
tags() - Method in class chemaxon.calculations.nmr.NMRCalculator
tags() - Method in class chemaxon.calculations.PolarizabilityPlugin
tags() - Method in class chemaxon.calculations.ResonancePlugin
tags() - Method in class chemaxon.calculations.solubility.SolubilityCalculator
tags() - Method in class chemaxon.calculations.StereoisomerPlugin: Deprecated.
tags() - Method in class chemaxon.calculations.TautomerPlugin
tags() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the tags of the action as a string, divided by comma characters
TAGS - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: tags of action
TAIL - Static variable in class chemaxon.struc.graphics.MPolyline: Arrow tail (feather).
tanimoto() - Method in class chemaxon.alignment.Alignment: Calculates the atomic colored volume Tanimoto similarity of two 3D molecules.
tanimoto(float[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates Tanimoto dissimilarity for floating point values.
tanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics: Calculates Tanimoto dissimilarity for floating point values.
TANIMOTO - Enum constant in enum class chemaxon.descriptors.MetricsType
target - Variable in class chemaxon.search.api.MolComparator: The target molecule.
TARGET - Static variable in class chemaxon.chemterms.SearchContext
TARGET_LABEL - Static variable in class chemaxon.search.hitdisplay.HitDisplayOptions: Label for the target part of the similarity hit.
TargetHomologyMatchingMode - Enum Class in chemaxon.search.api.options: Option to control homology matching on target side.
TAUTOMER_SEARCH_DEFAULT - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for indicating that tautomer duplicate search option is not explicitly set.
TAUTOMER_SEARCH_OFF - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for switching tautomer searching off.
TAUTOMER_SEARCH_ON - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for switching tautomer searching on.
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.
TautomerEqualityMode - Enum Class in chemaxon.search.api.options: Tautomer equality mode.
TAUTOMERIZATION_CANONICAL - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
TAUTOMERIZATION_DOMINANTS - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
TAUTOMERIZATION_GENERIC - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
TAUTOMERIZATION_MAJOR - Enum constant in enum class chemaxon.calculations.api.CalculatorTag
TautomerizeAction - Class in chemaxon.standardizer.actions: Standardizer action that generates canonical tautomer form of the molecule.
TautomerizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.TautomerizeAction: Initializes the action
TautomerizeAction.TautomerForm - Enum Class in chemaxon.standardizer.actions: Tautomer form to be used by TautomerizeAction.
TautomerPlugin - Class in chemaxon.calculations: Plugin class for generating tautomer structures.
TautomerPlugin() - Constructor for class chemaxon.calculations.TautomerPlugin: Constructor.
TautomerSubstructureMode - Enum Class in chemaxon.search.api.options: Shows the way tautomer substructure search is handled.
TautomerTransformationMode - Enum Class in chemaxon.search.api.options: Tautomer transformation mode.
Tb - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Tb.
Tc - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Tc.
Te - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Te.
tell() - Method in class chemaxon.formats.MolImporter: Returns the current file offset.
TEMPLATE_FILE_KEY - Static variable in class chemaxon.standardizer.actions.Clean2DAction: Key of template file for parsing and property change
TEMPLATE_TOOLBAR_CUSTOMIZABLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "templateToolbarCustomizable".
TEMPLATEBASED - Enum constant in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Template based clean
TEMPLATES - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "tmpls".
TEMPLATES_KEY - Static variable in class chemaxon.standardizer.actions.Clean2DAction: Key for templates property change
testEncoding(String) - Static method in class chemaxon.formats.MFileFormatUtil: Tests whether the given charset name is supported by this JVM
TETRAHEDRAL - Enum constant in enum class chemaxon.calculations.stereo.stereocenters.StereoType: Tetrahedral stereo center.
TETRAHEDRAL - Enum constant in enum class chemaxon.calculations.stereo.StereoisomerSettings.StereoisomerType: Tetrahedral stereoisomers.
TETRAHEDRAL - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoType
TETRAHEDRAL - Static variable in class chemaxon.calculations.StereoisomerPlugin: Deprecated.
TetrahedralStereoCenter - Class in chemaxon.calculations.stereo.stereocenters: Tetrahedral stereo center implementation.
TetrahedralStereoCenter(AtomSelection, CIPStereoValue.TetrahedralStereoIUPACValue) - Constructor for class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter: Constructs a new instance of tetrahedral stereo center.
TetrahedralStereoCenter(AtomSelection, CIPStereoValue.TetrahedralStereoIUPACValue, EnhancedStereo) - Constructor for class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter: Constructs a new instance of tetrahedral stereo center.
TetrahedralStereoCenter(AtomSelection, CIPStereoValue.TetrahedralStereoIUPACValue, EnhancedStereo, List<AttachedData>) - Constructor for class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter: Constructs a new instance of tetrahedral stereo center with attached data.
TetrahedralStereoCenter(AtomSelection, CIPStereoValue.TetrahedralStereoIUPACValue, Optional<EnhancedStereo>, List<AttachedData>) - Constructor for class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter: Constructs a new instance of tetrahedral stereo center with attached data.
tetrahedralStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the tetrahedral stereogenic centers.
tetrahedralStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the tetrahedral stereogenic centers (with attached data).
TetrahedralStereoDescriptor - Class in chemaxon.core.calculations.stereo: Tetrahedral stereo descriptor.
TetrahedralStereoDescriptor(CIPStereoValue.TetrahedralStereoValue, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.TetrahedralStereoDescriptor
TetrahedralStereoDescriptor(CIPStereoValue.TetrahedralStereoValue, StereoActivePart, int) - Constructor for class chemaxon.core.calculations.stereo.TetrahedralStereoDescriptor
TetrahedralStereoIUPACDescriptor - Class in chemaxon.core.calculations.stereo: Tetrahedral stereo descriptor.
TetrahedralStereoIUPACDescriptor(CIPStereoValue.TetrahedralStereoIUPACValue, StereoActivePart) - Constructor for class chemaxon.core.calculations.stereo.TetrahedralStereoIUPACDescriptor
TetrahedralStereoIUPACDescriptor(CIPStereoValue.TetrahedralStereoIUPACValue, StereoActivePart, int) - Constructor for class chemaxon.core.calculations.stereo.TetrahedralStereoIUPACDescriptor
TEXT - Enum constant in enum class chemaxon.marvin.common.CellType
TEXT - Static variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: Property display type: display in text.
TEXT - Static variable in class chemaxon.formats.MolExporter: Use this flag to write text files with OS dependent line separators.
TFINGERPRINT - Static variable in class chemaxon.chemterms.SearchContext
Th - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Th.
theAtoms - Variable in class chemaxon.struc.MoleculeGraph: The atoms (nodes).
theBonds - Variable in class chemaxon.struc.MolAtom: The bonds.
theBonds - Variable in class chemaxon.struc.MoleculeGraph: The bonds (edges).
THICKNESS_SET_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline: Thickness is set flag.
THREE_DIM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that 3D coordinates have been found in the molecule
THREE_LETTER_PEPTIDE_DISPLAY_S - Static variable in interface chemaxon.rendering.constants.DispOptConsts
ThreeDimensionChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting atoms with 3D coordinates (non-zero Z coordinates).
ThreeDimensionChecker() - Constructor for class chemaxon.checkers.ThreeDimensionChecker: Default constructor
thresholds - Variable in class chemaxon.descriptors.MDParameters: dissimilarity thresholds values
Ti - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ti.
TIFF - Static variable in class chemaxon.formats.MFileFormat: Tagged Image File Format.
TIME - Enum constant in enum class chemaxon.calculations.api.CalculatorLogger.Level
timeoutLimitMilliseconds - Variable in class chemaxon.search.api.options.SearchOptions: The search on a single target timeouts reaching this number of milliseconds.
title - Variable in class chemaxon.calculations.gui.CalculatorPluginDisplay: The result frame title.
Tl - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Tl.
Tm - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Tm.
toAnyBondStyle(String) - Static method in enum class chemaxon.rendering.constants.AnyBondStyle
toBinaryString() - Method in class chemaxon.descriptors.ChemicalFingerprint: Converts the fingerprint into a 0,1 string.
toBinaryString() - Method in class chemaxon.descriptors.ECFP: Converts the fingerprint into a fixed-length 0,1 string.
toBinaryString() - Method in class chemaxon.descriptors.MolecularDescriptor: Creates the binary string representation of a MolecularDescriptor object.
toBinaryString() - Method in class chemaxon.descriptors.ReactionFingerprint: Converts the fingerprint into a 0,1 string.
toBinaryString() - Method in class chemaxon.descriptors.ShapeDescriptor
toBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter: Returns a binary representation of the given molecule.
toCoordinateBondStyle(String) - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
toCoordinateBondStyle(String) - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle
toData() - Method in class chemaxon.alignment.AlignmentMolecule: Deprecated.
use ShapeData.toData() instead.
toData() - Method in class chemaxon.alignment.ShapeData: Serializes the current object to a byte array
toData() - Method in class chemaxon.descriptors.BCUT: Converts a BCUT object into a byte array.
toData() - Method in class chemaxon.descriptors.ChemicalFingerprint: Converts a chemical fingerprint object into a byte array.
toData() - Method in class chemaxon.descriptors.CustomDescriptor: Converts a CustomDescriptor object into a byte array.
toData() - Method in class chemaxon.descriptors.ECFP: Converts an ECFP object into a byte array.
toData() - Method in class chemaxon.descriptors.MolecularDescriptor: Converts the internal (memory) representation of a MolecularDescriptor instance into an external format that can be stored in a database.
toData() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Converts a PharmacophoreFingerprint object into a byte array.
toData() - Method in class chemaxon.descriptors.ReactionFingerprint: Converts a reaction fingerprint object into a byte array.
toData() - Method in class chemaxon.descriptors.ScalarDescriptor: Converts a ScalarDescriptor object into an array of bytes.
toData() - Method in class chemaxon.descriptors.ShapeDescriptor
toDecimalString() - Method in class chemaxon.descriptors.BCUT: Converts the BCUT descriptor into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.ChemicalFingerprint: Converts the fingerprint into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.CustomDescriptor: Converts the descriptor into a readable string of decimal numbers (float or integer, depending on descriptor type).
toDecimalString() - Method in class chemaxon.descriptors.ECFP: Converts the ECFP fingerprint into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.MolecularDescriptor: Creates the string representation of a MolecularDescriptor object.
toDecimalString() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Converts the fingerprint into a string of decial numbers.
toDecimalString() - Method in class chemaxon.descriptors.ReactionFingerprint: Converts the fingerprint into a tab separated string.
toDecimalString() - Method in class chemaxon.descriptors.ScalarDescriptor: Converts the descriptor value into a readable string.
toDecimalString() - Method in class chemaxon.descriptors.ShapeDescriptor
toFlag() - Method in enum class chemaxon.rendering.constants.AnyBondStyle
toFlag() - Method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
toFlag() - Method in enum class chemaxon.rendering.constants.CoordinateBondStyle
toFloatArray() - Method in class chemaxon.descriptors.BCUT: Creates the float array representation of a BCUT descriptor object.
toFloatArray() - Method in class chemaxon.descriptors.ChemicalFingerprint: Creates the float array representation of the fingerprint.
toFloatArray() - Method in class chemaxon.descriptors.CustomDescriptor: Creates the float array representation of a CustomDescriptor object.
toFloatArray() - Method in class chemaxon.descriptors.ECFP: Creates the float array representation of a ECFP fingerprint object.
toFloatArray() - Method in class chemaxon.descriptors.MolecularDescriptor: Creates the float array representation of a MolecularDescriptor object.
toFloatArray() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Creates the float array representation of a MolecularDescriptor object.
toFloatArray() - Method in class chemaxon.descriptors.ReactionFingerprint: Creates the float array representation of the fingerprint.
toFloatArray() - Method in class chemaxon.descriptors.ScalarDescriptor: Creates the float array representation of the descriptor.
toFloatArray() - Method in class chemaxon.descriptors.ShapeDescriptor
toFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter: Returns a string representation of the given molecule.
toHistogramString(String, boolean) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Creates the string representation of the fingerprint.
toIdentiferSet() - Method in class chemaxon.descriptors.ECFP: Deprecated, for removal: This API element is subject to removal in a future version.
Use ECFP.toIdentifierSet() instead
toIdentifierSet() - Method in class chemaxon.descriptors.ECFP: Converts the fingerprint to a set of Integer identifiers.
toInt() - Method in enum class chemaxon.rendering.constants.AnyBondStyle
toInt() - Method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
toInt() - Method in enum class chemaxon.rendering.constants.CoordinateBondStyle
toInt() - Method in enum class chemaxon.rendering.constants.RenderingStyle
toIntArray() - Method in class chemaxon.descriptors.ECFP: Converts the fingerprint to an array of int identifiers.
token - Variable in exception class chemaxon.naming.NamePrefixException
toList() - Method in class chemaxon.search.api.options.MolSearchOptions
toList() - Method in class chemaxon.search.api.options.SearchOptions: Returns the text representation of this options object as a list of "optionname:optionvalue" strings.
toMolecule() - Method in interface chemaxon.alignment.AlignmentResult: The two molecules from AlignmentResult.getMolecule1Aligned() and AlignmentResult.getMolecule2Aligned() fused as fragments of a single structure.
toMolecule() - Method in class chemaxon.alignment.MMPAlignmentResult: Creates a single two-fragment molecule from the reference and aligned molecule.
toMolecule() - Method in class chemaxon.alignment.ShapeData
toObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter: Returns a String, byte[] or Image representation of the given molecule.
TOOLBAR_FLOATABLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "toolbarFloatable".
TOOLBAR_TEMPLATES - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "ttmpls".
topLevelContainer - Static variable in class chemaxon.marvin.beans.MarvinPane: The top level container of the pane
toPoint2D() - Method in class chemaxon.struc.Point3D
TOPOLOGY_CHAIN - Static variable in class chemaxon.struc.MolBond: Bond is in a chain.
TOPOLOGY_MASK - Static variable in class chemaxon.struc.MolBond: Bond topology mask.
TOPOLOGY_RING - Static variable in class chemaxon.struc.MolBond: Bond is in a ring.
TopologyAnalysisPlugin - Class in chemaxon.calculations: Calculates topological data.
TopologyAnalysisPlugin() - Constructor for class chemaxon.calculations.TopologyAnalysisPlugin: Constructor.
TopologyAnalyzer - Class in chemaxon.core.calculations: Provides functions for analyzing the topology of a molecule.
TopologyAnalyzer() - Constructor for class chemaxon.core.calculations.TopologyAnalyzer
toProperties() - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Exports this checker into the format defined by HeavyAtomLimitChecker.fromProperties(Properties).
toRenderingStyle(String) - Static method in enum class chemaxon.rendering.constants.RenderingStyle
toString() - Method in class chemaxon.alignment.AlignmentMolecule
toString() - Method in class chemaxon.alignment.DihedralScanResult.BondInfo
toString() - Method in class chemaxon.alignment.DihedralScanResult.ScanStep
toString() - Method in class chemaxon.alignment.Pharmacophore3D
toString() - Method in record class chemaxon.calculations.admet.HergActivityPrediction: Returns a string representation of this record class.
toString() - Method in record class chemaxon.calculations.admet.HergClassPrediction: Returns a string representation of this record class.
toString() - Method in record class chemaxon.calculations.api.HeavyAtomLimitChecker: Returns a string representation of this record class.
toString() - Method in record class chemaxon.calculations.elemental.FormulaAtom: Returns a string representation of this record class.
toString() - Method in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType
toString() - Method in class chemaxon.calculations.nmr.NMRMultiplet
toString() - Method in class chemaxon.calculations.nmr.NMRShift
toString() - Method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
toString() - Method in class chemaxon.calculations.services.DynamicArgument
toString() - Method in class chemaxon.calculations.services.ServiceArgument
toString() - Method in class chemaxon.calculations.services.ServiceDescriptor
toString() - Method in class chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
toString() - Method in class chemaxon.calculations.stereo.ErrorReport
toString() - Method in class chemaxon.calculations.stereo.stereocenters.AtomSelection: Creates a string representation.
toString() - Method in class chemaxon.calculations.stereo.stereocenters.AtropStereoCenter
toString() - Method in class chemaxon.calculations.stereo.stereocenters.AxialStereoCenter
toString() - Method in class chemaxon.calculations.stereo.stereocenters.CisTransStereoCenter
toString() - Method in class chemaxon.calculations.stereo.stereocenters.EnhancedStereoGroup
toString() - Method in class chemaxon.calculations.stereo.stereocenters.TetrahedralStereoCenter
toString() - Method in class chemaxon.calculations.stereo.StereoisomerSettings
toString() - Method in class chemaxon.checkers.AbstractStructureChecker
toString() - Method in class chemaxon.checkers.AtomLabels
toString() - Method in class chemaxon.checkers.AtomQueryPropertyChecker
toString() - Method in class chemaxon.checkers.AttachedDataChecker.DataExclusionList
toString() - Method in enum class chemaxon.checkers.FixMode
toString() - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
toString() - Method in class chemaxon.checkers.StructureCheckerDescriptor
toString() - Method in class chemaxon.checkers.SubstructureChecker
toString() - Method in class chemaxon.core.calculations.stereo.AbstractAtropStereoDescriptor
toString() - Method in class chemaxon.core.calculations.stereo.AbstractAxialStereoDescriptor
toString() - Method in class chemaxon.core.calculations.stereo.AbstractCisTransStereoDescriptor
toString() - Method in class chemaxon.core.calculations.stereo.AbstractTetrahedralStereoDescriptor
toString() - Method in record class chemaxon.core.calculations.stereo.CIPStereoCalculator.CIPStereoCalculatorResult: Returns a string representation of this record class.
toString() - Method in class chemaxon.core.calculations.stereo.StereoActivePart
toString() - Method in class chemaxon.descriptors.BCUT: Converts the descriptor into a readable string.
toString() - Method in class chemaxon.descriptors.BCUTParameters: Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.ChemicalFingerprint: Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.CustomDescriptor: Converts the descriptor into a readable string.
toString() - Method in class chemaxon.descriptors.ECFP: Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.MDParameters: Returns the parameter values in string.
toString() - Method in class chemaxon.descriptors.MolecularDescriptor: Creates the string representation of a MolecularDescriptor object.
toString() - Method in class chemaxon.descriptors.PFParameters: Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.pharmacophore.PSymbols
toString() - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.ReactionFingerprint: Converts the fingerprint into a readable string.
toString() - Method in class chemaxon.descriptors.ScalarDescriptor: Converts the descriptor value into a readable string.
toString() - Method in class chemaxon.descriptors.scalars.HBParameters: Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.scalars.LDParameters: Returns the XML configuration in a string.
toString() - Method in class chemaxon.descriptors.ShapeDescriptor
toString() - Method in class chemaxon.fixers.StructureFixerDescriptor
toString() - Method in class chemaxon.formats.Encoding: Converts the encoding object to string.
toString() - Method in class chemaxon.formats.MFileFormat: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.formats.OptionDescriptor: Overrides Object.toString() to ease debugging.
toString() - Method in record class chemaxon.formats.Recognizer.RecognizerResult: Returns a string representation of this record class.
toString() - Method in class chemaxon.marvin.common.MAction: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.marvin.datatransfer.MarvinTransferable
toString() - Method in class chemaxon.reaction.AtomIdentifier
toString() - Method in enum class chemaxon.rendering.constants.AnyBondStyle
toString() - Method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle
toString() - Method in enum class chemaxon.rendering.constants.CoordinateBondStyle
toString() - Method in enum class chemaxon.rendering.constants.RenderingStyle
toString() - Method in enum class chemaxon.search.api.options.HaltOnErrorOption: Returns the string representation.
toString() - Method in enum class chemaxon.search.api.options.HomologyTranslationOption
toString() - Method in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption
toString() - Method in class chemaxon.search.api.options.SearchOptions: Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
toString() - Method in enum class chemaxon.search.api.options.SetOfSmallestRingsOption
toString() - Method in enum class chemaxon.search.api.options.TargetHomologyMatchingMode
toString() - Method in class chemaxon.search.api.SearchHit
toString() - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns a String representation of this object, which can be used in HitDisplayOptions.setOptions(HitDisplayOptions, String) to fill another HitDisplayOptions object with parameters.
toString() - Method in class chemaxon.standardizer.AbstractSgroupAction
toString() - Method in class chemaxon.standardizer.AbstractStandardizerAction
toString() - Method in class chemaxon.standardizer.actions.AliasToGroupAction
toString() - Method in class chemaxon.standardizer.actions.AromatizeAction
toString() - Method in enum class chemaxon.standardizer.actions.AromatizeAction.Type
toString() - Method in class chemaxon.standardizer.actions.Clean2DAction
toString() - Method in enum class chemaxon.standardizer.actions.Clean2DAction.Type
toString() - Method in class chemaxon.standardizer.actions.ClearStereoAction
toString() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
toString() - Method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
toString() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
toString() - Method in class chemaxon.standardizer.actions.CreateGroupAction
toString() - Method in class chemaxon.standardizer.actions.ExpandAction
toString() - Method in class chemaxon.standardizer.actions.GroupDefinition
toString() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
toString() - Method in class chemaxon.standardizer.actions.MapAction
toString() - Method in class chemaxon.standardizer.actions.MapReactionAction
toString() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
toString() - Method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
toString() - Method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method
toString() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
toString() - Method in class chemaxon.standardizer.actions.RemoveSolventsAction
toString() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
toString() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
toString() - Method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type
toString() - Method in class chemaxon.standardizer.actions.StripSaltsAction
toString() - Method in class chemaxon.standardizer.actions.TautomerizeAction
toString() - Method in class chemaxon.standardizer.actions.TransformAction
toString() - Method in class chemaxon.standardizer.Changes
toString() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
toString() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
toString() - Method in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
toString() - Method in class chemaxon.struc.BicycloStereoDescriptor
toString() - Method in class chemaxon.struc.graphics.MAnalysisBoxTerm
toString() - Method in class chemaxon.struc.graphics.MAtomSetPoint
toString() - Method in class chemaxon.struc.graphics.MElectron
toString() - Method in class chemaxon.struc.graphics.MFont
toString() - Method in class chemaxon.struc.graphics.MMidPoint: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.graphics.MRectanglePoint
toString() - Method in class chemaxon.struc.graphics.MTextAttributes: Returns the string representation of the attributes.
toString() - Method in class chemaxon.struc.graphics.MTextDocument.Portion: Gets the string representation of the portion.
toString() - Method in class chemaxon.struc.graphics.MTextDocument: Gets the string representation of the document.
toString() - Method in class chemaxon.struc.MDocument: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MObject: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MolAtom: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MolBond: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MoleculeGraph: Overrides MoleculeGraph.toString() to ease debugging.
toString() - Method in class chemaxon.struc.MPoint
toString() - Method in class chemaxon.struc.MProp: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.Point3D: Gets a string representation of the point
toString() - Method in class chemaxon.struc.prop.MBooleanProp
toString() - Method in class chemaxon.struc.prop.MByteArrayProp: Create base64 representation of the byte array.
toString() - Method in class chemaxon.struc.prop.MDoubleArrayProp
toString() - Method in class chemaxon.struc.prop.MDoubleProp
toString() - Method in class chemaxon.struc.prop.MFontProp
toString() - Method in class chemaxon.struc.prop.MHashProp
toString() - Method in class chemaxon.struc.prop.MHCoords3DProp
toString() - Method in class chemaxon.struc.prop.MIntegerArrayProp
toString() - Method in class chemaxon.struc.prop.MIntegerProp
toString() - Method in class chemaxon.struc.prop.MListProp
toString() - Method in class chemaxon.struc.prop.MMoleculeProp: String representation of this object: number of atoms, number of bonds.
toString() - Method in class chemaxon.struc.prop.MObjectProp: Create the serialized object base64 string representation.
toString() - Method in class chemaxon.struc.prop.MStringProp: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.RgMolecule: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.RgroupBridgeId
toString() - Method in class chemaxon.struc.RxnMolecule: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.sgroup.AttachmentPoint: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.Sgroup: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.Transform3D: Gets a string representation of the matrix.
toString() - Method in class chemaxon.struc.ValenceCheckOptions
toString() - Method in class chemaxon.structurechecker.CheckerFixerFactory.ClassDescriptor
toString(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Returns a string representation of the group.
toString(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Returns a string representation of the group.
toString(int) - Method in class chemaxon.struc.Sgroup: Gets a string representation of the S-group.
toString(PSymbols) - Method in class chemaxon.descriptors.pharmacophore.PMap: Returns the string representation of the feature map: for each atom the symbols representing the features of the atom are separated by '/' characters and these feature strings are separated by ';' characters.
toString(String) - Method in class chemaxon.search.api.options.SearchOptions: Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
toString(String) - Method in class chemaxon.search.hitdisplay.HitDisplayOptions: Returns a String representation of this object, which can be used in HitDisplayOptions.setOptions(HitDisplayOptions, String) to fill another HitDisplayOptions object with parameters.
toString(String, boolean) - Method in class chemaxon.descriptors.PharmacophoreFingerprint: Creates the string representation of the pharmacophore fingerprint.
toString(Node) - Method in class chemaxon.descriptors.MDParameters: Returns parts of the parameter values in string.
TOWARDS_EITHER_BRIDGE - Static variable in class chemaxon.struc.BicycloStereoDescriptor: Direction of the ligand is not defined, it can be oriented towards both of the bridges (e.g.
TOWARDS_HIGHER_BRIDGE - Static variable in class chemaxon.struc.BicycloStereoDescriptor: The ligand is towards the bridge with the higher index.
TOWARDS_LOWER_BRIDGE - Static variable in class chemaxon.struc.BicycloStereoDescriptor: The ligand is towards the bridge with the lower index.
TOXIC - Enum constant in enum class chemaxon.calculations.admet.HergClass
TPSA - Class in chemaxon.descriptors.scalars: Implements TPSA (Topological Polar Surface Area) value as a scalar descriptor.
TPSA - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction: Topological polar surface area.
TPSA - Enum constant in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Topological polar surface area.
TPSA() - Constructor for class chemaxon.descriptors.scalars.TPSA: Creates a new, empty logD descriptor.
TPSA(ScalarDescriptor) - Constructor for class chemaxon.descriptors.scalars.TPSA: Copy constructor.
TPSA(SDParameters) - Constructor for class chemaxon.descriptors.scalars.TPSA: Creates a new instance according to the parameters given.
TPSA(String) - Constructor for class chemaxon.descriptors.scalars.TPSA: Creates a new instance according to the parameters given.
TPSAPlugin - Class in chemaxon.calculations: Plugin class for TPSA (topological polar surface area) calculation.
TPSAPlugin() - Constructor for class chemaxon.calculations.TPSAPlugin: Constructor.
TRANS - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoValue: Trans stereo value.
TRANS - Static variable in interface chemaxon.struc.StereoConstants: Trans double bond.
transDoubleBonds() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the TRANS double bonds.
transfer - Variable in class chemaxon.marvin.datatransfer.MarvinTransferable: The Transferable which represents the clipboard data.
TRANSFER_BUTTON_ICON - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "transferButtonIcon".
TRANSFER_BUTTON_TEXT - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "transferButtonText".
TRANSFER_BUTTON_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "transferButtonVisible".
TransferableDescriptor - Class in chemaxon.marvin.datatransfer: Data object to store lookup information for MTransferable objects.
TransferableDescriptor(String, String, Integer, Integer, boolean, boolean) - Constructor for class chemaxon.marvin.datatransfer.TransferableDescriptor: Deprecated.
since 5.3.3 new descriptor parameter added.
TransferableDescriptor(String, String, Integer, Integer, boolean, boolean, boolean) - Constructor for class chemaxon.marvin.datatransfer.TransferableDescriptor: Constructs a TransferableDescriptor object.
transform(Molecule) - Method in interface chemaxon.standardizer.ConcurrentStandardizerProcessor.MolTransformer: Transforms and returns the molecule (the transformed input molecule is returned, no new molecule object is created).
transform(Point3D) - Method in class chemaxon.struc.Transform3D: Transforms a point.
transform(Transform3D) - Method in class chemaxon.struc.MDocument: Transforms all object's coordinates.
transform(Transform3D) - Method in class chemaxon.struc.MoleculeGraph: Apply a transformation matrix to the atomic coordinates.
transform(Transform3D) - Method in interface chemaxon.struc.MTransformable: Transformation.
transform(Transform3D) - Method in class chemaxon.struc.NoStructure: Transforms the location of the object
transform(Transform3D) - Method in class chemaxon.struc.prop.MHCoords3DProp: Transforms the coordinates.
transform(Transform3D) - Method in class chemaxon.struc.SelectionMolecule: Apply a transformation matrix to the atomic coordinates.
transform(Transform3D, boolean) - Method in class chemaxon.struc.MolAtom: Apply a transformation matrix to the coordinates.
transform(Transform3D, boolean) - Method in class chemaxon.struc.Molecule: Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.
transform(Transform3D, boolean) - Method in class chemaxon.struc.MoleculeGraph: Apply a transformation matrix to the atomic coordinates.
transform(Transform3D, boolean) - Method in class chemaxon.struc.RgMolecule: Apply a transformation matrix to the atomic coordinates.
transform(Transform3D, boolean) - Method in class chemaxon.struc.RxnMolecule: Apply a transformation matrix to the atomic coordinates and the reaction arrow.
transform(Transform3D, boolean) - Method in class chemaxon.struc.sgroup.SgroupAtom: Apply a transformation matrix to the coordinates.
transform(Transform3D, int) - Method in class chemaxon.struc.MDocument: Transforms all object's coordinates.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Does not perform any operation.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MBracket: Transforms the bracket.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct: Transforms all points.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MEFlowBasePoint: Does not perform any operation.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MMidPoint: Transforms all points.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie: Transforms all points.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MNameTextBox: Transforms all points, scales the arrow head widths and lengths.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MPolyline: Transforms all points, scales the arrow head widths and lengths.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MRectangle: Transforms the rectangle.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MRectanglePoint: Transforms all points.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.graphics.MTextBox: Transforms all points and scales the font size.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.MDocument: Transforms all object's coordinates.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.MObject: Transforms the object.
transform(Transform3D, int, Transform3D) - Method in class chemaxon.struc.MPoint: Transforms all points.
transform(Transform3D, Transform3D, int, Transform3D) - Method in class chemaxon.struc.MDocument: Transforms all object's coordinates.
TRANSFORM_DISTORT - Static variable in class chemaxon.struc.MObject: Distorting transformations are allowed.
Transform3D - Class in chemaxon.struc: Transformation matrix in three-dimensional space.
Transform3D() - Constructor for class chemaxon.struc.Transform3D: Constructs an identity transformation.
Transform3D(Transform3D) - Constructor for class chemaxon.struc.Transform3D: Copy constructor.
TransformAction - Class in chemaxon.standardizer.actions: Standardizer action that applies a specified transformation to the molecule.
TransformAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.TransformAction: Initializes the action with parameters
TRANSFORMATION_ENABLED - Static variable in class chemaxon.marvin.common.SketchParameterConstants
transformByParent(Transform3D, boolean) - Method in class chemaxon.struc.sgroup.DataSgroup: Applies a transformation matrix to the Data Sgroup coordinates.
transformByParent(Transform3D, boolean) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Applies a transformation matrix to the Sgroup coordinates.
transformByParent(Transform3D, boolean) - Method in class chemaxon.struc.Sgroup: Applies a transformation matrix to the coordinates.
transformCT(MolAtom, MolAtom, int) - Method in class chemaxon.struc.MolBond: Transform cis/trans stereo information into the `reference frame' of this bond.
transformReactionArrow(Transform3D) - Method in class chemaxon.struc.RxnMolecule: Apply a transformation matrix to the reaction arrow.
transformTo2D() - Method in class chemaxon.struc.graphics.MRectangle: Rotate to the XY plane.
TRANSLATE_ROTATE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.DegreeOfFreedomType: Translate and rotate only as a rigid body.
TRANSLATE_ROTATE_FLEXIBLE - Enum constant in enum class chemaxon.alignment.AlignmentProperties.DegreeOfFreedomType: Translate and rotate, and tweak rotatable bonds to adapt conformation.
TRANSLATE_ROTATE_FLEXIBLE_EXTRA - Enum constant in enum class chemaxon.alignment.AlignmentProperties.DegreeOfFreedomType: As of AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).
TRIPLE - Enum constant in enum class chemaxon.struc.BondType: Triple bond type.
TRIPLE - Static variable in class chemaxon.struc.MolBond: Triple bond type.
tripletIndex(int, int, int) - Method in class chemaxon.descriptors.PFParameters: Calculates the index of a feature pair and distance triplet in the linearised representation of histograms.
TRIVALENT - Enum constant in enum class chemaxon.struc.Radical: Trivalent radical center.
TRIVALENT_DOUBLET - Enum constant in enum class chemaxon.struc.Radical: Trivalent radical center with doublet electronic configuration.
TRIVALENT_QUARTET - Enum constant in enum class chemaxon.struc.Radical: Trivalent radical center with quartet electronic configuration.
TRUE - Static variable in class chemaxon.calculations.CalculatorPlugin
TRUE - Static variable in class chemaxon.chemterms.ChemTermsExpression: Logical result value: TRUE.
TRUE - Static variable in interface chemaxon.chemterms.CustomFunction: Possible result with the value of 1.0.
tryToRecognize(String, int) - Method in class chemaxon.formats.Recognizer: Checks whether the parameter line can be part of a valid (format-specified) file on the given file position.
Ts - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Ts.
tversky(float[], float, float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates Tversky dissimilarity for floating point values.
tversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates Tversky dissimilarity index for integer values.
TVERSKY - Enum constant in enum class chemaxon.descriptors.MetricsType
tverskyA - Variable in class chemaxon.descriptors.MDParameters: alpha values for tversky dissimilarity
tverskyB - Variable in class chemaxon.descriptors.MDParameters: beta values for tversky dissimilarity
twicesumbonds(boolean, boolean) - Method in class chemaxon.struc.MolAtom: Calculates the total number of bonding electrons, excluding implicit hydrogens.
TWO_HEADED_DOUBLE - Static variable in class chemaxon.struc.RxnMolecule: Two headed double reaction arrow type.
TWO_HEADED_SINGLE - Static variable in class chemaxon.struc.RxnMolecule: Two headed single reaction arrow type.
TXT - Enum constant in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType
type - Variable in class chemaxon.calculations.services.ServiceArgument: type of the argument
TYPE - Static variable in class chemaxon.naming.document.DocumentToStructure: Molecule property key on results: the type of source for the structure.
TYPE_3D_COORDS - Static variable in class chemaxon.struc.MProp
TYPE_ARRAY_BYTE - Static variable in class chemaxon.struc.MProp
TYPE_ARRAY_DOUBLE - Static variable in class chemaxon.struc.MProp
TYPE_ARRAY_INTEGER - Static variable in class chemaxon.struc.MProp
TYPE_BOOLEAN - Static variable in class chemaxon.struc.MProp
TYPE_CAS - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a CAS Registry Number^®.
TYPE_CDX - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is an embedded ChemDraw structure.
TYPE_COLLECTION_HASH - Static variable in class chemaxon.struc.MProp
TYPE_COLLECTION_LIST - Static variable in class chemaxon.struc.MProp
TYPE_COMMON - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a common name.
TYPE_COUNT - Static variable in class chemaxon.struc.RxnMolecule: Number of structure types.
TYPE_DISTR - Static variable in class chemaxon.calculations.IsoelectricPointPlugin: Type constant for microspecies distribution.
TYPE_DISTR - Static variable in class chemaxon.calculations.PkaPlugin: Type constant for microspecies distribution.
TYPE_DOUBLE - Static variable in class chemaxon.struc.MProp
TYPE_EC - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is an EC Number.
TYPE_FONT - Static variable in class chemaxon.struc.MProp
TYPE_GENERIC - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a generic name, for instance "C1-C4 alkyl".
TYPE_INCHI - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is an InChI string.
TYPE_INTEGER - Static variable in class chemaxon.struc.MProp
TYPE_ION - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is an ion abbreviation, for instance K+ or Ca2+.
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.AromatizeAction: Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.Clean2DAction: Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.ClearStereoAction: Key of type for parsing
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.ConvertDoubleBondsAction: Key of type for parsing and property change
TYPE_KEY - Static variable in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction: Key of type for parsing and property change
TYPE_MASK - Static variable in class chemaxon.struc.MolBond: The lowest bits of the flags that store the bond type.
TYPE_MASK - Static variable in class chemaxon.struc.RxnMolecule: Component type mask.
TYPE_MDOCUMENT_PROP - Static variable in class chemaxon.struc.MProp
TYPE_MOLECULE - Static variable in class chemaxon.struc.MProp
TYPE_MRV - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is an embedded Chemaxon MRV structure.
TYPE_OBJECT - Static variable in class chemaxon.struc.MProp
TYPE_OSR - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a structure image recognized by Optical Structure Recognition.
TYPE_PEPTIDE - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a peptide notation, for instance Val-Gly-Ser-Ala.
TYPE_SMILES - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a SMILES string.
TYPE_STRING - Static variable in class chemaxon.struc.MProp
TYPE_SYMYX - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is an embedded Symyx/ISIS draw structure.
TYPE_SYSTEMATIC - Static variable in class chemaxon.naming.document.DocumentToStructure: Possible value for the DocumentToStructure.TYPE property: the source is a systematic name.
typeLabel(int) - Method in class chemaxon.alignment.NodeColor.ExtendedAtomColoring
typeLabel(int) - Method in class chemaxon.alignment.NodeColor: Returns a label for the given type based on the coloring scheme.
typeLabel(int) - Static method in class chemaxon.alignment.Pharmacophore3D
types - Variable in class chemaxon.checkers.AtomTypeChecker: A List of String which represents the types should be checked in the molecule
Typical usage: - Search tag in class chemaxon.descriptors.ChemicalFingerprint: Section

U

U - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element U.
UI_DISABLED_GROUP_TYPES - Static variable in class chemaxon.marvin.common.SketchParameterConstants
UNBALANCED_REACTION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the reactions scheme has more atoms on one side of the reaction arrow than on the other
UnbalancedReactionChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting reaction schemes having more atoms on one side of the reaction arrow than on the other.
UnbalancedReactionChecker() - Constructor for class chemaxon.checkers.UnbalancedReactionChecker: Creates a new UnbalancedReactionChecker instance.
UNDECIDED - Static variable in class chemaxon.chemterms.ChemTermsExpression: Logical result value: UNDECIDED.
UNDECIDED - Static variable in interface chemaxon.chemterms.CustomFunction: Special result value which will propagate through the call chain of Chemical Terms functions and will be returned by the methods of ChemTermsExpression.
UNDEF_R_MATCHING_ALL - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
UNDEF_R_MATCHING_GROUP - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
UNDEF_R_MATCHING_GROUP_H - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
UNDEF_R_MATCHING_GROUP_H_EMPTY - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
UNDEF_R_MATCHING_UNDEF_R - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant.
UndefinedSolubilityCategory() - Constructor for class chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
UNDETACH_BY_X - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "undetachByX".
undo() - Method in class chemaxon.marvin.beans.MSketchPane: Invokes an undo command.
UNDO - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "undo".
UngroupFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which ungroups all abbreviated groups in the molecule
UngroupFixer() - Constructor for class chemaxon.fixers.UngroupFixer
ungroupSgroup(int, int) - Method in class chemaxon.struc.Molecule: Deprecated.
as of Marvin 6.3. use Molecule.ungroupSgroup(Sgroup) instead.
ungroupSgroup(Sgroup) - Method in class chemaxon.struc.Molecule: Ungroups the specified S-group and expands it if it is an Expandable S-group.
ungroupSgroup(Sgroup, int) - Method in class chemaxon.struc.Molecule: Expand and ungroup the specified S-group.
ungroupSgroups() - Method in class chemaxon.struc.Molecule: Expands and ungroups all S-groups.
ungroupSgroups(EnumSet<SgroupType>) - Method in class chemaxon.struc.Molecule: Ungroups all S-groups of the specified types in this molecule.
UngroupSgroupsAction - Class in chemaxon.standardizer.actions: Standardizer action that ungroups S-groups of the molecule.
UngroupSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.UngroupSgroupsAction: Initializes the action
unhighlight(MObject) - Method in class chemaxon.struc.MDocument: Unhighlights an object.
unhighlightAll() - Method in class chemaxon.struc.MDocument: Unhighlights all objects.
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoValue
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoValue
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoValue: Unknown stereo value.
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue
UNKNOWN - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoValue
unknownAtropStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the UNKNOWN atrop stereocenters.
unknownAxialStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the UNKNOWN axial stereocenters.
unknownResolvedStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the unknown, resolved tetrahedral stereogenic centers.
unknownResolvedStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the unknown, resolved tetrahedral stereogenic centers (with attached data).
unmap(Molecule) - Static method in class chemaxon.reaction.mapper.AutoMapper: Remove atom maps from the given structure
UnmapAction - Class in chemaxon.standardizer.actions: Standardizer action that removes atom map numbers from the molecule.
UnmapAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.UnmapAction: Initializes the action
unorderedIterator() - Method in class chemaxon.struc.prop.MCollectionProp: Gets an unordered iterator for the entries.
unorderedIterator() - Method in class chemaxon.struc.prop.MHashProp: Gets an iterator for the entries.
unorderedIterator() - Method in class chemaxon.struc.prop.MListProp: Gets an iterator for the entries.
unresolvedStereoCenters() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the unresolved tetrahedral stereogenic centers.
unresolvedStereoCentersWithAttachedData() - Method in class chemaxon.calculations.stereo.StereoAnalysis: Calculates the unresolved tetrahedral stereogenic centers (with attached data).
unRgroupAtoms(Set<?>) - Method in class chemaxon.struc.RgMolecule: Ungroup R-groups consisting of the specified atoms and make them be part of root.
unselectContents() - Method in class chemaxon.struc.graphics.MChemicalStruct: Unselects atoms.
unselectContents() - Method in class chemaxon.struc.graphics.MMoleculeMovie: Unselects atoms.
unselectContents() - Method in class chemaxon.struc.graphics.MPolyline: Unselects the points.
unselectContents() - Method in class chemaxon.struc.graphics.MTextBox: Unselects text.
unselectContents() - Method in class chemaxon.struc.MObject: Unselects sub-objects.
unSelectInDocument(MDocument) - Static method in class chemaxon.struc.NoStructure: Removes the selection from all NoStructure labels in the document.
UNSPECIFIED_AROMATICITY - Static variable in class chemaxon.struc.MolAtom: Atom aromaticity is not specified explicitly.
UNSUPPORTED - Enum constant in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType
UnsupportedQueryException - Exception Class in chemaxon.search.api: Exception class which helps to differentiate query problems from others.
UnsupportedQueryException(String) - Constructor for exception class chemaxon.search.api.UnsupportedQueryException
UnsupportedQueryException(String, Exception) - Constructor for exception class chemaxon.search.api.UnsupportedQueryException
UNUSED_RGROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that the molecule contains unused R-group definitions
UnusedRGroupChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting unused R-group definitions.
UnusedRGroupChecker() - Constructor for class chemaxon.checkers.UnusedRGroupChecker: Initializes the checker
UP - Static variable in class chemaxon.struc.MolBond: Single bond up flag.
updateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Deprecated.
as of Marvin 6.2, use SuperatomSgroup.calculateAttachmentPoints() instead
updateBoundingRect(double[], Transform3D) - Method in class chemaxon.struc.graphics.MBracket
updateBoundingRect(double[], Transform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
updateBoundingRect(double[], Transform3D) - Method in class chemaxon.struc.graphics.MPolyline: Calculate the bounding rectangle.
updateBoundingRect(double[], Transform3D) - Method in class chemaxon.struc.graphics.MReactionSign
updateBoundingRect(double[], Transform3D) - Method in class chemaxon.struc.MObject: Calculate the bounding rectangle.
updateBoundingRect(double[], Transform3D, double) - Method in class chemaxon.struc.MObject: Calculate the bounding rectangle.
updateComponentRoles() - Method in class chemaxon.struc.RxnMolecule: Updates fragment roles in the molecule.
updateDifLoc(Point3D) - Method in class chemaxon.struc.graphics.MElectron
updateDifLoc(Point3D[]) - Method in class chemaxon.struc.graphics.MElectronContainer
updateDim(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph: Updates the dimensions when fusing two structures.
updateFields(MDocument) - Method in class chemaxon.marvin.common.TableOptions: Update fields of SDF table
updateFields(MDocument[]) - Method in class chemaxon.marvin.common.TableOptions: Update fields of SDF table
updateStatistics(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator: Updates statistics gathered on fingerprints generated.
updateStatistics(MolecularDescriptor) - Method in class chemaxon.descriptors.ShapeGenerator
updateSubLevel(double[], double, int) - Method in class chemaxon.struc.graphics.MTextDocument
URL - Static variable in class chemaxon.calculations.services.ServiceDescriptor: Property key for service URL as String
Usage: - Search tag in class chemaxon.alignment.AtropIsomerDetector: Section
USE_DEFAULT_SALTS_KEY - Static variable in class chemaxon.standardizer.actions.StripSaltsAction: Property key for use default salts modification
USE_DEFAULT_SOLVENTS_KEY - Static variable in class chemaxon.standardizer.actions.RemoveSolventsAction: Property key for use default solvent modification
USE_DO_LABEL - Static variable in class chemaxon.marvin.common.MAction: Use short `do' label instead of name for the created menu item.
USE_WARNINGS - Static variable in class chemaxon.marvin.common.ParameterConstants: Constant key to set wether the user wants to see warnings or not.
USE_WHAT_LABEL - Static variable in class chemaxon.marvin.common.MAction: Use short `what' label instead of name for the created menu item.
useCorrectionLibrary(boolean) - Method in class chemaxon.calculations.PkaPlugin: Deprecated.
Use PkaPlugin.setCorrectionLibrary(String)
USED_JARS - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "usedJars".
USEFUL - Static variable in class chemaxon.search.api.MolComparator: Describes that the MolComparator should be used with the current search object and the current query, regardless of the target.
useOnlyFirstAtomInStereoCalculation - Variable in class chemaxon.struc.MoleculeGraph
useOnlyFirstAtomInStereoCalculation(boolean) - Method in class chemaxon.struc.MoleculeGraph: Set how the parity module should interpret wedges.
useOpticalCharacterRecognition - Variable in class chemaxon.naming.document.DocumentAnnotatorOptions: Whether to use Optical Character Recognition on images.
useOpticalCharacterRecognition(Boolean) - Method in class chemaxon.naming.document.DocumentAnnotatorOptions.Builder
usePopups(boolean) - Method in class chemaxon.naming.document.DocumentAnnotator
USER_DEFINED - Enum constant in enum class chemaxon.calculations.LogPMethod: User defined logP calculation method.
USER_DEFINED_CHECKERCONFIG_XML - Static variable in class chemaxon.structurechecker.CheckerFixerFactory: Users checker configuration file name
USER_DEFINED_STANDARDIZERCONFIG_XML - Static variable in class chemaxon.standardizer.StandardizerActionFactory: Users standardizer action configuration file name
USER_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.StandardizerConfigurationReader: path to user-defined standardizer action configuration list
UserSettings - Class in chemaxon.marvin.common: Represents the settings of the MarvinSketch and MarvinView applications.
UserSettings() - Constructor for class chemaxon.marvin.common.UserSettings: Construct a UserSettings object based on the default configuration, and the marvin.properties file stored in the chemaxon settings directory in the home directory of the user.
UserSettings(UserSettings) - Constructor for class chemaxon.marvin.common.UserSettings: Copy consturctor.
UserSettings(InputStream) - Constructor for class chemaxon.marvin.common.UserSettings
UserSettings(String) - Constructor for class chemaxon.marvin.common.UserSettings: Construct a UserSettings object based on the default configuration, and the file stored in the chemaxon settings directory in the home of the user.

V

V - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element V.
VAGUE_BOND_DEFAULT - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant for vague bond level HALF.
VAGUE_BOND_LEVEL_HALF - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1.
VAGUE_BOND_LEVEL1 - Static variable in interface chemaxon.search.api.SearchConstants: Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries.
VAGUE_BOND_LEVEL2 - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search.
VAGUE_BOND_LEVEL3 - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search.
VAGUE_BOND_LEVEL4 - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search.
VAGUE_BOND_OFF - Static variable in interface chemaxon.search.api.SearchConstants: Option value constant to disable vague bond matching.
VALENCE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that valence errors have been found in the molecule
VALENCE_CHECK - Static variable in class chemaxon.struc.MoleculeGraph: Valence check calculation bit in flags.
VALENCE_CHECK_ENABLED - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "valenceCheckEnabled".
VALENCE_CHECKED - Static variable in class chemaxon.struc.MolAtom: Valence checked if this flag is set.
VALENCE_ERROR - Static variable in class chemaxon.struc.MolAtom: The atom has valence error if this flag is set.
VALENCE_ERROR_VISIBLE - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "valenceErrorVisible".
VALENCE_ERROR_VISIBLE_IN_VIEW - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "valenceErrorVisibleInView".
VALENCE_PROP_VISIBILITY_FLAG - Static variable in interface chemaxon.rendering.constants.DispOptConsts: Show valence settings flag.
VALENCE_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that atoms with specified valence properties have been found in the molecule
VALENCE_PROPERTY_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "valencePropertyVisible".
valenceCheck() - Method in class chemaxon.struc.MolAtom: Valence checking.
valenceCheck() - Method in class chemaxon.struc.MoleculeGraph: Check valence and query property errors for atoms.
valenceCheck(List<MolAtom>) - Method in class chemaxon.struc.MoleculeGraph: Check valence and query property errors.
ValenceCheckOptions - Class in chemaxon.struc: Provides options for valence calculation.
ValenceCheckOptions.Builder - Class in chemaxon.struc: Builder for ValenceCheckOptions.
VALENCEERROR_H - Static variable in class chemaxon.struc.MolAtom: Hydrogen atom(s) connected to an atom which have valence error.
ValenceErrorChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting atoms with invalid valences.
ValenceErrorChecker() - Constructor for class chemaxon.checkers.ValenceErrorChecker: Default constructor
ValenceErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ValenceErrorChecker: Parameterized constructor.
ValenceFilter - Class in chemaxon.core.util: Molecule filter that excludes molecules having valence errors.
ValenceFilter() - Constructor for class chemaxon.core.util.ValenceFilter
ValenceFixer - Class in chemaxon.fixers: A descendant of AbstractStructureFixer which fixes valence problem in the molecule if it is possible with removing explicit hydrogens or by adding charge
ValenceFixer() - Constructor for class chemaxon.fixers.ValenceFixer
ValencePropertyChecker - Class in chemaxon.checkers: A descendant of AtomChecker detecting atoms having an explicitly set valence property.
ValencePropertyChecker() - Constructor for class chemaxon.checkers.ValencePropertyChecker: Creates a new ValencePropertyChecker instance.
ValencePropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ValencePropertyChecker: Creates a new ValencePropertyChecker instance.
value - Variable in class chemaxon.calculations.services.ServiceArgument: value of the argument
value() - Method in record class chemaxon.calculations.admet.HergActivityPrediction: Returns the value of the value record component.
value() - Method in record class chemaxon.calculations.admet.HergClassPrediction: Returns the value of the value record component.
value() - Method in class chemaxon.calculations.bbb.BBB.Property
value() - Method in class chemaxon.calculations.cnsmpo.CnsMpo.Property
value() - Element in annotation interface chemaxon.chemterms.ChemTermsContext.ProvidesFunctionContainer
value() - Element in annotation interface chemaxon.fixers.Fixes: The error type values
value() - Element in annotation interface chemaxon.fixers.FixesExternal: The error code values
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentAccuracyMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.ColoringScheme: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.ColorNotSpecifiedCase: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.DegreeOfFreedomType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.NodeType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.OrientationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties.ProximityPotentialType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AlignmentProperties: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.alignment.AtropIsomerDetector.Accuracy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.admet.HergClass: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.api.CalculatorLogger.Level: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.api.CalculatorTag: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.bbb.BBBFunction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.dipole.DipoleResult.Unit: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.elemental.FormulaGenerationRule: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.LogPMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRErrorClassification: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.PkaTrainingResult.PkaType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.services.JsonServiceDescriptor.Method: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.solubility.SolubilityUnit: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.stereo.stereocenters.EnhancedStereoType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.stereo.stereocenters.StereoType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.stereo.StereoisomerSettings.StereoisomerType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.CheckerSeverity: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.FixMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.checkers.StructureCheckerErrorType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.common.annotations.RemovalDate: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoValue: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.descriptors.MetricsType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.marvin.common.CellType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.naming.document.DocumentAnnotatorOptions.ImageFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.reaction.mapper.ReactionMapper.MappingStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.rendering.constants.AnyBondStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.rendering.constants.RenderingStyle: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.HaltOnErrorOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.HomologyTranslationOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.SetOfSmallestRingsOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.TargetHomologyMatchingMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.TautomerEqualityMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.TautomerSubstructureMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.api.options.TautomerTransformationMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.mcs.McsSearchMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.search.mcs.RingHandlingMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.BondType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.EZConfiguration: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.Radical: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class chemaxon.struc.SgroupType: Returns the enum constant of this class with the specified name.
values() - Static method in enum class chemaxon.alignment.AlignmentAccuracyMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.ColoringScheme: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.ColorNotSpecifiedCase: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.DegreeOfFreedomType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.FlexibilityMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.NodeType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.OrientationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties.ProximityPotentialType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AlignmentProperties: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.alignment.AtropIsomerDetector.Accuracy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.admet.HergClass: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.api.CalculatorLogger.Level: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.api.CalculatorTag: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.bbb.BBBFunction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.dipole.DipoleResult.Unit: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.elemental.FormulaGenerationRule: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.ElementalAnalysisPlugin.ResultType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.LogPMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.nmr.NMRErrorClassification: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.nmr.NMRSpectrum.Unit: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.PkaTrainingResult.PkaType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.services.JsonServiceDescriptor.Method: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.solubility.DefaultSolubilityCategory: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.solubility.SolubilityUnit: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.stereo.stereocenters.EnhancedStereoType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.stereo.stereocenters.StereoType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.stereo.StereoisomerSettings.StereoisomerType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.calculations.StructuralFrameworksPlugin.FrameworkTypes: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.CheckerSeverity: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.FixMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.checkers.StructureCheckerErrorType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.common.annotations.RemovalDate: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoValue: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.descriptors.MetricsType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.marvin.common.CellType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.naming.document.DocumentAnnotatorOptions.ImageFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.reaction.mapper.ReactionMapper.MappingStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.rendering.constants.AnyBondStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.rendering.constants.CoordinateBondOnMulticenterStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.rendering.constants.CoordinateBondStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.rendering.constants.RenderingStyle: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.HaltOnErrorOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.HomologyTranslationOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.MarkushAromaticityHandlingOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.SetOfSmallestRingsOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.TargetHomologyMatchingMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.TautomerEqualityMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.TautomerSubstructureMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.api.options.TautomerTransformationMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.mcs.McsSearchMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.search.mcs.RingHandlingMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.AromatizeAction.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.Clean2DAction.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Method: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.BondType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.EZConfiguration: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.Radical: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class chemaxon.struc.SgroupType: Returns an array containing the constants of this enum class, in the order they are declared.
VAN_DER_WAALS - Static variable in class chemaxon.calculations.MSAPlugin: Surface area type: 3D van der Waals surface area.
VARARG - Static variable in interface chemaxon.chemterms.ChemTermsContext: A possible value for ChemTermsContext.ProvidesFunction.maxParameterCount(), signaling that there is no maximum.
VARARG - Static variable in interface chemaxon.chemterms.CustomFunction: The multiplicity that marks a function vararg.
verbose - Variable in class chemaxon.search.api.options.SearchOptions: For debugging purposes.
verbose(Object) - Method in interface chemaxon.calculations.StructuralFrameworksPlugin.VerbosePrinter: Log a verbose message
verify3d() - Method in class chemaxon.calculations.stereo.StereoisomerSettings: Returns true if 3D structure will be checked for a valid stereo conformation.
verifyParameters() - Method in interface chemaxon.calculations.gui.ParameterPanelHandler: Verifies parameters on the parameter panel.
VERSION - Static variable in class chemaxon.marvin.beans.MarvinPane: Marvin version.
VersionInfo - Class in chemaxon.common.version: Provides version information of Chemaxon products.
VersionInfo() - Constructor for class chemaxon.common.version.VersionInfo
VH_AUTO - Static variable in class chemaxon.marvin.common.TableOptions: Automatic view selection.
VH_GRIDBAG - Static variable in class chemaxon.marvin.common.TableOptions: Molecule matrix view.
VH_SPREADSHEET - Static variable in class chemaxon.marvin.common.TableOptions: Record oriented view.
VIEW_ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "viewAnyBond".
VIEW_CARBON_VISIBILITY - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "viewCarbonVisibility".
VIEW_HELP - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "viewHelp".
VIEW_LIGAND_ORDER_VISIBILITY - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "viewLigandOrderVisibility".
VIEW_NAVIGATION_MODE_2D - Static variable in class chemaxon.marvin.common.ParameterConstants
VIEW_NAVIGATION_MODE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
VIEW_ONLY - Static variable in class chemaxon.marvin.beans.MViewPane: Editing mode identifier meaning the structures cannot be edited.
VIEW_ONLY - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "viewonly".
VIEW_PANEL_LAST_HEIGHT - Static variable in class chemaxon.marvin.common.ViewParameterConstants
VIEW_PANEL_LAST_WIDTH - Static variable in class chemaxon.marvin.common.ViewParameterConstants
ViewParameterConstants - Class in chemaxon.marvin.common: Parameters of MViewPane.
VISIBLE_COLS - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "visibleCols".
VISIBLE_ROWS - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "visibleRows".
visitAt(AtropStereoCenter) - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenterVisitor: Visits atrop stereo centers.
visitAx(AxialStereoCenter) - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenterVisitor: Visits axial stereo centers.
visitCT(CisTransStereoCenter) - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenterVisitor: Visits cis-trans stereo centers.
visitTH(TetrahedralStereoCenter) - Method in interface chemaxon.calculations.stereo.stereocenters.StereoCenterVisitor: Visits tetrahedral stereo centers.
VMN - Static variable in class chemaxon.formats.MFileFormat

W

W - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element W.
WARNING - Enum constant in enum class chemaxon.calculations.api.CalculatorLogger.Level
WARNING - Enum constant in enum class chemaxon.checkers.CheckerSeverity: This severity level should be used for StructureChecker implementations that search for problematic features in a Molecule.
warningMsgOn - Static variable in class chemaxon.calculations.TautomerPlugin
WAVY - Static variable in class chemaxon.struc.MolBond: Single bond wavy flag.
WedgeCleanAction - Class in chemaxon.standardizer.actions: Standardizer action that rearranges the wedge bond representations of the molecule.
WedgeCleanAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.WedgeCleanAction: Initializes the action
WEDGED_H - Static variable in class chemaxon.struc.MolAtom: Hydrogen atom(s) with wedge bonds.
WEIGHT - Static variable in class chemaxon.alignment.MinMaxDistance
weightedAsymmetricEuclidean(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric Euclidean distance.
weightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric Euclidean distance.
weightedAsymmetricNormalizedEuclidean(float[], float[], float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric normalized Euclidean distance.
weightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted asymmetric normalized Euclidean distance.
weightedEuclidean(float[], float[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted Euclidean distance.
weightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted Euclidean distance.
weightedNormalizedEuclidean(float[], float[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted normalized Euclidean distance.
weightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics: Calculates the weighted normalized Euclidean distance.
weights - Variable in class chemaxon.descriptors.MDParameters: weights for parametrized metrics
wienerIndex() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
wienerPolarity() - Method in class chemaxon.core.calculations.TopologyAnalyzer: Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.
WIGGLY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that wiggly bonds have been found in the molecule
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoIUPACValue
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AtropStereoValue
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoIUPACValue
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.AxialStereoValue
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoValue: Wiggly stereo value, that is, CIS or TRANS.
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoIUPACValue
WIGGLY - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.TetrahedralStereoValue
WIGGLY - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type: Wiggly double bond type
WIGGLY_BOND_TETRAHEDRAL - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType: Represents that wiggly bonds on tetrahedral stereo centers have been found in the molecule
WigglyBondChecker - Class in chemaxon.checkers: A descendant of AbstractStructureChecker detecting wiggly bonds on tetrahedral stereo centers.
WigglyBondChecker() - Constructor for class chemaxon.checkers.WigglyBondChecker: Initializes a wiggly bond checker
WigglyDoubleBondChecker - Class in chemaxon.checkers: A descendant of BondChecker detecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.
WigglyDoubleBondChecker() - Constructor for class chemaxon.checkers.WigglyDoubleBondChecker: Default constructor
WINDOW_SCALE - Static variable in class chemaxon.marvin.common.ViewParameterConstants: Identifier of parameter: "winScale".
WIRE_THICKNESS - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier of parameter: "wireThickness".
WIREFRAME - Enum constant in enum class chemaxon.rendering.constants.RenderingStyle: Wireframe rendering style.
withoutAnchorLabel(int) - Method in class chemaxon.alignment.NodeColor: Returns the type without the anchor label if it is an anchor type.
withoutType(int, int) - Static method in class chemaxon.alignment.Pharmacophore3D
wordLength() - Method in class chemaxon.formats.Encoding: Gets the word length in bytes.
wrapTextAndSetActualPoints(Transform3D, double) - Method in class chemaxon.struc.graphics.MReactionSign
wrapTextAndSetActualPoints(Transform3D, double) - Method in class chemaxon.struc.graphics.MTextBox
write(Molecule) - Method in class chemaxon.formats.MolExporter: Writes a molecule into the stream.
write16doubles(ObjectOutput) - Method in class chemaxon.struc.Transform3D: Writes the 4x4 matrix components as double precision floating point numbers.
write16floats(ObjectOutput) - Method in class chemaxon.struc.Transform3D: Writes the 4x4 matrix components as single precision floating point numbers.
writeConfiguration(StandardizerConfiguration, OutputStream) - Method in class chemaxon.standardizer.configuration.StandardizerActionStringWriter
writeConfiguration(StandardizerConfiguration, OutputStream) - Method in interface chemaxon.standardizer.configuration.StandardizerConfigurationWriter: Writes the target configuration to output stream
writeConfiguration(StandardizerConfiguration, OutputStream) - Method in class chemaxon.standardizer.configuration.StandardizerConfigurationXmlWriter
writeConfiguration(OutputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory: Writes the factory configuration to the output stream
writeConfiguration(OutputStream) - Method in class chemaxon.structurechecker.CheckerFixerFactory: Writes the factory configuration to the output stream
writeConfiguration(List<StructureChecker>, OutputStream) - Method in class chemaxon.structurechecker.configuration.StructureCheckerActionStringWriter
writeConfiguration(List<StructureChecker>, OutputStream) - Method in interface chemaxon.structurechecker.configuration.StructureCheckerConfigurationWriter: Writes the checker list to output
writeConfiguration(List<StructureChecker>, OutputStream) - Method in class chemaxon.structurechecker.configuration.StructureCheckerConfigurationXmlWriter
writeExternal(ObjectOutput) - Method in class chemaxon.formats.Encoding: Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MarvinPane: Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MSketch: Saves the sketcher's state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MSketchPane: Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MView: Saves the viewer's state.
writeExternal(ObjectOutput) - Method in class chemaxon.marvin.beans.MViewPane: Saves object state.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.graphics.MTextAttributes
writeExternal(ObjectOutput) - Method in class chemaxon.struc.graphics.MTextDocument: Saves the document.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.MPropertyContainer: Saves the property container's state.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.PageSettings
writeExternal(ObjectOutput) - Method in class chemaxon.struc.Point3D: Serializes a 3D point.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.Transform3D: Serializes a transformation matrix.
writeMetricParameter(ArrayList, String, int, boolean) - Method in class chemaxon.descriptors.MDParameters: Writes a given parameter of the specified metric into the corresponding tree node.
writeMol(ObjectOutput, Molecule) - Static method in class chemaxon.marvin.beans.MarvinPane
writeServiceDescriptors(List<ServiceDescriptor>, OutputStream) - Method in interface chemaxon.calculations.services.ServiceDescriptorWriter: Writes the descriptors to the specified output

X

x - Variable in class chemaxon.struc.Point3D: The x coordinate.
xCoordinate - Variable in class chemaxon.struc.MolAtom: X coordinate.
Xe - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Xe.
XML - Enum constant in enum class chemaxon.naming.document.DocumentAnnotator.DocumentType
XML_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor: xml token of the action
XmlToHtmlConverter - Class in chemaxon.naming.document: This class implements the default conversion from XML to HTML.
xmlToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo: Returns the XML tokens of the action as a string, divided by comma characters
XSTATE_C - Static variable in class chemaxon.struc.Sgroup: S-group is contracted.
XSTATE_NONE - Static variable in class chemaxon.struc.Sgroup: S-group is in an undetermined state.
XSTATE_X - Static variable in class chemaxon.struc.Sgroup: S-group is expanded.
XSTATE_XC - Static variable in class chemaxon.struc.Sgroup: S-group is expanded, but its atoms have the same coordinates as in contracted state.
xyz - Variable in class chemaxon.descriptors.PFParameters: The calculateXYZ() methods (in PharmacophoreFingerprint sub-classes) calculate three numbers (denoted by x,y and z), but methods in java cannot have output parameters.
XYZ - Static variable in class chemaxon.formats.MFileFormat: XYZ files.

Y

y - Variable in class chemaxon.struc.Point3D: The y coordinate.
Y - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Y.
Yb - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Yb.
yCoordinate - Variable in class chemaxon.struc.MolAtom: Y coordinate.
YES - Enum constant in enum class chemaxon.search.api.options.HaltOnErrorOption: Stop on any errors during the search.

Z

z - Variable in class chemaxon.struc.Point3D: The z coordinate.
Z - Enum constant in enum class chemaxon.core.calculations.stereo.CIPStereoValue.CisTransStereoIUPACValue
Z - Enum constant in enum class chemaxon.struc.EZConfiguration
Z_OR_UNSPEC - Enum constant in enum class chemaxon.struc.EZConfiguration
zCoordinate - Variable in class chemaxon.struc.MolAtom: Z coordinate.
ZERO_BASED_ATOM_INDEXING - Static variable in class chemaxon.marvin.common.ParameterConstants: Identifier for parameter: "zeroBasedAtomIndexing" See Parameters and Events documentation.
ZERO_VECTOR - Static variable in class chemaxon.struc.Point3D
Zn - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Zn.
ZOOM_TO_SCAFFOLD_ON_LOAD - Static variable in class chemaxon.marvin.common.SketchParameterConstants: Identifier of parameter: "zoomToScaffoldOnLoad".
Zr - Static variable in class chemaxon.struc.PeriodicTable: Atomic number of the element Zr.

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